1
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Cieri N, Hookeri N, Stromhaug K, Li L, Keating J, Díaz-Fernández P, Gómez-García de Soria V, Stevens J, Kfuri-Rubens R, Shao Y, Kooshesh KA, Powell K, Ji H, Hernandez GM, Abelin J, Klaeger S, Forman C, Clauser KR, Sarkizova S, Braun DA, Penter L, Kim HT, Lane WJ, Oliveira G, Kean LS, Li S, Livak KJ, Carr SA, Keskin DB, Muñoz-Calleja C, Ho VT, Ritz J, Soiffer RJ, Neuberg D, Stewart C, Getz G, Wu CJ. Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation. Nat Biotechnol 2024:10.1038/s41587-024-02348-3. [PMID: 39169264 DOI: 10.1038/s41587-024-02348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/02/2024] [Indexed: 08/23/2024]
Abstract
T cell alloreactivity against minor histocompatibility antigens (mHAgs)-polymorphic peptides resulting from donor-recipient (D-R) disparity at sites of genetic polymorphisms-is at the core of the therapeutic effect of allogeneic hematopoietic cell transplantation (allo-HCT). Despite the crucial role of mHAgs in graft-versus-leukemia (GvL) and graft-versus-host disease (GvHD) reactions, it remains challenging to consistently link patient-specific mHAg repertoires to clinical outcomes. Here we devise an analytic framework to systematically identify mHAgs, including their detection on HLA class I ligandomes and functional verification of their immunogenicity. The method relies on the integration of polymorphism detection by whole-exome sequencing of germline DNA from D-R pairs with organ-specific transcriptional- and proteome-level expression. Application of this pipeline to 220 HLA-matched allo-HCT D-R pairs demonstrated that total and organ-specific mHAg load could independently predict the occurrence of acute GvHD and chronic pulmonary GvHD, respectively, and defined promising GvL targets, confirmed in a validation cohort of 58 D-R pairs, for the prevention or treatment of post-transplant disease recurrence.
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Affiliation(s)
- Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nidhi Hookeri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kari Stromhaug
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Liang Li
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Julia Keating
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paula Díaz-Fernández
- Department of Immunology, Instituto de Investigación Sanitaria Princesa (IIS-IP), Hospital Universitario de La Princesa, Madrid, Spain
| | - Valle Gómez-García de Soria
- Department of Hematology, Instituto de Investigación Sanitaria Princesa (IIS-IP), Hospital Universitario de La Princesa, Madrid, Spain
| | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Raphael Kfuri-Rubens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Yiren Shao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kaila Powell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Helen Ji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabrielle M Hernandez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jennifer Abelin
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Susan Klaeger
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Proteomic and Genomic Technologies, Genentech Inc, South San Francisco, CA, USA
| | - Cleo Forman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Haesook T Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William J Lane
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Leslie S Kean
- Harvard Medical School, Boston, MA, USA
- Division Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Cecilia Muñoz-Calleja
- Department of Immunology, Instituto de Investigación Sanitaria Princesa (IIS-IP), Hospital Universitario de La Princesa, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Vincent T Ho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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2
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Zhang Y, Naderi Yeganeh P, Zhang H, Wang SY, Li Z, Gu B, Lee DJ, Zhang Z, Ploumakis A, Shi M, Wu H, Greer EL, Hide W, Lieberman J. Tumor editing suppresses innate and adaptive antitumor immunity and is reversed by inhibiting DNA methylation. Nat Immunol 2024:10.1038/s41590-024-01932-8. [PMID: 39169233 DOI: 10.1038/s41590-024-01932-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/13/2024] [Indexed: 08/23/2024]
Abstract
Cancer cells edit gene expression to evade immunosurveillance. However, genome-wide studies of gene editing during early tumorigenesis are lacking. Here we used single-cell RNA sequencing in a breast cancer genetically engineered mouse model (GEMM) to identify edited genes without bias. Late tumors repressed antitumor immunity genes, reducing infiltrating immune cells and tumor-immune cell communications. Innate immune genes, especially interferon-stimulated genes, dominated the list of downregulated tumor genes, while genes that regulate cell-intrinsic malignancy were mostly unedited. Naive and activated CD8+ T cells in early tumors were replaced with exhausted or precursor-exhausted cells in late tumors. Repression of immune genes was reversed by inhibiting DNA methylation using low-dose decitabine, which suppressed tumor growth and restored immune control, increasing the number, functionality and memory of tumor-infiltrating lymphocytes and reducing the number of myeloid suppressor cells. Decitabine induced important interferon, pyroptosis and necroptosis genes, inflammatory cell death and immune control in GEMM and implanted breast and melanoma tumors.
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Affiliation(s)
- Ying Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Pourya Naderi Yeganeh
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Haiwei Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Simon Yuan Wang
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Zhouyihan Li
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bowen Gu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dian-Jang Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Zhibin Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Athanasios Ploumakis
- Harvard Medical School, Boston, MA, USA
- Spatial Technologies Unit, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ming Shi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Departments of Pediatrics and Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Winston Hide
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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3
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Idiiatullina E, Al-Azab M, Lin M, Hrovat-Schaale K, Liu Z, Li X, Guo C, Chen X, Li Y, Gao S, Cui J, Zhou W, Liu L, Zhang Y, Masters SL. Heterozygous de novo dominant negative mutation of REXO2 results in interferonopathy. Nat Commun 2024; 15:6685. [PMID: 39107301 PMCID: PMC11303720 DOI: 10.1038/s41467-024-50878-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Mitochondrial RNA (mtRNA) in the cytosol can trigger the innate immune sensor MDA5, and autoinflammatory disease due to type I IFN. Here, we show that a dominant negative mutation in the gene encoding the mitochondrial exonuclease REXO2 may cause interferonopathy by triggering the MDA5 pathway. A patient characterized by this heterozygous de novo mutation (p.T132A) presented with persistent skin rash featuring hyperkeratosis, parakeratosis and acanthosis, with infiltration of lymphocytes and eosinophils around small blood vessels. In addition, circulating IgE levels and inflammatory cytokines, including IFNα, are found consistently elevated. Transcriptional analysis highlights a type I IFN gene signature in PBMC. Mechanistically, REXO2 (T132A) lacks the ability to cleave RNA and inhibits the activity of wild-type REXO2. This leads to an accumulation of mitochondrial dsRNA in the cytosol, which is recognized by MDA5, leading to the associated type I IFN gene signature. These results demonstrate that in the absence of appropriate regulation by REXO2, aberrant cellular nucleic acids may accumulate and continuously trigger innate sensors, resulting in an inborn error of immunity.
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Affiliation(s)
- Elina Idiiatullina
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
- Department of Therapy and Nursing, Bashkir State Medical University, Ufa, Russia
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, USA
| | - Mahmoud Al-Azab
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
- Department of Medical Microbiology, Faculty of Medicine, University of Science and Technology, Aden, Yemen
| | - Meng Lin
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Katja Hrovat-Schaale
- Department of Therapy and Nursing, Bashkir State Medical University, Ufa, Russia
- Department of Medical Microbiology, Faculty of Medicine, University of Science and Technology, Aden, Yemen
| | - Ziyang Liu
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Xiaotian Li
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Caiqin Guo
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Xixi Chen
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Yaoying Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun Cui
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenhao Zhou
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.
| | - Yuxia Zhang
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.
| | - Seth L Masters
- Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Australia.
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
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4
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Ohnezeit D, Huang J, Westerkamp U, Brinschwitz V, Schmidt C, Günther T, Czech-Sioli M, Weißelberg S, Schlemeyer T, Nakel J, Mai J, Schreiner S, Schneider C, Friedel CC, Schwanke H, Brinkmann MM, Grundhoff A, Fischer N. Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling. PLoS Pathog 2024; 20:e1012426. [PMID: 39110744 PMCID: PMC11333005 DOI: 10.1371/journal.ppat.1012426] [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: 08/09/2023] [Revised: 08/19/2024] [Accepted: 07/15/2024] [Indexed: 08/21/2024] Open
Abstract
Merkel cell polyomavirus (MCPyV) is the causative agent of the majority of Merkel cell carcinomas (MCC). The virus has limited coding capacity, with its early viral proteins, large T (LT) and small T (sT), being multifunctional and contributing to infection and transformation. A fundamental difference in early viral gene expression between infection and MCPyV-driven tumorigenesis is the expression of a truncated LT (LTtr) in the tumor. In contrast, sT is expressed in both conditions and contributes significantly to oncogenesis. Here, we identified novel functions of early viral proteins by performing genome-wide transcriptome and chromatin studies in primary human fibroblasts. Due to current limitations in infection and tumorigenesis models, we mimic these conditions by ectopically expressing sT, LT or LTtr, individually or in combination, at different time points. In addition to its known function in cell cycle and inflammation modulation, we reveal a fundamentally new function of sT. We show that sT regulates the type I interferon (IFN) response downstream of the type I interferon receptor (IFNAR) by interfering with the interferon-stimulated gene factor 3 (ISGF3)-induced interferon-stimulated gene (ISG) response. Expression of sT leads to a reduction in the expression of interferon regulatory factor 9 (IRF9) which is a central component of the ISGF3 complex. We further show that this function of sT is conserved in BKPyV. We provide a first mechanistic understanding of which early viral proteins trigger and control the type I IFN response, which may influence MCPyV infection, persistence and, during MCC progression, regulation of the tumor microenvironment.
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Affiliation(s)
- Denise Ohnezeit
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ute Westerkamp
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Veronika Brinschwitz
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Schmidt
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Manja Czech-Sioli
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samira Weißelberg
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tabea Schlemeyer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Julia Mai
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, Freiburg, Germany
| | - Sabrina Schreiner
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, Freiburg, Germany
| | | | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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5
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Felício R, Franco A, Corrêa-Moreira D, Martinez de Carvalho F, Guimarães A, Vargas FR. Humoral immune transcriptome signature in myelomeningocele patients. J Reprod Immunol 2024; 163:104224. [PMID: 38479055 DOI: 10.1016/j.jri.2024.104224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 06/03/2024]
Abstract
INTRODUCTION Myelomeningocele (MMC) results from incomplete closure of the neural tube, and has a complex multifactorial etiology, including an inflammatory microenvironment. OBJECTIVE We evaluated the contribution of humoral immune response for development of inflammatory milieu. METHODS Using public repository Gene Expression Omnibus (GEO), we retrieve dataset transcriptome from the amniotic fluid of ten fetuses with myelomeningocele and ten healthy control fetuses to found differential gene expression associated with disturbances and inflammatory signatures in MMC. The identified DEGs were submitted to enrichment, network, and matrix correlation analyses. RESULTS Our initial analysis revealed 90 DEGs in MMC, mainly associated with signaling pathways of inflammation, including the immune modules, humoral immune response and IFN-type I signatures. Protein-protein analysis (PPI) revealed an association with three protein networks; positive regulation of B cell proliferation constituted the largest network. Matrix correlation analyses showed that MMC alters the co-expression of genes related to inflammatory processes that promote microenvironment inflammation. CONCLUSION These results revealed an altered humoral immune response in MMC patients, contributing to an inflammatory profile and providing opportunities for identifying potential biomarkers in myelomeningocele disease.
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Affiliation(s)
- Rfm Felício
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Almm Franco
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Ciências Biológicas (Genética), Universidade Federal do Rio de Janeiro, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - D Corrêa-Moreira
- Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Laboratory of Taxonomy, Biochesmistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - F Martinez de Carvalho
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Programa de Pós-Graduação em Ciências Biológicas (Genética), Universidade Federal do Rio de Janeiro, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Acr Guimarães
- Laboratory of Taxonomy, Biochesmistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - F R Vargas
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Programa de Pós-Graduação em Ciências Biológicas (Genética), Universidade Federal do Rio de Janeiro, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Departamento de Genética e Biologia Molecular, Universidade Federal do Estado do Rio de Janeiro, Brazil.
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6
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Jauze L, Vie M, Miagoux Q, Rossiaud L, Vidal P, Montalvo-Romeral V, Saliba H, Jarrige M, Polveche H, Nozi J, Le Brun PR, Bocchialini L, Francois A, Cosette J, Rouillon J, Collaud F, Bordier F, Bertil-Froidevaux E, Georger C, van Wittenberghe L, Miranda A, Daniele NF, Gross DA, Hoch L, Nissan X, Ronzitti G. Synergism of dual AAV gene therapy and rapamycin rescues GSDIII phenotype in muscle and liver. JCI Insight 2024; 9:e172614. [PMID: 38753465 PMCID: PMC11382881 DOI: 10.1172/jci.insight.172614] [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: 05/26/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Glycogen storage disease type III (GSDIII) is a rare metabolic disorder due to glycogen debranching enzyme (GDE) deficiency. Reduced GDE activity leads to pathological glycogen accumulation responsible for impaired hepatic metabolism and muscle weakness. To date, there is no curative treatment for GSDIII. We previously reported that 2 distinct dual AAV vectors encoding for GDE were needed to correct liver and muscle in a GSDIII mouse model. Here, we evaluated the efficacy of rapamycin in combination with AAV gene therapy. Simultaneous treatment with rapamycin and a potentially novel dual AAV vector expressing GDE in the liver and muscle resulted in a synergic effect demonstrated at biochemical and functional levels. Transcriptomic analysis confirmed synergy and suggested a putative mechanism based on the correction of lysosomal impairment. In GSDIII mice livers, dual AAV gene therapy combined with rapamycin reduced the effect of the immune response to AAV observed in this disease model. These data provide proof of concept of an approach exploiting the combination of gene therapy and rapamycin to improve efficacy and safety and to support clinical translation.
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Affiliation(s)
- Louisa Jauze
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Mallaury Vie
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Quentin Miagoux
- CECS, I-STEM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Corbeil-Essonnes, France
| | - Lucille Rossiaud
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
- CECS, I-STEM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Corbeil-Essonnes, France
| | - Patrice Vidal
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Valle Montalvo-Romeral
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Hanadi Saliba
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Margot Jarrige
- CECS, I-STEM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Corbeil-Essonnes, France
| | - Helene Polveche
- CECS, I-STEM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Corbeil-Essonnes, France
| | - Justine Nozi
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | | | - Luca Bocchialini
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Amandine Francois
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | | | - Jérémy Rouillon
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Fanny Collaud
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | | | | | | | | | | | | | - David-Alexandre Gross
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
| | - Lucile Hoch
- CECS, I-STEM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Corbeil-Essonnes, France
| | - Xavier Nissan
- CECS, I-STEM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Corbeil-Essonnes, France
| | - Giuseppe Ronzitti
- Généthon, Évry, France
- Université Paris-Saclay, Univ Évry, Inserm, Généthon, Integrare research unit UMR_S951, 91000 Évry, France
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7
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Bodega-Mayor I, Delgado-Wicke P, Arrabal A, Alegría-Carrasco E, Nicolao-Gómez A, Jaén-Castaño M, Espadas C, Dopazo A, Martín-Gayo E, Gaspar ML, de Andrés B, Fernández-Ruiz E. Tyrosine kinase 2 modulates splenic B cells through type I IFN and TLR7 signaling. Cell Mol Life Sci 2024; 81:199. [PMID: 38683377 PMCID: PMC11058799 DOI: 10.1007/s00018-024-05234-y] [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: 07/26/2023] [Revised: 01/29/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
Tyrosine kinase 2 (TYK2) is involved in type I interferon (IFN-I) signaling through IFN receptor 1 (IFNAR1). This signaling pathway is crucial in the early antiviral response and remains incompletely understood on B cells. Therefore, to understand the role of TYK2 in B cells, we studied these cells under homeostatic conditions and following in vitro activation using Tyk2-deficient (Tyk2-/-) mice. Splenic B cell subpopulations were altered in Tyk2-/- compared to wild type (WT) mice. Marginal zone (MZ) cells were decreased and aged B cells (ABC) were increased, whereas follicular (FO) cells remained unchanged. Likewise, there was an imbalance in transitional B cells in juvenile Tyk2-/- mice. RNA sequencing analysis of adult MZ and FO cells isolated from Tyk2-/- and WT mice in homeostasis revealed altered expression of IFN-I and Toll-like receptor 7 (TLR7) signaling pathway genes. Flow cytometry assays corroborated a lower expression of TLR7 in MZ B cells from Tyk2-/- mice. Splenic B cell cultures showed reduced proliferation and differentiation responses after activation with TLR7 ligands in Tyk2-/- compared to WT mice, with a similar response to lipopolysaccharide (LPS) or anti-CD40 + IL-4. IgM, IgG, IL-10 and IL-6 secretion was also decreased in Tyk2-/- B cell cultures. This reduced response of the TLR7 pathway in Tyk2-/- mice was partially restored by IFNα addition. In conclusion, there is a crosstalk between TYK2 and TLR7 mediated by an IFN-I feedback loop, which contributes to the establishment of MZ B cells and to B cell proliferation and differentiation.
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Affiliation(s)
- Irene Bodega-Mayor
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain
- Immunobiology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Pablo Delgado-Wicke
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain
| | - Alejandro Arrabal
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain
- Immunobiology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Estíbaliz Alegría-Carrasco
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain
| | - Ana Nicolao-Gómez
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain
| | - Marta Jaén-Castaño
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain
| | - Cristina Espadas
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Enrique Martín-Gayo
- Immunology Department, Hospital Universitario de La Princesa and IIS-Princesa, Madrid, Spain
- Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Luisa Gaspar
- Immunobiology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Belén de Andrés
- Immunobiology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Fernández-Ruiz
- Molecular Biology Unit, Hospital Universitario de La Princesa and Research Institute (IIS-Princesa), Madrid, Spain.
- Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain.
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8
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Duffy BC, King KM, Nepal B, Nonnemacher MR, Kortagere S. Acute Administration of HIV-1 Tat Protein Drives Glutamatergic Alterations in a Rodent Model of HIV-Associated Neurocognitive Disorders. Mol Neurobiol 2024:10.1007/s12035-024-04113-8. [PMID: 38514527 DOI: 10.1007/s12035-024-04113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
HIV-1-associated neurocognitive disorders (HAND) are a major comorbidity of HIV-1 infection, marked by impairment of executive function varying in severity. HAND affects nearly half of people living with HIV (PLWH), with mild forms predominating since the use of anti-retroviral therapies (ART). The HIV-1 transactivator of transcription (Tat) protein is found in the cerebrospinal fluid of patients adherent to ART, and its administration or expression in animals causes cognitive symptoms. Studies of Tat interaction with the N-methyl-D-aspartate receptor (NMDAR) suggest that glutamate toxicity contributes to Tat-induced impairments. To identify changes in regional glutamatergic circuitry underlying cognitive impairment, we injected recombinant Tat86 or saline to medial prefrontal cortex (mPFC) of male Sprague-Dawley rats. Rats were assessed with behavioral tasks that involve intact functioning of mPFC including the novel object recognition (NOR), spatial object recognition (SOR), and temporal order (TO) tasks at 1 and 2 postoperative weeks. Following testing, mPFC tissue was collected and analyzed by RT-PCR. Results showed Tat86 in mPFC-induced impairment in SOR, and upregulation of Grin1 and Grin2a transcripts. To further understand the mechanism of Tat toxicity, we assessed the effects of full-length Tat101 on gene expression in mPFC by RNA sequencing. The results of RNAseq suggest that glutamatergic effects of Tat86 are maintained with Tat101, as Grin2a was upregulated in Tat101-injected tissue, among other differentially expressed genes. Spatial learning and memory impairment and Grin2a upregulation suggest that exposure to Tat protein drives adaptation in mPFC, altering the function of circuitry supporting spatial learning and memory.
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Affiliation(s)
- Brenna C Duffy
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kirsten M King
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Binod Nepal
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
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9
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Marks KD, Anderson DM. Protection from plague via single dose administration of antibody to neutralize the type I interferon response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584497. [PMID: 38559124 PMCID: PMC10979884 DOI: 10.1101/2024.03.11.584497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Yersinia pestis is a gram-negative bacterium and the causative agent for the plague. Yersinia spp . use effector proteins of the type III secretion system (T3SS) to skew the host immune response toward a bacterial advantage during infection. Previous work established that mice which lack the type I IFN receptor (IFNAR), exhibit resistance to pulmonary infection by Y. pestis . In this work, we addressed the efficacy of a single dose administration of neutralizing antibody to IFNAR (MAR1) as a preventive treatment for plague. We show that single dose administration of MAR1 provides protection from mortality due to secondary septicemic plague where it appears to reduce the production of serum TNFα during the disease phase. We further demonstrate that the T3SS effector protein YopJ is necessary for MAR1-induced protection, however IFNAR-dependent serum TNFα was observed independent of YopJ. We further define tissue-specific anti-bacterial roles of IFNAR that are blocked by YopJ activity indicating that YopJ and IFNAR work in parallel to promote disease. The combined data suggest that therapeutic targeting of IFNAR signaling may reduce the hyper-inflammatory response associated with plague.
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10
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Zhao X, Perez JM, Faull PA, Chan C, Munting FW, Canadeo LA, Cenik C, Huibregtse JM. Cellular targets and lysine selectivity of the HERC5 ISG15 ligase. iScience 2024; 27:108820. [PMID: 38303729 PMCID: PMC10831901 DOI: 10.1016/j.isci.2024.108820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
ISG15 is a type I interferon-induced ubiquitin-like modifier that functions in innate immune responses. The major human ISG15 ligase is hHERC5, a ribosome-associated HECT E3 that broadly ISGylates proteins cotranslationally. Here, we characterized the hHERC5-dependent ISGylome and identified over 2,000 modified lysines in over 1,100 proteins in IFN-β-stimulated cells. In parallel, we compared the substrate selectivity hHERC5 to the major mouse ISG15 ligase, mHERC6, and analysis of sequences surrounding ISGylation sites revealed that hHERC5 and mHERC6 have distinct preferences for amino acid sequence context. Several features of the datasets were consistent with ISGylation of ribosome-tethered nascent chains, and mHERC6, like hHERC5, cotranslationally modified nascent polypeptides. The ISGylome datasets presented here represent the largest numbers of protein targets and modification sites attributable to a single Ub/Ubl ligase and the lysine selectivities of the hHERC5 and mHERC6 enzymes may have implications for the activities of HECT domain ligases, generally.
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Affiliation(s)
- Xu Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jessica M. Perez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Peter A. Faull
- Biological Mass Spectrometry Facility, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Chan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Femke W. Munting
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Larissa A. Canadeo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jon M. Huibregtse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- John Ring LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
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11
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Mills M, Emori C, Kumar P, Boucher Z, George J, Bolcun-Filas E. Single-cell and bulk transcriptional profiling of mouse ovaries reveals novel genes and pathways associated with DNA damage response in oocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578648. [PMID: 38352597 PMCID: PMC10862846 DOI: 10.1101/2024.02.02.578648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Immature oocytes enclosed in primordial follicles stored in female ovaries are under constant threat of DNA damage induced by endogenous and exogenous factors. Checkpoint kinase 2 (CHEK2) is a key mediator of the DNA damage response in all cells. Genetic studies have shown that CHEK2 and its downstream targets, p53 and TAp63, regulate primordial follicle elimination in response to DNA damage, however the mechanism leading to their demise is still poorly characterized. Single-cell and bulk RNA sequencing were used to determine the DNA damage response in wildtype and Chek2-deficient ovaries. A low but oocyte-lethal dose of ionizing radiation induces a DNA damage response in ovarian cells that is solely dependent on CHEK2. DNA damage activates multiple ovarian response pathways related to apoptosis, p53, interferon signaling, inflammation, cell adhesion, and intercellular communication. These pathways are differentially employed by different ovarian cell types, with oocytes disproportionately affected by radiation. Novel genes and pathways are induced by radiation specifically in oocytes, shedding light on their sensitivity to DNA damage, and implicating a coordinated response between oocytes and pre-granulosa cells within the follicle. These findings provide a foundation for future studies on the specific mechanisms regulating oocyte survival in the context of aging, as well as therapeutic and environmental genotoxic exposures.
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Affiliation(s)
- Monique Mills
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- The Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 5650871, Japan
| | - Parveen Kumar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Zachary Boucher
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Joshy George
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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12
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Badla BA, Hanifa MS, Jain R, Naofal ME, Halabi N, Yaslam S, Ramaswamy S, Taylor A, Alfalasi R, Shenbagam S, Khansaheb H, Al Suwaidi H, Nowotny N, Popatia R, Al Khayat A, Alsheikh-Ali A, Loney T, AlDabal LM, Abou Tayoun A. Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients: a case series. Sci Rep 2023; 13:20294. [PMID: 37985737 PMCID: PMC10661561 DOI: 10.1038/s41598-023-47718-0] [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: 08/17/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Studies of genetic factors associated with severe COVID-19 in young adults have been limited in non-Caucasian populations. Here, we clinically characterize a case series of patients with COVID-19, who were otherwise healthy, young adults (N = 55; mean age 34.1 ± SD 5.0 years) from 16 Asian, Middle Eastern, and North African countries. Using whole exome sequencing, we identify rare, likely deleterious variants affecting 16 immune-related genes in 17 out of 55 patients (31%), including 7 patients (41% of all carriers or 12.7% of all patients) who harbored multiple such variants mainly in interferon and toll-like receptor genes. Protein network analysis as well as transcriptomic analysis of nasopharyngeal swabs from an independent COVID-19 cohort (N = 50; 42% Asians and 22% Arabs) revealed that most of the altered genes, as identified by whole exome sequencing, and the associated molecular pathways were significantly altered in COVID-19 patients. Genetic variants tended to be associated with mortality, intensive care admission, and ventilation support. Our clinical cases series, genomic and transcriptomic findings suggest a possible role for interferon pathway genes in severe COVID-19 and highlight the importance of extending genetic studies to diverse populations to better understand the human genetics of disease.
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Affiliation(s)
- Beshr Abdulaziz Badla
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Mohamed Samer Hanifa
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Ruchi Jain
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Maha El Naofal
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Nour Halabi
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Sawsan Yaslam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Sathishkumar Ramaswamy
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Alan Taylor
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Roudha Alfalasi
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Shruti Shenbagam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Hamda Khansaheb
- Medical Education and Research Department, Dubai Health, Dubai, UAE
| | - Hanan Al Suwaidi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Rizwana Popatia
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | | | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Dubai Health, Dubai, UAE
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | | | - Ahmad Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE.
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
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13
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Di Lollo V, Canciello A, Peserico A, Orsini M, Russo V, Cerveró-Varona A, Dufrusine B, El Khatib M, Curini V, Mauro A, Berardinelli P, Tournier C, Ancora M, Cammà C, Dainese E, Mincarelli LF, Barboni B. Unveiling the immunomodulatory shift: Epithelial-mesenchymal transition Alters immune mechanisms of amniotic epithelial cells. iScience 2023; 26:107582. [PMID: 37680464 PMCID: PMC10481295 DOI: 10.1016/j.isci.2023.107582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) changes cell phenotype by affecting immune properties of amniotic epithelial cells (AECs). The present study shows how the response to lipopolysaccharide of cells collected pre- (eAECs) and post-EMT (mAECs) induces changes in their transcriptomics profile. In fact, eAECs mainly upregulate genes involved in antigen-presenting response, whereas mAECs over-express soluble inflammatory mediator transcripts. Consistently, network analysis identifies CIITA and Nrf2 as main drivers of eAECs and mAECs immune response, respectively. As a consequence, the depletion of CIITA and Nrf2 impairs the ability of eAECs and mAECs to inhibit lymphocyte proliferation or macrophage-dependent IL-6 release, thus confirming their involvement in regulating immune response. Deciphering the mechanisms controlling the immune function of AECs pre- and post-EMT represents a step forward in understanding key physiological events wherein these cells are involved (pregnancy and labor). Moreover, controlling the immunomodulatory properties of eAECs and mAECs may be essential in developing potential strategies for regenerative medicine applications.
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Affiliation(s)
- Valeria Di Lollo
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Angelo Canciello
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Alessia Peserico
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Massimiliano Orsini
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
- Istituto Zooprofilattico Sperimentale delle Venezie, Department of Microbiology, Viale dell’Università 10, 35020 Legnaro (PD), Italy
| | - Valentina Russo
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Adrián Cerveró-Varona
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Beatrice Dufrusine
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Mohammad El Khatib
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Valentina Curini
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Annunziata Mauro
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Paolo Berardinelli
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Cathy Tournier
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Massimo Ancora
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Enrico Dainese
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
| | - Luana Fiorella Mincarelli
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Barbara Barboni
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
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14
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Kang B, Zhang J, Schwoerer MP, Nelson AN, Schoeman E, Guo A, Ploss A, Myhrvold C. Highly multiplexed mRNA quantitation with CRISPR-Cas13. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553527. [PMID: 37645785 PMCID: PMC10461975 DOI: 10.1101/2023.08.16.553527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
RNA quantitation tools are often either high-throughput or cost-effective, but rarely are they both. Existing methods can profile the transcriptome at great expense or are limited to quantifying a handful of genes by labor constraints. A technique that permits more throughput at a reduced cost could enable multi-gene kinetic studies, gene regulatory network analysis, and combinatorial genetic screens. Here, we introduce quantitative Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (qCARMEN): an RNA quantitation technique which leverages the programmable RNA-targeting capabilities of CRISPR-Cas13 to address this challenge by quantifying over 4,500 gene-sample pairs in a single experiment. Using qCARMEN, we studied the response profiles of interferon-stimulated genes (ISGs) during interferon (IFN) stimulation and flavivirus infection. Additionally, we observed isoform switching kinetics during epithelial-mesenchymal transition. qCARMEN is a simple and inexpensive technique that greatly enhances the scalability of RNA quantitation for novel applications with performance similar to gold-standard methods.
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Affiliation(s)
- Brian Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Jiayu Zhang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Amy N. Nelson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Emily Schoeman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Andrew Guo
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544
- Department of Chemistry, Princeton University, Princeton, NJ 08544
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15
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Hobson BD, Stanley AT, De Los Santos MB, Culbertson B, Mosharov EV, Sims PA, Sulzer D. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain Behav Immun 2023; 111:277-291. [PMID: 37100211 PMCID: PMC10460506 DOI: 10.1016/j.bbi.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023] Open
Abstract
Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it has been unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We found that IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were similar in neurons and glia, but with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, which were the only cells to undergo cellular proliferation and express MHC classII (MHC-II) and associated genes. To determine if neurons respond directly via cell-autonomous IFN-γ receptor (IFNGR) signaling, we produced mutant mice with a deletion of the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, which resulted in a complete loss of dopaminergic neuronal responses to IFN-γ. Our results demonstrate that IFN-γ induces neuronal IFNGR signaling and upregulation of MHC-I and related genes in vivo, although the expression level is low compared to oligodendrocytes, astrocytes, and microglia.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Adrien T Stanley
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Mark B De Los Santos
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Bruce Culbertson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Eugene V Mosharov
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, United States; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
| | - David Sulzer
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
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16
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Sacchi A, Giannessi F, Sabatini A, Percario ZA, Affabris E. SARS-CoV-2 Evasion of the Interferon System: Can We Restore Its Effectiveness? Int J Mol Sci 2023; 24:ijms24119353. [PMID: 37298304 DOI: 10.3390/ijms24119353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Type I and III Interferons (IFNs) are the first lines of defense in microbial infections. They critically block early animal virus infection, replication, spread, and tropism to promote the adaptive immune response. Type I IFNs induce a systemic response that impacts nearly every cell in the host, while type III IFNs' susceptibility is restricted to anatomic barriers and selected immune cells. Both IFN types are critical cytokines for the antiviral response against epithelium-tropic viruses being effectors of innate immunity and regulators of the development of the adaptive immune response. Indeed, the innate antiviral immune response is essential to limit virus replication at the early stages of infection, thus reducing viral spread and pathogenesis. However, many animal viruses have evolved strategies to evade the antiviral immune response. The Coronaviridae are viruses with the largest genome among the RNA viruses. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic. The virus has evolved numerous strategies to contrast the IFN system immunity. We intend to describe the virus-mediated evasion of the IFN responses by going through the main phases: First, the molecular mechanisms involved; second, the role of the genetic background of IFN production during SARS-CoV-2 infection; and third, the potential novel approaches to contrast viral pathogenesis by restoring endogenous type I and III IFNs production and sensitivity at the sites of infection.
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Affiliation(s)
- Alessandra Sacchi
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Flavia Giannessi
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Andrea Sabatini
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Zulema Antonia Percario
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Elisabetta Affabris
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
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17
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Chida T, Ishida Y, Morioka S, Sugahara G, Han C, Lam B, Yamasaki C, Sugahara R, Li M, Tanaka Y, Liang TJ, Tateno C, Saito T. Persistent hepatic IFN system activation in HBV-HDV infection determines viral replication dynamics and therapeutic response. JCI Insight 2023; 8:162404. [PMID: 37154158 DOI: 10.1172/jci.insight.162404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/22/2023] [Indexed: 05/10/2023] Open
Abstract
Hepatitis delta virus (HDV), a satellite virus of HBV, is regarded as the most severe type of hepatitis virus because of the substantial morbidity and mortality. The IFN system is the first line of defense against viral infections and an essential element of antiviral immunity; however, the role of the hepatic IFN system in controlling HBV-HDV infection remains poorly understood. Herein, we showed that HDV infection of human hepatocytes induced a potent and persistent activation of the IFN system whereas HBV was inert in triggering hepatic antiviral response. Moreover, we demonstrated that HDV-induced constitutive activation of the hepatic IFN system resulted in a potent suppression of HBV while modestly inhibiting HDV. Thus, these pathogens are equipped with distinctive immunogenicity and varying sensitivity to the antiviral effectors of IFN, leading to the establishment of a paradoxical mode of viral interference wherein HDV, the superinfectant, outcompetes HBV, the primary pathogen. Furthermore, our study revealed that HDV-induced constitutive IFN system activation led to a state of IFN refractoriness, rendering therapeutic IFNs ineffective. The present study provides potentially novel insights into the role of the hepatic IFN system in regulating HBV-HDV infection dynamics and its therapeutic implications through elucidating the molecular basis underlying the inefficacy of IFN-based antiviral strategies against HBV-HDV infection.
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Affiliation(s)
- Takeshi Chida
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
| | - Yuji Ishida
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
- PhoenixBio, Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | - Sho Morioka
- PhoenixBio, Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | - Go Sugahara
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
- PhoenixBio, Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | - Christine Han
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
| | - Bill Lam
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
| | | | - Remi Sugahara
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
| | - Meng Li
- Bioinformatics Service, Norris Medical Library, USC, Los Angeles, California, USA
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Chise Tateno
- PhoenixBio, Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | - Takeshi Saito
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California (USC), Los Angeles, California, USA
- Department of Molecular Microbiology & Immunology
- Department of Pathology, and
- USC Research Center for Liver Diseases, Keck School of Medicine, USC, Los Angeles, California, USA
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18
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Kuhl N, Linder A, Philipp N, Nixdorf D, Fischer H, Veth S, Kuut G, Xu TT, Theurich S, Carell T, Subklewe M, Hornung V. STING agonism turns human T cells into interferon-producing cells but impedes their functionality. EMBO Rep 2023; 24:e55536. [PMID: 36705069 PMCID: PMC9986811 DOI: 10.15252/embr.202255536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
The cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) axis is the predominant DNA sensing system in cells of the innate immune system. However, human T cells also express high levels of STING, while its role and physiological trigger remain largely unknown. Here, we show that the cGAS-STING pathway is indeed functional in human primary T cells. In the presence of a TCR-engaging signal, both cGAS and STING activation switches T cells into type I interferon-producing cells. However, T cell function is severely compromised following STING activation, as evidenced by increased cell death, decreased proliferation, and impaired metabolism. Interestingly, these different phenotypes bifurcate at the level of STING. While antiviral immunity and cell death require the transcription factor interferon regulatory factor 3 (IRF3), decreased proliferation is mediated by STING independently of IRF3. In summary, we demonstrate that human T cells possess a functional cGAS-STING signaling pathway that can contribute to antiviral immunity. However, regardless of its potential antiviral role, the activation of the cGAS-STING pathway negatively affects T cell function at multiple levels. Taken together, these results could help inform the future development of cGAS-STING-targeted immunotherapies.
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Affiliation(s)
- Niklas Kuhl
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine II, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Andreas Linder
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine II, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Nora Philipp
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Daniel Nixdorf
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Hannah Fischer
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Simon Veth
- Department of Chemistry and Center for NanoScience (CeNS)Ludwig‐Maximilians‐Universität MünchenMunichGermany
| | - Gunnar Kuut
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Teng Teng Xu
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Sebastian Theurich
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
- German Cancer Consortium (DKTK), Partner site MunichHeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Thomas Carell
- Department of Chemistry and Center for NanoScience (CeNS)Ludwig‐Maximilians‐Universität MünchenMunichGermany
| | - Marion Subklewe
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Veit Hornung
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
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19
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453 DOI: 10.12688/gatesopenres.14327.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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20
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453.2 DOI: 10.12688/gatesopenres.14327.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/09/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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21
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Santer DM, Li D, Ghosheh Y, Zahoor MA, Prajapati D, Hansen BE, Tyrrell DLJ, Feld JJ, Gehring AJ. Interferon-λ treatment accelerates SARS-CoV-2 clearance despite age-related delays in the induction of T cell immunity. Nat Commun 2022; 13:6992. [PMID: 36385011 PMCID: PMC9667439 DOI: 10.1038/s41467-022-34709-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
Interferons induced early after SARS-CoV-2 infection are crucial for shaping immunity and preventing severe COVID-19. We previously demonstrated that injection of pegylated interferon-lambda accelerated viral clearance in COVID-19 patients (NCT04354259). To determine if the viral decline is mediated by enhanced immunity, we assess in vivo responses to interferon-lambda by single cell RNA sequencing and measure SARS-CoV-2-specific T cell and antibody responses between placebo and interferon-lambda-treated patients. Here we show that interferon-lambda treatment induces interferon stimulated genes in peripheral immune cells expressing IFNLR1, including plasmacytoid dendritic cells and B cells. Interferon-lambda does not affect SARS-CoV-2-specific antibody levels or the magnitude of virus-specific T cells. However, we identify delayed T cell responses in older adults, suggesting that interferon-lambda can overcome delays in adaptive immunity to accelerate viral clearance in high-risk patients. Altogether, interferon-lambda offers an early COVID-19 treatment option for outpatients to boost innate antiviral defenses without dampening peripheral adaptive immunity.
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Affiliation(s)
- Deanna M. Santer
- grid.21613.370000 0004 1936 9609Department of Immunology, University of Manitoba, Winnipeg, MB Canada
| | - Daniel Li
- grid.17063.330000 0001 2157 2938Institute of Medical Science, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428Toronto Centre for Liver Disease, University Health Network, Toronto, ON Canada
| | - Yanal Ghosheh
- grid.231844.80000 0004 0474 0428Toronto Centre for Liver Disease, University Health Network, Toronto, ON Canada
| | - Muhammad Atif Zahoor
- grid.231844.80000 0004 0474 0428Toronto Centre for Liver Disease, University Health Network, Toronto, ON Canada
| | - Dhanvi Prajapati
- grid.21613.370000 0004 1936 9609Department of Immunology, University of Manitoba, Winnipeg, MB Canada
| | - Bettina E. Hansen
- grid.231844.80000 0004 0474 0428Toronto Centre for Liver Disease, University Health Network, Toronto, ON Canada
| | - D. Lorne J. Tyrrell
- grid.17089.370000 0001 2190 316XDepartment of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
| | - Jordan J. Feld
- grid.17063.330000 0001 2157 2938Institute of Medical Science, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428Toronto Centre for Liver Disease, University Health Network, Toronto, ON Canada
| | - Adam J. Gehring
- grid.17063.330000 0001 2157 2938Institute of Medical Science, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428Toronto Centre for Liver Disease, University Health Network, Toronto, ON Canada
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22
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Kelly JN, Laloli L, V’kovski P, Holwerda M, Portmann J, Thiel V, Dijkman R. Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis. Front Immunol 2022; 13:978824. [PMID: 36268025 PMCID: PMC9576848 DOI: 10.3389/fimmu.2022.978824] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/01/2022] [Indexed: 12/04/2022] Open
Abstract
The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.
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Affiliation(s)
- Jenna N. Kelly
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philip V’kovski
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Ronald Dijkman
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center (EVBC), Jena, Germany
- *Correspondence: Ronald Dijkman,
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Córdoba-David G, García-Giménez J, Cardoso Castelo-Branco R, Carrasco S, Cannata P, Ortiz A, Ramos AM. Crosstalk between TBK1/IKKε and the type I interferon pathway contributes to tubulointerstitial inflammation and kidney tubular injury. Front Pharmacol 2022; 13:987979. [PMID: 36386242 PMCID: PMC9647636 DOI: 10.3389/fphar.2022.987979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/22/2022] [Indexed: 09/01/2023] Open
Abstract
The type I interferon (TI-IFN) pathway regulates innate immunity, inflammation, and apoptosis during infection. However, the contribution of the TI-IFN pathway or upstream signaling pathways to tubular injury in kidney disease is poorly understood. Upon observing evidence of activation of upstream regulators of the TI-IFN pathway in a transcriptomics analysis of murine kidney tubulointerstitial injury, we have now addressed the impact of the TI-IFN and upstream signaling pathways on kidney tubulointerstitial injury. In cultured tubular cells and kidney tissue, IFNα/β binding to IFNAR activated the TI-IFN pathway and recruited antiviral interferon-stimulated genes (ISG) and NF-κB-associated proinflammatory responses. TWEAK and lipopolysaccharide (LPS) signaled through TBK1/IKKε and IRF3 to activate both ISGs and NF-κB. In addition, TWEAK recruited TLR4 to stimulate TBK1/IKKε-dependent ISG and inflammatory responses. Dual pharmacological inhibition of TBK1/IKKε with amlexanox decreased TWEAK- or LPS-induced ISG and cytokine responses, as well as cell death induced by a complex inflammatory milieu that included TWEAK. TBK1 or IRF3 siRNA prevented the TWEAK-induced ISG and inflammatory gene expression while IKKε siRNA did not. In vivo, kidney IFNAR and IFNβ were increased in murine LPS and folic acid nephrotoxicity while IFNAR was increased in human kidney biopsies with tubulointerstitial damage. Inhibition of TBK1/IKKε with amlexanox or IFNAR neutralization decreased TI-IFN pathway activation and protected from kidney injury induced by folic acid or LPS. In conclusion, TI-IFNs, TWEAK, and LPS engage interrelated proinflammatory and antiviral responses in tubular cells. Moreover, inhibition of TBK1/IKKε with amlexanox, and IFNAR targeting, may protect from tubulointerstitial kidney injury.
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Affiliation(s)
- Gina Córdoba-David
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jorge García-Giménez
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Susana Carrasco
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS 2040, Madrid, Spain
| | - Pablo Cannata
- Department of Pathology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS 2040, Madrid, Spain
- Department of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Adrián M. Ramos
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS 2040, Madrid, Spain
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Rb-E2F-HDAC Repressor Complexes Control Interferon-Induced Repression of Adenovirus To Promote Persistent Infection. J Virol 2022; 96:e0044222. [PMID: 35546119 DOI: 10.1128/jvi.00442-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interferons (IFNs) are cytokines that induce a global change in the cell to establish antiviral immunity. We previously demonstrated that human adenovirus (HAdV) exploits IFN-induced viral repression to persist in infected cells. Although this in vitro persistence model has been described, the mechanism behind how persistent HAdV infection is established is not well understood. In this study, we demonstrate that IFN signaling is essential for viral repression and promoting persistent infection. Cyclin-dependent kinase 4 (CDK4), an antagonist of retinoblastoma (Rb) family proteins, was shown to disrupt the viral repression induced by IFNs. Consistent with this result, knockout of the Rb family proteins pRb, p107, and/or p130 drastically reduced the effect of IFNs on viral replication. The pRb protein specifically contributed the greatest effect to IFN inhibition of viral replication. Interestingly, IFNs did not impact pRb through direct changes in protein or phosphorylation levels. Cells treated with IFNs continued to cycle normally, consistent with observations that persistently infected cells remain for long periods of time in the host and in our in vitro persistent infection model. Finally, we observed that histone deacetylase (HDAC) inhibitors activated productive viral replication in persistently infected cells in the presence of IFN. Thus, HDACs, specifically class I HDACs, which are commonly associated with Rb family proteins, play a major role in the maintenance of persistent HAdV infection in vitro. This study uncovers the critical role of pRb and class I HDACs in the IFN-induced formation of a repressor complex that promotes persistent HAdV infections. IMPORTANCE Adenoviruses are ubiquitous viruses infecting more than 90% of the human population. HAdVs cause persistent infections that may lead to serious complications in immunocompromised patients. Therefore, exploring how HAdVs establish persistent infections is critical for understanding viral reactivation in immunosuppressed individuals. The mechanism underlying HAdV persistence has not been fully explored. Here, we provide insight into the contributions of the host cell to IFN-mediated persistent HAdV infection. We found that HAdV-C5 productive infection is inhibited by an Rb-E2F-HDAC repressor complex. Treatment with HDAC inhibitors converted a persistent infection to a lytic infection. Our results suggest that this process involves the noncanonical regulation of Rb-E2F signaling. This study provides insight into a highly prevalent human pathogen, bringing a new level of complexity and understanding to the replicative cycle.
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Abuhammour W, Yavuz L, Jain R, Abu Hammour K, Al-Hammouri GF, El Naofal M, Halabi N, Yaslam S, Ramaswamy S, Taylor A, Wafadari D, Alsarhan A, Khansaheb H, Deesi ZO, Varghese RM, Uddin M, Al Suwaidi H, Al-Hammadi S, Alkhaja A, AlDabal LM, Loney T, Nowotny N, Al Khayat A, Alsheikh-Ali A, Abou Tayoun A. Genetic and Clinical Characteristics of Patients in the Middle East With Multisystem Inflammatory Syndrome in Children. JAMA Netw Open 2022; 5:e2214985. [PMID: 35639375 PMCID: PMC9157271 DOI: 10.1001/jamanetworkopen.2022.14985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
IMPORTANCE Clinical, genetic, and laboratory characteristics of Middle Eastern patients with multisystem inflammatory syndrome in children (MIS-C) have not yet been documented. OBJECTIVE To assess the genetic and clinical characteristics of patients with MIS-C of primarily Arab and Asian origin. DESIGN, SETTING, AND PARTICIPANTS A prospective, multicenter cohort study was conducted from September 1, 2020, to August 31, 2021, in the United Arab Emirates and Jordan. Forty-five patients with MIS-C and a matched control group of 25 healthy children with a confirmed SARS-CoV-2 infection status were recruited. Whole exome sequencing in all 70 participants was performed to identify rare, likely deleterious variants in patients with MIS-C and to correlate genetic findings with the clinical course of illness. EXPOSURES SARS-CoV-2. MAIN OUTCOMES AND MEASURES Fever, organ system complications, laboratory biomarkers, whole exome sequencing findings, treatments, and clinical outcomes were measured. The Mann-Whitney U test was used to assess the association between genetic variants and MIS-C attributes. The Fisher exact test was used to compute the genetic burden in MIS-C relative to controls. RESULTS A total of 45 patients with MIS-C (23 [51.1%] male; 30 [66.7%] of Middle Eastern origin; mean [SD] age, 6.7 [3.6] years) and 25 controls (17 [68.0%] male; 24 [96.0%] of Middle Eastern origin; mean [SD] age 7.4 [4.0] years) participated in the study. Key inflammatory markers were significantly dysregulated in all patients with MIS-C. Mucocutaneous and gastrointestinal manifestations were each reported in 36 patients (80.0%; 95% CI, 66.1%-89.1%), cardiac findings were reported in 22 (48.9%; 95% CI, 35.0%-63.0%), and neurologic findings were reported in 14 (31.1%; 95% CI, 19.5%-45.6%). Rare, likely deleterious heterozygous variants in immune-related genes, including TLR3, TLR6, IL22RA2, IFNB1, and IFNA6, were identified in 19 patients (42.2%; 95% CI, 29.0%-56.7%), of whom 7 had multiple variants. There was higher enrichment of genetic variants in patients relative to controls (29 vs 3, P < .001). Patients with those variants tended to have earlier disease onset (7 patients [36.8%; 95% CI, 19.1%-58.9%] with genetic findings vs 2 [7.7%; 95% CI, 2.1%-24.1%] without genetic findings were younger than 3 years at onset) and resistance to treatment (8 patients [42.1%; 95% CI, 23.1%-63.7%] with genetic findings vs 3 patients [11.5%; 95% CI, 4.0%-29.0%] without genetic findings received 2 doses of intravenous immunoglobulin). CONCLUSIONS AND RELEVANCE The results of this cohort study suggest that rare, likely deleterious genetic variants may contribute to MIS-C disease. This finding paves the way for additional studies with larger, diverse populations to fully characterize the genetic contribution to this new disease entity.
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Affiliation(s)
| | - Lemis Yavuz
- Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Ruchi Jain
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Khawla Abu Hammour
- Department of Biopharmaceutics and Clinical Pharmacy, The University of Jordan, Amman, Jordan
| | | | - Maha El Naofal
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Nour Halabi
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Sawsan Yaslam
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | | | - Alan Taylor
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Deena Wafadari
- Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Ali Alsarhan
- Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Hamda Khansaheb
- Medical Education and Research Department, Dubai Health Authority, Dubai, United Arab Emirates
| | - Zulfa Omar Deesi
- Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Hospital for Women and Children, Dubai, United Arab Emirates
| | - Rupa Murthy Varghese
- Virology Laboratory, Microbiology and Infection Control Unit, Latifa Hospital for Women and Children, Dubai, United Arab Emirates
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Hanan Al Suwaidi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Suleiman Al-Hammadi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Abdulmajeed Alkhaja
- Medical Education and Research Department, Dubai Health Authority, Dubai, United Arab Emirates
| | - Laila Mohamed AlDabal
- Medical Affairs Department, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Dubai Health Authority, Dubai, United Arab Emirates
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Chuah JJM, Hertzog PJ, Campbell NK. Immunoregulation by type I interferons in the peritoneal cavity. J Leukoc Biol 2021; 111:337-353. [PMID: 34612523 DOI: 10.1002/jlb.3mr0821-147r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The peritoneal cavity, a fluid-containing potential space surrounding the abdominal and pelvic organs, is home to a rich network of immune cells that maintain tissue homeostasis and provide protection against infection. However, under pathological conditions such as peritonitis, endometriosis, and peritoneal carcinomatosis, the peritoneal immune system can become dysregulated, resulting in nonresolving inflammation and disease progression. An enhanced understanding of the factors that regulate peritoneal immune cells under both homeostatic conditions and in disease contexts is therefore required to identify new treatment strategies for these often life-limiting peritoneal pathologies. Type I interferons (T1IFNs) are a family of cytokines with broad immunoregulatory functions, which provide defense against viruses, bacteria, and cancer. There have been numerous reports of immunoregulation by T1IFNs within the peritoneal cavity, which can contribute to both the resolution or propagation of peritoneal disease states, depending on the specifics of the disease setting and local environment. In this review, we provide an overview of the major immune cell populations that reside in the peritoneal cavity (or infiltrate it under inflammatory conditions) and highlight their contribution to the initiation, progression, or resolution of peritoneal diseases. Additionally, we will discuss the role of T1IFNs in the regulation of peritoneal immune cells, and summarize the results of laboratory studies and clinical trials which have investigated T1IFNs in peritonitis/sepsis, endometriosis, and peritoneal carcinomatosis.
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Affiliation(s)
- Jasmine J M Chuah
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Nicole K Campbell
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
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Tunable heat shock protein-mediated NK cell responses are orchestrated by STAT1 in Antigen Presenting Cells. Sci Rep 2021; 11:16106. [PMID: 34373574 PMCID: PMC8352880 DOI: 10.1038/s41598-021-95578-3] [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: 10/07/2020] [Accepted: 07/27/2021] [Indexed: 11/30/2022] Open
Abstract
The release of Heat Shock Proteins (HSPs) from aberrant cells can initiate immune responses following engagement of the HSPs with antigen presenting cells (APCs). This is an important mechanism for cancer immunosurveillance and can also be modeled by vaccination with HSPs through various routes, targeting specific APCs expressing the HSP receptor CD91. Immunological outcomes can be varied as a result of the broad expression of CD91 in different dendritic cell and macrophage populations. We investigated the cellular response of different APCs to the prototypical immunogenic HSP, gp96, in the context of Th1 immunity. Although APCs generally express similar levels of the HSP receptor CD91, we uncovered APC-distinct, downstream signaling pathways activating STAT1, and differential STAT1 induced genes. As a result of this differential and unique signaling we determined that gp96-activated macrophages, but not DCs are capable of activating NK cells to produce IFN-\documentclass[12pt]{minimal}
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\begin{document}$$\gamma$$\end{document}γ. These data demonstrate that different APC subsets elicit unique intracellular signaling responses to HSPs which result in different patterns of downstream cellular activation and immune responses. Collectively this provides a novel tunable and autochthonous immune response to extracellular HSPs which has important implications on the development of immunity to cancer and infectious disease, as well as homeostasis.
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28
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Teafatiller T, Agrawal S, De Robles G, Rahmatpanah F, Subramanian VS, Agrawal A. Vitamin C Enhances Antiviral Functions of Lung Epithelial Cells. Biomolecules 2021; 11:1148. [PMID: 34439814 PMCID: PMC8394979 DOI: 10.3390/biom11081148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Vitamin C is well documented to have antiviral functions; however, there is limited information about its effect on airway epithelial cells-the first cells to encounter infections. Here, we examined the effect of vitamin C on human bronchial epithelium transformed with Ad12-SV40 2B (BEAS-2B) cells, and observed that sodium-dependent vitamin C transporter 2 (SVCT2) was the primary vitamin C transporter. Transcriptomic analysis revealed that treating BEAS-2B cells with vitamin C led to a significant upregulation of several metabolic pathways and interferon-stimulated genes (ISGs) along with a downregulation of pathways involved in lung injury and inflammation. Remarkably, vitamin C also enhanced the expression of the viral-sensing receptors retinoic acid-inducible gene 1 (RIG-1) and melanoma differentiation-associated protein 5 (MDA-5), which was confirmed at the protein and functional levels. In addition, the lungs of l-gulono-γ-lactone oxidase knockout (GULO-KO) mice also displayed a marked decrease in these genes compared to wild-type controls. Collectively, our findings indicate that vitamin C acts at multiple levels to exert its antiviral and protective functions in the lungs.
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Affiliation(s)
- Trevor Teafatiller
- Division of Gastroenterology, Department of Medicine, University of California, Irvine, CA 92697, USA;
| | - Sudhanshu Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, CA 92697, USA;
| | - Gabriela De Robles
- Department of Pathology, University of California, Irvine, CA 92697, USA; (G.D.R.); (F.R.)
| | - Farah Rahmatpanah
- Department of Pathology, University of California, Irvine, CA 92697, USA; (G.D.R.); (F.R.)
| | - Veedamali S. Subramanian
- Division of Gastroenterology, Department of Medicine, University of California, Irvine, CA 92697, USA;
| | - Anshu Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, CA 92697, USA;
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29
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NAD + depletion by type I interferon signaling sensitizes pancreatic cancer cells to NAMPT inhibition. Proc Natl Acad Sci U S A 2021; 118:2012469118. [PMID: 33597293 DOI: 10.1073/pnas.2012469118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence suggests that intratumoral interferon (IFN) signaling can trigger targetable vulnerabilities. A hallmark of pancreatic ductal adenocarcinoma (PDAC) is its extensively reprogrammed metabolic network, in which nicotinamide adenine dinucleotide (NAD) and its reduced form, NADH, are critical cofactors. Here, we show that IFN signaling, present in a subset of PDAC tumors, substantially lowers NAD(H) levels through up-regulating the expression of NAD-consuming enzymes PARP9, PARP10, and PARP14. Their individual contributions to this mechanism in PDAC have not been previously delineated. Nicotinamide phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme in the NAD salvage pathway, a dominant source of NAD in cancer cells. We found that IFN-induced NAD consumption increased dependence upon NAMPT for its role in recycling NAM to salvage NAD pools, thus sensitizing PDAC cells to pharmacologic NAMPT inhibition. Their combination decreased PDAC cell proliferation and invasion in vitro and suppressed orthotopic tumor growth and liver metastases in vivo.
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30
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Gocher AM, Workman CJ, Vignali DAA. Interferon-γ: teammate or opponent in the tumour microenvironment? Nat Rev Immunol 2021; 22:158-172. [PMID: 34155388 DOI: 10.1038/s41577-021-00566-3] [Citation(s) in RCA: 240] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
Cancer immunotherapy offers substantive benefit to patients with various tumour types, in some cases leading to complete tumour clearance. However, many patients do not respond to immunotherapy, galvanizing the field to define the mechanisms of pre-existing and acquired resistance. Interferon-γ (IFNγ) is a cytokine that has both protumour and antitumour activities, suggesting that it may serve as a nexus for responsiveness to immunotherapy. Many cancer immunotherapies and chemotherapies induce IFNγ production by various cell types, including activated T cells and natural killer cells. Patients resistant to these therapies commonly have molecular aberrations in the IFNγ signalling pathway or express resistance molecules driven by IFNγ. Given that all nucleated cells can respond to IFNγ, the functional consequences of IFNγ production need to be carefully dissected on a cell-by-cell basis. Here, we review the cells that produce IFNγ and the different effects of IFNγ in the tumour microenvironment, highlighting the pleiotropic nature of this multifunctional and abundant cytokine.
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Affiliation(s)
- Angela M Gocher
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA. .,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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31
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García-de-Gracia F, Gaete-Argel A, Riquelme-Barrios S, Pereira-Montecinos C, Rojas-Araya B, Aguilera P, Oyarzún-Arrau A, Rojas-Fuentes C, Acevedo ML, Chnaiderman J, Valiente-Echeverría F, Toro-Ascuy D, Soto-Rifo R. CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev. RNA Biol 2021; 18:745-758. [PMID: 33103564 PMCID: PMC8078705 DOI: 10.1080/15476286.2020.1832375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Translation initiation of the human immunodeficiency virus type-1 (HIV-1) full-length RNA has been shown to occur through cap-dependent and IRES-driven mechanisms. Previous studies suggested that the nuclear cap-binding complex (CBC) rather than eIF4E drives cap-dependent translation of the full-length RNA and we have recently reported that the CBC subunit CBP80 supports the function of the viral protein Rev during nuclear export and translation of this viral transcript. Ribosome recruitment during CBC-dependent translation of cellular mRNAs relies on the activity CBP80/20 translation initiation factor (CTIF), which bridges CBP80 and the 40S ribosomal subunit through interactions with eIF3g. Here, we report that CTIF inhibits HIV-1 and HIV-2 Gag synthesis from the full-length RNA. Our results indicate that CTIF associates with HIV-1 Rev through its N-terminal domain and is recruited onto the full-length RNA ribonucleoprotein complex in order to interfere with Gag synthesis. We also demonstrate that CTIF induces the cytoplasmic accumulation of Rev impeding the association of the viral protein with CBP80. We finally show that Rev interferes with the association of CTIF with CBP80 indicating that CTIF and Rev compete for the CBC subunit.
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Affiliation(s)
- Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Camila Pereira-Montecinos
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Bárbara Rojas-Araya
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Paulina Aguilera
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aarón Oyarzún-Arrau
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Cecilia Rojas-Fuentes
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Mónica L. Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jonás Chnaiderman
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Daniela Toro-Ascuy
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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Apatinib combined with PD-L1 blockade synergistically enhances antitumor immune responses and promotes HEV formation in gastric cancer. J Cancer Res Clin Oncol 2021; 147:2209-2222. [PMID: 33891173 DOI: 10.1007/s00432-021-03633-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Apatinib, an antiangiogenic drug, has shown beneficial effects only in a fraction of advanced gastric cancer (GC) patients. Given the recent success of immunotherapies, combination of apatinib with immune checkpoint inhibitor may provide sustained and potent antitumor responses. METHODS Immunocompetent mice with subcutaneous MFC tumors grown were given a combination of apatinib and anti-PD-L1 antibody therapy. GC tissues from patients undergoing curative resection in China were collected, and the density of HEVs, MSI status and tumor-infiltrated lymphocytes were analyzed by immunohistochemical staining. RESULTS Combined apatinib and PD-L1 blockade therapy synergistically delayed tumor growth and increased survival in MFC-bearing immunocompetent mice. The combination therapy promoted antitumor immunity by increasing the ratio of CD8+ cytotoxic T cells to Foxp3+ Treg cells, the accumulation of CD20+ B cells and the Th1/Th2 cytokine ratio (IFN-γ/IL-10). The combination therapy induced the formation of HEVs through activation of LTβR signaling, thus promoting CD8+ cytotoxic T cell and CD20+ B cell infiltration in tumors. In clinical GC samples, the density of HEVs positively correlated with the intratumoral infiltration of CD8+ cytotoxic T cells and CD20+ B cells. MSI-high GC showed a higher density of HEVs, CD8+ cytotoxic T cells and CD20+ B cells than MSS/MSI-low GC. GC patients with high densities of HEVs, CD8+ cytotoxic T cells and CD20+ B cells had an improved prognosis with superior overall survival. CONCLUSION Combining apatinib with PD-L1 blockade treatment synergistically enhances antitumor immune responses and promotes HEV formation in GC.
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Mini-TrpRS is essential for IFNγ-induced monocyte-derived giant cell formation. Cytokine 2021; 142:155486. [PMID: 33721618 DOI: 10.1016/j.cyto.2021.155486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/07/2021] [Accepted: 02/24/2021] [Indexed: 11/24/2022]
Abstract
Truncated tryptophanyl-tRNA synthetase (mini-TrpRS), like any other aminoacyl-tRNA synthetases, canonically functions as a protein synthesis enzyme. Here we provide evidence for an additional signaling role of mini-TrpRS in the formation of monocyte-derived multinuclear giant cells (MGCs). Interferon-gamma (IFNγ) readily induced monocyte aggregation leading to MGC formation with paralleled marked upregulation of mini-TrpRS. Small interfering (si)RNA, targeting mini-TrpRS in the presence of IFNγ prevented monocyte aggregation. Moreover, blockade of mini-TrpRS, either by siRNA, or the cognate amino acid and decoy substrate D-Tryptophan to prevent mini-TrpRS signaling, resulted in a marked reduction in expression of the purinergic receptor P2X 7 (P2RX7) in monocytes activated by IFNγ. Our findings identify mini-TrpRS as a critical signaling molecule in a mechanism by which IFNγ initiates monocyte-derived giant cell formation.
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Type I IFNs facilitate innate immune control of the opportunistic bacteria Burkholderia cenocepacia in the macrophage cytosol. PLoS Pathog 2021; 17:e1009395. [PMID: 33684179 PMCID: PMC7971856 DOI: 10.1371/journal.ppat.1009395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/18/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
The mammalian immune system is constantly challenged by signals from both pathogenic and non-pathogenic microbes. Many of these non-pathogenic microbes have pathogenic potential if the immune system is compromised. The importance of type I interferons (IFNs) in orchestrating innate immune responses to pathogenic microbes has become clear in recent years. However, the control of opportunistic pathogens-and especially intracellular bacteria-by type I IFNs remains less appreciated. In this study, we use the opportunistic, Gram-negative bacterial pathogen Burkholderia cenocepacia (Bc) to show that type I IFNs are capable of limiting bacterial replication in macrophages, preventing illness in immunocompetent mice. Sustained type I IFN signaling through cytosolic receptors allows for increased expression of autophagy and linear ubiquitination mediators, which slows bacterial replication. Transcriptomic analyses and in vivo studies also show that LPS stimulation does not replicate the conditions of intracellular Gram-negative bacterial infection as it pertains to type I IFN stimulation or signaling. This study highlights the importance of type I IFNs in protection against opportunistic pathogens through innate immunity, without the need for damaging inflammatory responses.
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Hossain MU, Bhattacharjee A, Emon MTH, Chowdhury ZM, Mosaib MG, Mourin M, Das KC, Keya CA, Salimullah M. Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach. Gene 2021; 771:145368. [PMID: 33346100 PMCID: PMC7833977 DOI: 10.1016/j.gene.2020.145368] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/03/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has become an immense threat to global public health. In this study, we performed complete genome sequencing of a SARS-CoV-2 isolate. More than 67,000 genome sequences were further inspected from Global Initiative on Sharing All Influenza Data (GISAID). Using several in silico techniques, we proposed prospective therapeutics against this virus. Through meticulous analysis, several conserved and therapeutically suitable regions of SARS-CoV-2 such as RNA-dependent RNA polymerase (RdRp), Spike (S) and Membrane glycoprotein (M) coding genes were selected. Both S and M were chosen for the development of a chimeric vaccine that can generate memory B and T cells. siRNAs were also designed for S and M gene silencing. Moreover, six new drug candidates were suggested that might inhibit the activity of RdRp. Since SARS-CoV-2 and SARS-CoV-1 have 82.30% sequence identity, a Gene Expression Omnibus (GEO) dataset of Severe Acute Respiratory Syndrome (SARS) patients were analyzed. In this analysis, 13 immunoregulatory genes were found that can be used to develop type 1 interferon (IFN) based therapy. The proposed vaccine, siRNAs, drugs and IFN based analysis of this study will accelerate the development of new treatments.
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Affiliation(s)
- Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh; Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Tabassum Hossain Emon
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Golam Mosaib
- Department of Biochemistry and Molecular Biology, Faculty of Health & Medical Sciences, Gono Bishwabidyaloy, Ashulia, Savar, Dhaka 1344, Bangladesh
| | - Muntahi Mourin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh; Department of Microbiology, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh.
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Provine NM, Amini A, Garner LC, Spencer AJ, Dold C, Hutchings C, Silva Reyes L, FitzPatrick MEB, Chinnakannan S, Oguti B, Raymond M, Ulaszewska M, Troise F, Sharpe H, Morgan SB, Hinks TSC, Lambe T, Capone S, Folgori A, Barnes E, Rollier CS, Pollard AJ, Klenerman P. MAIT cell activation augments adenovirus vector vaccine immunogenicity. Science 2021; 371:521-526. [PMID: 33510029 PMCID: PMC7610941 DOI: 10.1126/science.aax8819] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/20/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate sensors of viruses and can augment early immune responses and contribute to protection. We hypothesized that MAIT cells may have inherent adjuvant activity in vaccine platforms that use replication-incompetent adenovirus vectors. In mice and humans, ChAdOx1 (chimpanzee adenovirus Ox1) immunization robustly activated MAIT cells. Activation required plasmacytoid dendritic cell (pDC)-derived interferon (IFN)-α and monocyte-derived interleukin-18. IFN-α-induced, monocyte-derived tumor necrosis factor was also identified as a key secondary signal. All three cytokines were required in vitro and in vivo. Activation of MAIT cells positively correlated with vaccine-induced T cell responses in human volunteers and MAIT cell-deficient mice displayed impaired CD8+ T cell responses to multiple vaccine-encoded antigens. Thus, MAIT cells contribute to the immunogenicity of adenovirus vectors, with implications for vaccine design.
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Affiliation(s)
- Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Claire Hutchings
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Laura Silva Reyes
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Blanche Oguti
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Meriel Raymond
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | | | - Fulvia Troise
- Nouscom, SRL, Rome, Italy
- Ceinge Biotechnologie Avanzate, Naples, Italy
| | | | - Sophie B Morgan
- Respiratory Medicine Unit, Nuffield Department of Medicine - Experimental Medicine, University of Oxford, Oxford, UK
| | - Timothy S C Hinks
- Respiratory Medicine Unit, Nuffield Department of Medicine - Experimental Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, University of Oxford, Oxford, UK
| | | | | | - Eleanor Barnes
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Jenner Institute, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Christine S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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Shobha V, Mohan A, Malini AV, Chopra P, Karunanithi P, Subramani Thulasingam S, Selvam S, Deyati A, Srivastava R, Basavanthappa S, Lemos N, Sunitha SM, Mazumder Tagore D, Anand A, Pant S, Jayaswal V, Ramarao M, Dudhgaonkar S. Identification and stratification of systemic lupus erythematosus patients into two transcriptionally distinct clusters based on IFN-I signature. Lupus 2021; 30:762-774. [PMID: 33497307 DOI: 10.1177/0961203321990107] [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: 01/01/2023]
Abstract
OBJECTIVE Despite the significant advancement in the understanding of the pathophysiology of systemic lupus erythematosus (SLE) variable clinical response to newer therapies remain a major concern, especially for patients with lupus nephritis and neuropsychiatric systemic lupus erythematosus (NPSLE). We performed this study with an objective to comprehensively characterize Indian SLE patients with renal and neuropsychiatric manifestation with respect to their gene signature, cytokine profile and immune cell phenotypes. METHODS We characterized 68 Indian SLE subjects with diverse clinical profiles and disease activity and tried to identify differentially expressed genes and enriched pathways. To understand the temporal profile, same patients were followed at 6 and 12-months intervals. Additionally, auto-antibody profile, levels of various chemokines, cytokines and the proportion of different immune cells and their activation status were captured in these subjects. RESULTS Multiple IFN-related pathways were enriched with significant increase in IFN-I gene signature in SLE patients as compared to normal healthy volunteers (NHV). We identified two transcriptionally distinct clusters within the same cohort of SLE patients with differential immune cell activation status, auto-antibody as well as plasma chemokines and cytokines profile. CONCLUSIONS Identification of two distinct clusters of patients based on IFN-I signature provided new insights into the heterogeneity of underlying disease pathogenesis of Indian SLE cohort. Importantly, patient within those clusters retain their distinct expression dynamics of IFN-I signature over the time course of one year despite change in disease activity. This study will guide clinicians and researchers while designing future clinical trials on Indian SLE cohort.
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Affiliation(s)
- Vineeta Shobha
- St. John's National Academy of Health Sciences, Bangalore, India
| | - Anu Mohan
- St. John's National Academy of Health Sciences, Bangalore, India
| | | | - Puneet Chopra
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | - Preethi Karunanithi
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | | | - Sabariya Selvam
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | - Avisek Deyati
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | - Ratika Srivastava
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | - Sushma Basavanthappa
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | - Nadine Lemos
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | - S Margaret Sunitha
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | | | - Amit Anand
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | | | - Vivek Jayaswal
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
| | | | - Shailesh Dudhgaonkar
- Biocon Bristol-Myers Squibb R&D Centre, Syngene International Ltd., Bangalore, India
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Liu CC, Lu IC, Wang LK, Chen JY, Li YY, Yang CP, Liu PH, Cheng WJ, Tan PH. Interferon-β suppresses inflammatory pain through activating µ-opioid receptor. Mol Pain 2021; 17:17448069211045211. [PMID: 34517736 PMCID: PMC8642049 DOI: 10.1177/17448069211045211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/02/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Interferons (IFNs) are cytokines secreted by infected cells that can interfere with viral replication. Besides activating antiviral defenses, type I IFNs also exhibit diverse biological functions. IFN-β has been shown to have a protective effect against neurotoxic and inflammatory insults on neurons. Therefore, we aimed to investigate the possible role of IFN-β in reducing mechanical allodynia caused by Complete Freund's Adjuvant (CFA) injection in rats. We assessed the antinociceptive effect of intrathecal IFN-β in naïve rats and the rats with CFA-induced inflammatory pain. After the behavioral test, the spinal cords of the rats were harvested for western blot and immunohistochemical double staining. We found that intrathecal administration of IFN-β in naïve rats can significantly increase the paw withdrawal threshold and paw withdrawal latency. Further, the intrathecal injection of a neutralizing IFN-β antibody can reduce the paw withdrawal threshold and paw withdrawal latency, suggesting that IFN-β is produced in the spinal cord in normal conditions and serves as a tonic inhibitor of pain. In addition, intrathecal injection of IFN-β at dosages from 1000 U to 10000 U demonstrates a significant transient dose-dependent inhibition of CFA-induced inflammatory pain. This analgesic effect is reversed by intrathecal naloxone, suggesting that IFN-β produces an analgesic effect through central opioid receptor-mediated signaling. Increased expression of phospho-µ-opioid receptors after IFN-β injection was observed on western blot, and immunohistochemical staining showed that µ-opioids co-localized with IFN-α/βR in the dorsal horn of the spinal cord. The findings of this study demonstrate that the analgesic effect of IFN-β is through µ-opioid receptors activation in spial cord.
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Affiliation(s)
- Chien Cheng Liu
- Department of Anesthesiology, E-Da Hospital/I-Shou University, Kaohsiung City, Taiwan
| | - I Cheng Lu
- Department of Anesthesiology, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Li Kai Wang
- Southern Taiwan University of Science and Technology, Tainan City, Taiwan
- Department of Anesthesiology, Chi Mei Medical Center, Tainan City, Taiwan
| | - Jen Yin Chen
- Department of Anesthesiology, Chi Mei Medical Center, Tainan City, Taiwan
| | - Yu Yu Li
- Department of Anesthesiology, Chi Mei Medical Center, Tainan City, Taiwan
| | - Chih Ping Yang
- Department of Anesthesiology, Chi Mei Medical Center, Tainan City, Taiwan
| | - Ping Hsin Liu
- Department of Anesthesiology, E-Da Hospital/I-Shou University, Kaohsiung City, Taiwan
| | - Wan Jung Cheng
- Department of Anesthesiology, Chi Mei Medical Center, Tainan City, Taiwan
| | - Ping Heng Tan
- Department of Anesthesiology, Chi Mei Medical Center, Tainan City, Taiwan
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Guo K, Shen G, Kibbie J, Gonzalez T, Dillon SM, Smith HA, Cooper EH, Lavender K, Hasenkrug KJ, Sutter K, Dittmer U, Kroehl M, Kechris K, Wilson CC, Santiago ML. Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis. PLoS Pathog 2020; 16:e1008986. [PMID: 33064743 PMCID: PMC7592919 DOI: 10.1371/journal.ppat.1008986] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 10/28/2020] [Accepted: 09/16/2020] [Indexed: 12/27/2022] Open
Abstract
The Type I Interferons (IFN-Is) are innate antiviral cytokines that include 12 different IFNα subtypes and IFNβ that signal through the IFN-I receptor (IFNAR), inducing hundreds of IFN-stimulated genes (ISGs) that comprise the 'interferome'. Quantitative differences in IFNAR binding correlate with antiviral activity, but whether IFN-Is exhibit qualitative differences remains controversial. Moreover, the IFN-I response is protective during acute HIV-1 infection, but likely pathogenic during the chronic stages. To gain a deeper understanding of the IFN-I response, we compared the interferomes of IFNα subtypes dominantly-expressed in HIV-1-exposed plasmacytoid dendritic cells (1, 2, 5, 8 and 14) and IFNβ in the earliest cellular targets of HIV-1 infection. Primary gut CD4 T cells from 3 donors were treated for 18 hours ex vivo with individual IFN-Is normalized for IFNAR signaling strength. Of 1,969 IFN-regulated genes, 246 'core ISGs' were induced by all IFN-Is tested. However, many IFN-regulated genes were not shared between the IFNα subtypes despite similar induction of canonical antiviral ISGs such as ISG15, RSAD2 and MX1, formally demonstrating qualitative differences between the IFNα subtypes. Notably, IFNβ induced a broader interferome than the individual IFNα subtypes. Since IFNβ, and not IFNα, is upregulated during chronic HIV-1 infection in the gut, we compared core ISGs and IFNβ-specific ISGs from colon pinch biopsies of HIV-1-uninfected (n = 13) versus age- and gender-matched, antiretroviral-therapy naïve persons with HIV-1 (PWH; n = 19). Core ISGs linked to inflammation, T cell activation and immune exhaustion were elevated in PWH, positively correlated with plasma lipopolysaccharide (LPS) levels and gut IFNβ levels, and negatively correlated with gut CD4 T cell frequencies. In sharp contrast, IFNβ-specific ISGs linked to protein translation and anti-inflammatory responses were significantly downregulated in PWH, negatively correlated with gut IFNβ and LPS, and positively correlated with plasma IL6 and gut CD4 T cell frequencies. Our findings reveal qualitative differences in interferome induction by diverse IFN-Is and suggest potential mechanisms for how IFNβ may drive HIV-1 pathogenesis in the gut.
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Affiliation(s)
- Kejun Guo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Guannan Shen
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Jon Kibbie
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Tania Gonzalez
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Stephanie M. Dillon
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Harry A. Smith
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Emily H. Cooper
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Kerry Lavender
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Canada
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, Hamilton, MT, United States of America
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisberg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisberg-Essen, Essen, Germany
| | - Miranda Kroehl
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Katerina Kechris
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Cara C. Wilson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Mario L. Santiago
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
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Schreiber G. The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19. Front Immunol 2020; 11:595739. [PMID: 33117408 PMCID: PMC7561359 DOI: 10.3389/fimmu.2020.595739] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Type I interferons (IFN-I) were first discovered over 60 years ago in a classical experiment by Isaacs and Lindenman, who showed that IFN-Is possess antiviral activity. Later, it became one of the first approved protein drugs using heterologous protein expression systems, which allowed its large-scale production. It has been approved, and widely used in a pleiotropy of diseases, including multiple-sclerosis, hepatitis B and C, and some forms of cancer. Preliminary clinical data has supported its effectiveness against potential pandemic pathogens such as Ebola and SARS. Still, more efficient and specific drugs have taken its place in treating such diseases. The COVID-19 global pandemic has again lifted the status of IFN-Is to become one of the more promising drug candidates, with initial clinical trials showing promising results in reducing the severity and duration of the disease. Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I-receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Furthermore, I discuss how these may guide the optimized use IFN-Is in combatting COVID-19.
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Affiliation(s)
- Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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41
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Ackerman EE, Shoemaker JE. Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning. Viruses 2020; 12:v12101087. [PMID: 32993136 PMCID: PMC7650805 DOI: 10.3390/v12101087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
In a short time, the COVID-19 pandemic has left the world with over 25 million cases and staggering death tolls that are still rising. Treatments for SARS-CoV-2 infection are desperately needed as there are currently no approved drug therapies. With limited knowledge of viral mechanisms, a network controllability method of prioritizing existing drugs for repurposing efforts is optimal for quickly moving through the drug approval pipeline using limited, available, virus-specific data. Based on network topology and controllability, 16 proteins involved in translation, cellular transport, cellular stress, and host immune response are predicted as regulators of the SARS-CoV-2 infected cell. Of the 16, eight are prioritized as possible drug targets where two, PVR and SCARB1, are previously unexplored. Known compounds targeting these genes are suggested for viral inhibition study. Prioritized proteins in agreement with previous analysis and viral inhibition studies verify the ability of network controllability to predict biologically relevant candidates.
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Affiliation(s)
- Emily E. Ackerman
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15260, USA;
| | - Jason E. Shoemaker
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15260, USA;
- The McGowan Institute for Regenerative Medicine (MIRM), University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Correspondence:
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Korvatska O, Kiianitsa K, Ratushny A, Matsushita M, Beeman N, Chien WM, Satoh JI, Dorschner MO, Keene CD, Bammler TK, Bird TD, Raskind WH. Triggering Receptor Expressed on Myeloid Cell 2 R47H Exacerbates Immune Response in Alzheimer's Disease Brain. Front Immunol 2020; 11:559342. [PMID: 33101276 PMCID: PMC7546799 DOI: 10.3389/fimmu.2020.559342] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/25/2020] [Indexed: 01/11/2023] Open
Abstract
The R47H variant in the microglial triggering receptor expressed on myeloid cell 2 (TREM2) receptor is a strong risk factor for Alzheimer’s disease (AD). To characterize processes affected by R47H, we performed an integrative network analysis of genes expressed in brains of AD patients with R47H, sporadic AD without the variant, and patients with polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL), systemic disease with early-onset dementia caused by loss-of-function mutations in TREM2 or its adaptor TYRO protein tyrosine kinase-binding protein (TYROBP). Although sporadic AD had few perturbed microglial and immune genes, TREM2 R47H AD demonstrated upregulation of interferon type I response and pro-inflammatory cytokines accompanied by induction of NKG2D stress ligands. In contrast, PLOSL had distinct sets of highly perturbed immune and microglial genes that included inflammatory mediators, immune signaling, cell adhesion, and phagocytosis. TREM2 knockout (KO) in THP1, a human myeloid cell line that constitutively expresses the TREM2- TYROBP receptor, inhibited response to the viral RNA mimetic poly(I:C) and phagocytosis of amyloid-beta oligomers; overexpression of ectopic TREM2 restored these functions. Compared with wild-type protein, R47H TREM2 had a higher stimulatory effect on the interferon type I response signature. Our findings point to a role of the TREM2 receptor in the control of the interferon type I response in myeloid cells and provide insight regarding the contribution of R47H TREM2 to AD pathology.
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Affiliation(s)
- Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, Seattle, WA, United States
| | - Alexander Ratushny
- Seattle Biomedical Research Institute and Institute for Systems Biology, Seattle, WA, United States
| | - Mark Matsushita
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, United States
| | - Neal Beeman
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, United States
| | - Wei-Ming Chien
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, United States
| | - Jun-Ichi Satoh
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Michael O Dorschner
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, Seattle, WA, United States
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, WA, United States.,Geriatric Research, Education and Clinical Center, Veteran Affairs Puget Sound Health Care System, Seattle, WA, United States
| | - Wendy H Raskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, United States.,Geriatric Research, Education and Clinical Center, Veteran Affairs Puget Sound Health Care System, Seattle, WA, United States.,Mental Illness Research, Education and Clinical Center, Department of Veteran Affairs, Seattle, WA, United States
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Blaauboer A, Booy S, van Koetsveld PM, Karels B, Dogan F, van Zwienen S, van Eijck CHJ, Hofland LJ. Interferon-beta enhances sensitivity to gemcitabine in pancreatic cancer. BMC Cancer 2020; 20:913. [PMID: 32967656 PMCID: PMC7513525 DOI: 10.1186/s12885-020-07420-0] [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: 07/01/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background Adjuvant gemcitabine for pancreatic cancer has limited efficacy in the clinical setting. Impaired drug metabolism is associated with treatment resistance. We aimed to evaluate the chemosensitising effect of interferon-beta (IFN-β). Methods BxPC-3, CFPAC-1, and Panc-1 cells were pre-treated with IFN-β followed by gemcitabine monotherapy. The effect on cell growth, colony formation, and cell cycle was determined. RT-qPCR was used to measure gene expression. BxPC-3 cells were used in a heterotopic subcutaneous mouse model. Results IFN-β increased sensitivity to gemcitabine (4-, 7.7-, and 1.7-fold EC50 decrease in BxPC-3, CFPAC-1, and Panc-1, respectively; all P < 0.001). Findings were confirmed when assessing colony formation. The percentage of cells in the S-phase was significantly increased after IFN-β treatment only in BxPC-3 and CFPAC-1 by 12 and 7%, respectively (p < 0.001 and p < 0.05, respectively). Thereby, IFN-β upregulated expression of the drug transporters SLC28A1 in BxPC-3 (252%) and SLC28A3 in BxPC-3 (127%) and CFPAC-1 (223%) (all p < 0.001). In vivo, combination therapy reduced tumor volume with 45% (P = 0.01). Both ex vivo and in vivo data demonstrate a significant reduction in the number of proliferating cells, whereas apoptosis was increased. Conclusions For the first time, we validated the chemosensitising effects of IFN-β when combined with gemcitabine in vitro, ex vivo, and in vivo. This was driven by cell cycle modulation and associated with an upregulation of genes involving intracellular uptake of gemcitabine. The use of IFN-β in combination with gemcitabine seems promising in patients with pancreatic cancer and needs to be further explored.
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Affiliation(s)
- Amber Blaauboer
- Department of Surgery, Erasmus Medical Center, Room Ee-514, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands. .,Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Stephanie Booy
- Department of Surgery, Erasmus Medical Center, Room Ee-514, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter M van Koetsveld
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bas Karels
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fadime Dogan
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Suzanne van Zwienen
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus Medical Center, Room Ee-514, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Leo J Hofland
- Department of Internal Medicine, Division of Endocrinology, Erasmus Medical Center, Rotterdam, The Netherlands
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Kleinpenning F, Steigenberger B, Wu W, Heck AJR. Fishing for newly synthesized proteins with phosphonate-handles. Nat Commun 2020; 11:3244. [PMID: 32591520 PMCID: PMC7320153 DOI: 10.1038/s41467-020-17010-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term PhosID. In this approach, click-able phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets. Here the authors describe PhosID, an enrichment strategy using phosphonate-handles, that combines click chemistry and IMAC-based phospho-enrichment for quantitative proteomics analysis of newly synthesized proteins.
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Affiliation(s)
- Fleur Kleinpenning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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45
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Kelly-Scumpia KM, Choi A, Shirazi R, Bersabe H, Park E, Scumpia PO, Ochoa MT, Yu J, Ma F, Pellegrini M, Modlin RL. ER Stress Regulates Immunosuppressive Function of Myeloid Derived Suppressor Cells in Leprosy that Can Be Overcome in the Presence of IFN-γ. iScience 2020; 23:101050. [PMID: 32339990 PMCID: PMC7190750 DOI: 10.1016/j.isci.2020.101050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023] Open
Abstract
Myeloid derived suppressor cells (MDSCs) are a population of immature myeloid cells that suppress adaptive immune function, yet the factors that regulate their suppressive function in patients with infection remain unclear. We studied MDSCs in patients with leprosy, a disease caused by Mycobacterium leprae, where clinical manifestations present on a spectrum that correlate with immunity to the pathogen. We found that HLA-DR-CD33+CD15+ MDSCs were increased in blood from patients with disseminated/progressive lepromatous leprosy and possessed T cell-suppressive activity as compared with self-limiting tuberculoid leprosy. Mechanistically, we found ER stress played a critical role in regulating the T cell suppressive activity in these MDSCs. Furthermore, ER stress augmented IL-10 production, contributing to MDSC activity, whereas IFN-γ allowed T cells to overcome MDSC suppressive activity. These studies highlight a regulatory mechanism that links ER stress to IL-10 in mediating MDSC suppressive function in human infectious disease. Cells with an MDSC phenotype are increased in blood and skin of patients with leprosy Only MDSCs from patients with leprosy with disseminated infection suppress T cell function MDSC function is dependent on increased ER stress and IL-10 production MDSC function can be reversed in the presence of IFN-γ
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Affiliation(s)
| | - Aaron Choi
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roksana Shirazi
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Hannah Bersabe
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Esther Park
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Philip O Scumpia
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Maria T Ochoa
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Yu
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Feiyang Ma
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Robert L Modlin
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
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46
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Oon S, Monaghan K, Ng M, Hoi A, Morand E, Vairo G, Maraskovsky E, Nash AD, Wicks IP, Wilson NJ. A potential association between IL-3 and type I and III interferons in systemic lupus erythematosus. Clin Transl Immunology 2019; 8:e01097. [PMID: 31890206 PMCID: PMC6928763 DOI: 10.1002/cti2.1097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 10/30/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Objectives Plasmacytoid dendritic cells (pDCs), through the production of type 1 interferons (IFNs) and other cytokines, are major contributors to systemic lupus erythematosus (SLE) pathogenesis. IL-3 promotes pDC survival, but its role in SLE is not well characterised. This study investigated serum IL-3 and IFN levels, and a whole blood 'IL-3 gene signature', in human SLE. Methods Serum cytokine levels were measured by ELISA in n = 42 SLE patients, and n = 44 healthy donors. IL-3-regulated genes were determined by RNASeq of healthy donor whole blood cells (WBCs) stimulated in vitro with IL-3 for 6 or 24 h. Whole blood cell RNASeq analysis was undertaken in a separate cohort of n = 31 SLE patients, and n = 28 healthy donors. Results Serum IL-3 levels correlated with IFNα (r = 0.612, 95% CI 0.455-0.733, P < 0.001) and type III IFN (r = 0.585, 95% CI 0.406-0.720, P < 0.0001). IL-3 stimulation of WBC in vitro altered 794 genes (-1 ≥ logFC ≥ 1, FDR < 0.05), of which 35 overlapped with genes differentially expressed between SLE and healthy donors. These 35 genes were expressed in 27/31 SLE donors, revealing the presence of an 'IL-3 gene signature'. There was strong correlation between the IL-3 signature and an IFN signature, as determined by hierarchical clustering of the 500 most variable genes in SLE donors (r = 0.939, 95% CI 0.898-0.964, P < 0.0001). Conclusion A dual IL-3/IFN gene signature is a feature of SLE. An association between IL-3 and IFN raises the possibility that dual blockade of IL-3 and IFN may be especially useful for SLE patients with this dual cytokine gene signature.
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Affiliation(s)
- Shereen Oon
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,The Royal Melbourne Hospital Parkville VIC Australia.,The University of Melbourne Parkville VIC Australia
| | | | | | | | | | | | - Eugene Maraskovsky
- The University of Melbourne Parkville VIC Australia.,CSL Limited Parkville VIC Australia
| | - Andrew D Nash
- The University of Melbourne Parkville VIC Australia.,CSL Limited Parkville VIC Australia
| | - Ian P Wicks
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,The Royal Melbourne Hospital Parkville VIC Australia.,The University of Melbourne Parkville VIC Australia
| | - Nicholas J Wilson
- The University of Melbourne Parkville VIC Australia.,CSL Limited Parkville VIC Australia
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47
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Tamaura M, Satoh-Takayama N, Tsumura M, Sasaki T, Goda S, Kageyama T, Hayakawa S, Kimura S, Asano T, Nakayama M, Koseki H, Ohara O, Okada S, Ohno H, Kobayashi M. Human gain-of-function STAT1 mutation disturbs IL-17 immunity in mice. Int Immunol 2019; 32:259-272. [DOI: 10.1093/intimm/dxz079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/18/2019] [Indexed: 01/17/2023] Open
Abstract
Abstract
Gain-of-function (GOF) mutations in the gene for signal transducer and activator of transcription 1 (STAT1) account for approximately one-half of patients with chronic mucocutaneous candidiasis (CMC) disease. Patients with GOF-STAT1 mutations display a broad variety of infectious and autoimmune manifestations in addition to CMC, and those with severe infections and/or autoimmunity have a poor prognosis. The establishment of safe and effective treatments based on a precise understanding of the molecular mechanisms of this disorder is required to improve patient care. To tackle this problem, we introduced the human R274Q GOF mutation into mice [GOF-Stat1 knock-in (GOF-Stat1R274Q)]. To investigate the immune responses, we focused on the small intestine (SI), which contains abundant Th17 cells. Stat1R274Q/R274Q mice showed excess phosphorylation of STAT1 in CD4+ T cells upon IFN-γ stimulation, consistent with the human phenotype in patients with the R274Q mutation. We identified two subpopulations of CD4+ T cells, those with ‘normal’ or ‘high’ level of basal STAT1 protein in Stat1R274Q/R274Q mice. Upon IFN-γ stimulation, the ‘normal’ level CD4+ T cells were more efficiently phosphorylated than those from WT mice, whereas the ‘high’ level CD4+ T cells were not, suggesting that the level of STAT1 protein does not directly correlate with the level of pSTAT1 in the SI. Inoculation of Stat1R274Q/R274Q mice with Candida albicans elicited decreased IL-17-producing CD4+RORγt+ cells. Stat1R274Q/R274Q mice also excreted larger amounts of C. albicans DNA in their feces than control mice. Under these conditions, there was up-regulation of T-bet in CD4+ T cells. GOF-Stat1R274Q mice thus should be a valuable model for functional analysis of this disorder.
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Affiliation(s)
- Moe Tamaura
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Naoko Satoh-Takayama
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Miyuki Tsumura
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takaharu Sasaki
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoshi Goda
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoko Kageyama
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Seiichi Hayakawa
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takaki Asano
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Manabu Nakayama
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoshi Okada
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Division of Immunobiology, Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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Aiello A, Giannessi F, Percario ZA, Affabris E. An emerging interplay between extracellular vesicles and cytokines. Cytokine Growth Factor Rev 2019; 51:49-60. [PMID: 31874738 DOI: 10.1016/j.cytogfr.2019.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Extracellular vesicles (EVs) are small membrane-bound particles that are naturally released from cells. They are recognized as potent vehicles of intercellular communication both in prokaryotes and eukaryotes. Because of their capacity to carry biological macromolecules such as proteins, lipids and nucleic acids, EVs influence different physiological and pathological functions of both parental and recipient cells. Although multiple pathways have been proposed for cytokine secretion beyond the classical ER/Golgi route, EVs have recently recognized as an alternative secretory mechanism. Interestingly, cytokines/chemokines exploit these vesicles to be released into the extracellular milieu, and also appear to modulate their release, trafficking and/or content. In this review, we provide an overview of the cytokines/chemokines that are known to be associated with EVs or their regulation with a focus on TNFα, IL-1β and IFNs.
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49
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Marks ZRC, Campbell N, deWeerd NA, Lim SS, Gearing LJ, Bourke NM, Hertzog PJ. PROPERTIES AND FUNCTIONS OF THE NOVEL TYPE I INTERFERON EPSILON. Semin Immunol 2019; 43:101328. [PMID: 31734130 DOI: 10.1016/j.smim.2019.101328] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 11/17/2022]
Abstract
Interferon epsilon (IFNε) is a type I IFN with unusual patterns of expression and therefore, function. It is constitutively expressed by reproductive tract epithelium and regulated by hormones during estrus cycle, reproduction, and menopause and by exogenous hormones. The IFNe protein is encoded by a gene in the type I IFN locus, binds to IFNAR1 and 2 which are required for signaling via the JAK STAT pathway. Its affinity for binding receptors and transducing signals is less potent than IFNα or β subtypes in vitro. Nevertheless, in vivo experiments indicate its efficacy in regulating mucosal immune responses and protecting from bacterial and viral infections. These studies demonstrate a different mechanism of action to type I IFNs. In this organ system with dynamic fluxes in cellularity, requirement to tolerate an implanted fetus, and be protected from disease, there is co-option of a special IFN from a family of effective immunoregulators, with unique controls and modified potency to make it a safe and effective constitutive reproductive tract cytokine.
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Affiliation(s)
- Zoe R C Marks
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Nicole Campbell
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Nicole A deWeerd
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Nollaig M Bourke
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia; Department of Medical Gerontology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia.
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50
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Kalinin S, Meares GP, Lin SX, Pietruczyk EA, Saher G, Spieth L, Nave KA, Boullerne AI, Lutz SE, Benveniste EN, Feinstein DL. Liver kinase B1 depletion from astrocytes worsens disease in a mouse model of multiple sclerosis. Glia 2019; 68:600-616. [PMID: 31664743 PMCID: PMC7337013 DOI: 10.1002/glia.23742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/19/2019] [Accepted: 10/05/2019] [Indexed: 12/15/2022]
Abstract
Liver kinase B1 (LKB1) is a ubiquitously expressed kinase involved in the regulation of cell metabolism, growth, and inflammatory activation. We previously reported that a single nucleotide polymorphism in the gene encoding LKB1 is a risk factor for multiple sclerosis (MS). Since astrocyte activation and metabolic function have important roles in regulating neuroinflammation and neuropathology, we examined the serine/threonine kinase LKB1 in astrocytes in a chronic experimental autoimmune encephalomyelitis mouse model of MS. To reduce LKB1, a heterozygous astrocyte-selective conditional knockout (het-cKO) model was used. While disease incidence was similar, disease severity was worsened in het-cKO mice. RNAseq analysis identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched in het-cKO mice relating to mitochondrial function, confirmed by alterations in mitochondrial complex proteins and reductions in mRNAs related to astrocyte metabolism. Enriched pathways included major histocompatibility class II genes, confirmed by increases in MHCII protein in spinal cord and cerebellum of het-cKO mice. We observed increased numbers of CD4+ Th17 cells and increased neuronal damage in spinal cords of het-cKO mice, associated with reduced expression of choline acetyltransferase, accumulation of immunoglobulin-γ, and reduced expression of factors involved in motor neuron survival. In vitro, LKB1-deficient astrocytes showed reduced metabolic function and increased inflammatory activation. These data suggest that metabolic dysfunction in astrocytes, in this case due to LKB1 deficiency, can exacerbate demyelinating disease by loss of metabolic support and increase in the inflammatory environment.
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Affiliation(s)
- Sergey Kalinin
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Gordon P Meares
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, West Virginia
| | - Shao Xia Lin
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | | | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Gottingen, Germany
| | - Lena Spieth
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Gottingen, Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Gottingen, Germany
| | - Anne I Boullerne
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Sarah E Lutz
- Department of Anatomy and Cell Biology, University of Illinois, Chicago, Illinois
| | - Etty N Benveniste
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Douglas L Feinstein
- Department of Anesthesiology, University of Illinois, Chicago, Illinois.,Department of Veterans Affairs, Jesse Brown VA Medical Center, Chicago, Illinois
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