1
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Naulaerts S, Datsi A, Borras DM, Antoranz Martinez A, Messiaen J, Vanmeerbeek I, Sprooten J, Laureano RS, Govaerts J, Panovska D, Derweduwe M, Sabel MC, Rapp M, Ni W, Mackay S, Van Herck Y, Gelens L, Venken T, More S, Bechter O, Bergers G, Liston A, De Vleeschouwer S, Van Den Eynde BJ, Lambrechts D, Verfaillie M, Bosisio F, Tejpar S, Borst J, Sorg RV, De Smet F, Garg AD. Multiomics and spatial mapping characterizes human CD8 + T cell states in cancer. Sci Transl Med 2023; 15:eadd1016. [PMID: 37043555 DOI: 10.1126/scitranslmed.add1016] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Clinically relevant immunological biomarkers that discriminate between diverse hypofunctional states of tumor-associated CD8+ T cells remain disputed. Using multiomics analysis of CD8+ T cell features across multiple patient cohorts and tumor types, we identified tumor niche-dependent exhausted and other types of hypofunctional CD8+ T cell states. CD8+ T cells in "supportive" niches, like melanoma or lung cancer, exhibited features of tumor reactivity-driven exhaustion (CD8+ TEX). These included a proficient effector memory phenotype, an expanded T cell receptor (TCR) repertoire linked to effector exhaustion signaling, and a cancer-relevant T cell-activating immunopeptidome composed of largely shared cancer antigens or neoantigens. In contrast, "nonsupportive" niches, like glioblastoma, were enriched for features of hypofunctionality distinct from canonical exhaustion. This included immature or insufficiently activated T cell states, high wound healing signatures, nonexpanded TCR repertoires linked to anti-inflammatory signaling, high T cell-recognizable self-epitopes, and an antiproliferative state linked to stress or prodeath responses. In situ spatial mapping of glioblastoma highlighted the prevalence of dysfunctional CD4+:CD8+ T cell interactions, whereas ex vivo single-cell secretome mapping of glioblastoma CD8+ T cells confirmed negligible effector functionality and a promyeloid, wound healing-like chemokine profile. Within immuno-oncology clinical trials, anti-programmed cell death protein 1 (PD-1) immunotherapy facilitated glioblastoma's tolerogenic disparities, whereas dendritic cell (DC) vaccines partly corrected them. Accordingly, recipients of a DC vaccine for glioblastoma had high effector memory CD8+ T cells and evidence of antigen-specific immunity. Collectively, we provide an atlas for assessing different CD8+ T cell hypofunctional states in immunogenic versus nonimmunogenic cancers.
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Affiliation(s)
- Stefan Naulaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
- Ludwig Institute for Cancer Research, Brussels 1200, Belgium
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
- De Duve Institute, UCLouvain, Brussels 1200, Belgium
| | - Angeliki Datsi
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Daniel M Borras
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Asier Antoranz Martinez
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Julie Messiaen
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Isaure Vanmeerbeek
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Raquel S Laureano
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Dena Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Marleen Derweduwe
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Michael C Sabel
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Marion Rapp
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Weiming Ni
- IsoPlexis Corporation, Branford, CT 06405-2801, USA
| | - Sean Mackay
- IsoPlexis Corporation, Branford, CT 06405-2801, USA
| | - Yannick Van Herck
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven and Department of General Medical Oncology, UZ Leuven, Leuven 3000, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Tom Venken
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
- VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Sanket More
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Oliver Bechter
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven and Department of General Medical Oncology, UZ Leuven, Leuven 3000, Belgium
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, Department of Oncology, VIB Center for Cancer Biology, KU Leuven, Leuven 3000, Belgium
- Department of Neurological Surgery, UCSF Comprehensive Cancer Center, UCSF, San Francisco, CA 94143-0350, USA
| | - Adrian Liston
- VIB Center for Brain and Disease Research, Leuven 3000, Belgium
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Steven De Vleeschouwer
- Department of Neurosurgery, University Hospitals Leuven, Leuven 3000, Belgium
- Laboratory of Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
- Leuven Brain Institute (LBI), Leuven 3000, Belgium
| | - Benoit J Van Den Eynde
- Ludwig Institute for Cancer Research, Brussels 1200, Belgium
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
- De Duve Institute, UCLouvain, Brussels 1200, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
- VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Michiel Verfaillie
- Neurosurgery Department, Europaziekenhuizen - Cliniques de l'Europe, Sint-Elisabeth, Brussels 1180, Belgium
| | - Francesca Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Sabine Tejpar
- Laboratory for Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Jannie Borst
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Rüdiger V Sorg
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Abhishek D Garg
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
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2
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Wauters E, Van Mol P, Garg AD, Jansen S, Van Herck Y, Vanderbeke L, Bassez A, Boeckx B, Malengier-Devlies B, Timmerman A, Van Brussel T, Van Buyten T, Schepers R, Heylen E, Dauwe D, Dooms C, Gunst J, Hermans G, Meersseman P, Testelmans D, Yserbyt J, Tejpar S, De Wever W, Matthys P, Neyts J, Wauters J, Qian J, Lambrechts D. Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages. Cell Res 2021; 31:272-290. [PMID: 33473155 PMCID: PMC8027624 DOI: 10.1038/s41422-020-00455-9] [Citation(s) in RCA: 194] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/20/2020] [Indexed: 02/08/2023] Open
Abstract
How the innate and adaptive host immune system miscommunicate to worsen COVID-19 immunopathology has not been fully elucidated. Here, we perform single-cell deep-immune profiling of bronchoalveolar lavage (BAL) samples from 5 patients with mild and 26 with critical COVID-19 in comparison to BALs from non-COVID-19 pneumonia and normal lung. We use pseudotime inference to build T-cell and monocyte-to-macrophage trajectories and model gene expression changes along them. In mild COVID-19, CD8+ resident-memory (TRM) and CD4+ T-helper-17 (TH17) cells undergo active (presumably antigen-driven) expansion towards the end of the trajectory, and are characterized by good effector functions, while in critical COVID-19 they remain more naïve. Vice versa, CD4+ T-cells with T-helper-1 characteristics (TH1-like) and CD8+ T-cells expressing exhaustion markers (TEX-like) are enriched halfway their trajectories in mild COVID-19, where they also exhibit good effector functions, while in critical COVID-19 they show evidence of inflammation-associated stress at the end of their trajectories. Monocyte-to-macrophage trajectories show that chronic hyperinflammatory monocytes are enriched in critical COVID-19, while alveolar macrophages, otherwise characterized by anti-inflammatory and antigen-presenting characteristics, are depleted. In critical COVID-19, monocytes contribute to an ATP-purinergic signaling-inflammasome footprint that could enable COVID-19 associated fibrosis and worsen disease-severity. Finally, viral RNA-tracking reveals infected lung epithelial cells, and a significant proportion of neutrophils and macrophages that are involved in viral clearance.
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Affiliation(s)
- Els Wauters
- grid.5596.f0000 0001 0668 7884Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium ,grid.410569.f0000 0004 0626 3338Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Van Mol
- grid.410569.f0000 0004 0626 3338Department of Pneumology, University Hospitals Leuven, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Abhishek Dinkarnath Garg
- grid.5596.f0000 0001 0668 7884Laboratory for Cell Stress & Immunity (CSI), Department of Cellular and Molecular Medicine (CMM), KU Leuven, Leuven, Belgium
| | - Sander Jansen
- grid.5596.f0000 0001 0668 7884Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Yannick Van Herck
- grid.5596.f0000 0001 0668 7884Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lore Vanderbeke
- grid.5596.f0000 0001 0668 7884Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Ayse Bassez
- grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Bram Boeckx
- grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Bert Malengier-Devlies
- grid.5596.f0000 0001 0668 7884Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anna Timmerman
- grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Thomas Van Brussel
- grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Tina Van Buyten
- grid.5596.f0000 0001 0668 7884Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Rogier Schepers
- grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Elisabeth Heylen
- grid.5596.f0000 0001 0668 7884Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dieter Dauwe
- grid.5596.f0000 0001 0668 7884Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Christophe Dooms
- grid.5596.f0000 0001 0668 7884Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium ,grid.410569.f0000 0004 0626 3338Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Jan Gunst
- grid.5596.f0000 0001 0668 7884Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Greet Hermans
- grid.5596.f0000 0001 0668 7884Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Philippe Meersseman
- grid.5596.f0000 0001 0668 7884Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Dries Testelmans
- grid.5596.f0000 0001 0668 7884Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium ,grid.410569.f0000 0004 0626 3338Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Jonas Yserbyt
- grid.5596.f0000 0001 0668 7884Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium ,grid.410569.f0000 0004 0626 3338Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Sabine Tejpar
- grid.5596.f0000 0001 0668 7884Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Walter De Wever
- grid.5596.f0000 0001 0668 7884Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Patrick Matthys
- grid.5596.f0000 0001 0668 7884Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Johan Neyts
- grid.5596.f0000 0001 0668 7884Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Joost Wauters
- grid.5596.f0000 0001 0668 7884Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Junbin Qian
- grid.13402.340000 0004 1759 700XDepartment of Gynecologic Oncology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006 China
| | - Diether Lambrechts
- grid.5596.f0000 0001 0668 7884Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology, VIB, Leuven, Belgium
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3
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James NE, Oliver MT, Ribeiro JR, Cantillo E, Rowswell-Turner RB, Kim KK, Chichester CO, DiSilvestro PA, Moore RG, Singh RK, Yano N, Zhao TC. Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6. Front Pharmacol 2019; 10:216. [PMID: 30941033 PMCID: PMC6433991 DOI: 10.3389/fphar.2019.00216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/20/2019] [Indexed: 01/07/2023] Open
Abstract
While selective overexpression of serum clinical biomarker Human epididymis secretory protein 4 (HE4) is indicative of ovarian cancer tumorigenesis, much is still known about the mechanistic role of the HE4 gene or gene product. Here, we examine the role of the secretory glycoprotein HE4 in ovarian cancer immune evasion. Through modified subtractive hybridization analyses of human peripheral blood mononuclear cells (PBMCs), we have characterized gene targets of HE4 and established a preliminary mechanism of HE4-mediated immune failure in ovarian tumors. Dual specificity phosphatase 6 (DUSP6) emerged as the most upregulated gene in PBMCs upon in vitro exposure to HE4. DUSP6 was found to be upregulated in CD8+ cells and CD56+ cells. HE4 exposure reduced Erk1/2 phosphorylation specifically in these cell populations and the effect was erased by co-incubation with a DUSP6 inhibitor, (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI). In co-culture with PBMCs, HE4-silenced SKOV3 human ovarian cancer cells exhibited enhanced proliferation upon exposure to external HE4, while this effect was partially attenuated by adding BCI to the culture. Additionally, the reversal effects of BCI were erased in the co-culture with CD8+ / CD56+ cell deprived PBMCs. Taken together, these findings show that HE4 enhances tumorigenesis of ovarian cancer by compromising cytotoxic CD8+ and CD56+ cells through upregulation of self-produced DUSP6.
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Affiliation(s)
- Nicole E James
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States.,Department of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Matthew T Oliver
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Jennifer R Ribeiro
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Evelyn Cantillo
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Rachael B Rowswell-Turner
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, United States
| | - Kyu-Kwang Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, United States
| | | | - Paul A DiSilvestro
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Richard G Moore
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, United States
| | - Rakesh K Singh
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, United States
| | - Naohiro Yano
- Program in Women's Oncology, Department of Obstetrics and Gynecology, Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States.,Department of Surgery, Roger Williams Medical Center, Boston University Medical School, Providence, RI, United States
| | - Ting C Zhao
- Department of Surgery, Roger Williams Medical Center, Boston University Medical School, Providence, RI, United States
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Schlafen2 mutation unravels a role for chronic ER stress in the loss of T cell quiescence. Oncotarget 2018; 7:39396-39407. [PMID: 27276683 PMCID: PMC5129940 DOI: 10.18632/oncotarget.9818] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 05/22/2016] [Indexed: 11/29/2022] Open
Abstract
Immunologically naïve lymphocytes are kept in a quiescent state until antigen engagement. These quiescent immune cells are characterized by small cell size, lack of spontaneous proliferation and low metabolic rate. Lymphocyte quiescence is actively enforced condition which ensures the preservation of proper differentiation and proliferation capabilities of naïve and memory lymphocytes. Previously we described a chemically induced mutation in Schlafen2 (Slfn2), termed elektra, which breaks quiescence and compromises immunity. However, the mechanism by which Slfn2 maintains quiescence remains unknown. Here we demonstrate that elektra T cells display chronic ER stress under steady state conditions. Modulation of ER stress response by depletion of either UPR mediators XBP1 or CHOP, improved viability and partially corrected the developmental abnormalities and proliferation capabilities of elektra T cells. Altogether, our results demonstrate a functional connection between Slfn2 induced quiescence in T cells and ER homeostasis, clarifying a novel mechanism by which immune cell quiescence is maintained.
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5
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Goldshtein A, Zerbib SM, Omar I, Cohen-Daniel L, Popkin D, Berger M. Loss of T-cell quiescence by targeting Slfn2 prevents the development and progression of T-ALL. Oncotarget 2018; 7:46835-46847. [PMID: 27206675 PMCID: PMC5216906 DOI: 10.18632/oncotarget.9390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 04/26/2016] [Indexed: 01/08/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes. Despite significant improvement in the treatment of T-ALL, approximately 20% of children and most adults undergo relapse. Previous findings demonstrated that loss of T-cell quiescence due to a mutation in the Slfn2 gene (elektra) leads to acquisition of an aberrant developmental program by which T-cells lose their renewal capabilities and undergo apoptosis. Here we show that the elektra mutation in Slfn2 completely prevents a severe lymphoproliferative disease caused by overexpression of BCL2 in combination with Fas deficiency in mice. Moreover, Slfn2 impaired-function protects mice from experimental disease similar to human T-ALL by severely impairing the proliferation potential and survival of leukemic T-cells, partially by activation of the p53 tumor suppressor protein. Our study suggest that in certain malignancies, such as T-ALL, a novel therapeutic strategy may be applied by imposing aberrant development of leukemic cells. Furthermore, as the elektra mutation in Slfn2 seems to impair only T-cells and monocytes, targeting Slfn2 is expected to be harmless to other cell types, and thereby could be a promising target for treating malignancies. Together our results demonstrate the potential of targeting Slfn2 and its human paralog for T-ALL treatment.
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Affiliation(s)
- Aviya Goldshtein
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Shani Mistriel Zerbib
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Ibrahim Omar
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Leonor Cohen-Daniel
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Daniel Popkin
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Michael Berger
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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6
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Omar I, Rom O, Aviram M, Cohen-Daniel L, Gebre AK, Parks JS, Berger M. Slfn2 mutation-induced loss of T-cell quiescence leads to elevated de novo sterol synthesis. Immunology 2017; 152:484-493. [PMID: 28672048 DOI: 10.1111/imm.12785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/12/2017] [Accepted: 06/22/2017] [Indexed: 01/04/2023] Open
Abstract
Acquisition of a 'quiescence programme' by naive T cells is important to provide a stress-free environment and resistance to apoptosis while preserving their responsiveness to activating stimuli. Therefore, the survival and proper function of naive T cells depends on their ability to maintain quiescence. Recently we demonstrated that by preventing chronic unresolved endoplasmic reticulum (ER) stress, Schlafen2 (Slfn2) maintains a stress-free environment to conserve a pool of naive T cells ready to respond to a microbial invasion. These findings strongly suggest an intimate association between quiescence and stress signalling. However, the connection between ER stress conditions and loss of T-cell quiescence is unknown. Here we demonstrate that homeostasis of cholesterol and lipids, is disrupted in T cells and monocytes from Slfn2-mutant, elektra, mice with higher levels of lipid rafts and lipid droplets found in these cells. Moreover, elektra T cells had elevated levels of free cholesterol and cholesteryl ester due to increased de novo synthesis and higher levels of the enzyme HMG-CoA reductase. As cholesterol plays an important role in the transition of T cells from resting to active state, and ER regulates cholesterol and lipid synthesis, we suggest that regulation of cholesterol levels through the prevention of ER stress is an essential component of the mechanism by which Slfn2 regulates quiescence.
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Affiliation(s)
- Ibrahim Omar
- The Lautenberg Centre for Immunology and Cancer Research, The Biomedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School Jerusalem, Jerusalem, Israel
| | - Oren Rom
- The Lipid Research Laboratory, Rambam Health Care Campus, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michael Aviram
- The Lipid Research Laboratory, Rambam Health Care Campus, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Leonor Cohen-Daniel
- The Lautenberg Centre for Immunology and Cancer Research, The Biomedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School Jerusalem, Jerusalem, Israel
| | - Abraham K Gebre
- Section on Molecular Medicine, Department of Internal Medicine, Medical Center Blvd, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John S Parks
- Section on Molecular Medicine, Department of Internal Medicine, Medical Center Blvd, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Michael Berger
- The Lautenberg Centre for Immunology and Cancer Research, The Biomedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School Jerusalem, Jerusalem, Israel
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7
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Hong CQ, Zhang F, You YJ, Qiu WL, Giuliano AE, Cui XJ, Zhang GJ, Cui YK. Elevated C1orf63 expression is correlated with CDK10 and predicts better outcome for advanced breast cancers: a retrospective study. BMC Cancer 2015; 15:548. [PMID: 26209438 PMCID: PMC4513615 DOI: 10.1186/s12885-015-1569-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 07/17/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Chromosome 1 open reading frame 63 (C1orf63) is located on the distal short arm of chromosome 1, whose allelic loss has been observed in several human cancers. C1orf63 has been reported to be up-regulated in IL-2-starved T lymphocytes, which suggests it might be involved in cell cycle control, a common mechanism for carcinogenesis. Here we investigated the expression and clinical implication of C1orf63 in breast cancer. METHODS Paraffin-embedded specimens, clinicopathological features and follow-up data of the breast cancer patients were collected. Publicly available microarray and RNA-seq datasets used in this study were downloaded from ArrayExpress of EBI and GEO of NCBI. KM plotter tool was also adopted. The expression of C1orf63 and CDK10, one known cell cycle-dependent tumor suppressor in breast cancer, was assessed by immunohistochemistry. Western blotting was performed to detect C1orf63 protein in human breast cancer cell lines, purchased from the Culture Collection of the Chinese Academy of Sciences, Shanghai. RESULTS In a group of 12 human breast tumors and their matched adjacent non-cancerous tissues, C1orf63 expression was observed in 7 of the 12 breast tumors, but not in the 12 adjacent non-cancerous tissues (P < 0.001). Similar results were observed of C1orf63 mRNA expression both in breast cancer and several other cancers, including lung cancer, prostate cancer and hepatocellular carcinoma. In another group of 182 breast cancer patients, C1orf63 expression in tumors was not correlated with any clinicopathological features collected in this study. Survival analyses showed that there was no significant difference of overall survival (OS) rates between the C1orf63 (+) group and the C1orf63 (-) group (P = 0.145). However, the analyses of KM plotter displayed a valid relationship between C1orf63 and RFS (relapse free survival)/OS (P < 0.001; P = 0.007). Notablely, in breast cancers with advanced TNM stages (III ~ IV) among these 182 patients, C1orf63 expression was an independent prognostic factor predicting better clinical outcome (HR: 0.41; 95 % CI: 0.17 ~ 0.97; P = 0.042). Additionally, we found that CDK10 mRNA expression was positively correlated with C1orf63, which was consistent with the relationship of protein expression between C1orf63 and CDK10 (r s = 0.391; P < 0.001). CONCLUSIONS Compared to adjacent non-cancerous tissues, C1orf63 expression was elevated in tumor tissues. However, C1orf63 predicts better prognosis for breast cancers with advanced TNM stage, and the underlying mechanism is unknown. In addition, C1orf63 is correlated with the cell cycle related gene, CDK10.
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Affiliation(s)
- Chao-Qun Hong
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
| | - Fan Zhang
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
| | - Yan-Jie You
- Department of pharmacy, Luohe Medical College, 148 Daxue-Road, Luohe, 462002, China.
| | - Wei-Li Qiu
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
| | - Armando E Giuliano
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - Xiao-Jiang Cui
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - Guo-Jun Zhang
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
| | - Yu-Kun Cui
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
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Yang XH, Wang B, Cunningham JM. Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles. BMC Med Genomics 2015; 8 Suppl 2:S6. [PMID: 26043758 PMCID: PMC4460748 DOI: 10.1186/1755-8794-8-s2-s6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Therapy-related, secondary acute myeloid leukemia (t-AML) is an increasingly frequent complication of intensive chemotherapy. This malignancy is often characterized by abnormalities of chromosome 7, including large deletions or chromosomal loss. A variety of studies suggest that decreased expression of the EZH2 gene located at 7q36.1 is critical in disease pathogenesis. This histone methyltransferase has been implicated in transcriptional repression through modifying histone H3 on lysine 27 (H3k27). However, the critical target genes of EZH2 and their regulatory roles remain unclear. Method To characterize the subset of EZH2 target genes that might contribute to t-AML pathogenesis, we developed a novel computational analysis to integrate tissue-specific histone modifications and genome-wide transcriptional regulation. Initial integrative analysis utilized a novel "seq2gene" strategy to explore largely the target genes of chromatin immuneprecipitation sequencing (ChIP-seq) enriched regions. By combining seq2gene with our Phenotype-Genotype-Network (PGNet) algorithm, we enriched genes with similar expression profiles and genomic or functional characteristics into "biomodules". Results Initial studies identified SEMA3A (semaphoring 3A) as a novel oncogenic candidate that is regulated by EZH2-silencing, using data derived from both normal and leukemic cell lines as well as murine cells deficient in EZH2. A microsatellite marker at the SEMA3A promoter has been associated with chemosensitivity and radiosensitivity. Notably, our subsequent studies in primary t-AML demonstrate an expected up-regulation of SEMA3A that is EZH2-modulated. Furthermore, we have identified three biomodules that are co-expressed with SEMA3A and up-regulated in t-AML, one of which consists of previously characterized EZH2-repressed gene targets. The other two biomodules include MAPK8 and TATA box targets. Together, our studies suggest an important role for EZH2 targets in t-AML pathogenesis that warrants further study. Conclusion These developed computational algorithms and systems biology strategies will enhance the knowledge discovery and hypothesis-driven analysis of multiple next generation sequencing data, for t-AML and other complex diseases.
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Shen C, Liu L, Jiang Z, Zheng X, Meng L, Yin X, Gao J, Sheng Y, Gao J, Li Y, Zhou F, Xiao F, Sun L, Cui Y, Yang S, Zuo X, Zhang X. Four genetic variants interact to confer susceptibility to atopic dermatitis in Chinese Han population. Mol Genet Genomics 2015; 290:1493-8. [DOI: 10.1007/s00438-015-1014-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/27/2015] [Indexed: 12/14/2022]
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Górnikiewicz B, Ronowicz A, Podolak J, Madanecki P, Stanisławska-Sachadyn A, Sachadyn P. Epigenetic basis of regeneration: analysis of genomic DNA methylation profiles in the MRL/MpJ mouse. DNA Res 2013; 20:605-21. [PMID: 23929942 PMCID: PMC3859327 DOI: 10.1093/dnares/dst034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Epigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the comparative analysis of genomic DNA methylation profiles of the MRL/MpJ and the control C57BL/6J mouse. Methylated DNA immunoprecipitation followed by microarray analysis using the Nimblegen '3 × 720 K CpG Island Plus RefSeq Promoter' platform was applied in order to carry out genome-wide DNA methylation profiling covering 20 404 promoter regions. We identified hundreds of hypo- and hypermethylated genes and CpG islands in the heart, liver, and spleen, and 37 of them in the three tissues. Decreased inter-tissue diversification and the shift of DNA methylation balance upstream the genes distinguish the genomic methylation patterns of the MRL/MpJ mouse from the C57BL/6J. Homeobox genes and a number of other genes involved in embryonic morphogenesis are significantly overrepresented among the genes hypomethylated in the MRL/MpJ mouse. These findings indicate that epigenetic patterning might be a likely molecular basis of regeneration capability in the MRL/MpJ mouse.
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Sigdel TK, Woo SH, Dai H, Khatri P, Li L, Myers B, Sarwal MM, Lafayette RA. Profiling of autoantibodies in IgA nephropathy, an integrative antibiomics approach. Clin J Am Soc Nephrol 2012; 6:2775-84. [PMID: 22157707 DOI: 10.2215/cjn.04600511] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES IgG commonly co-exists with IgA in the glomerular mesangium of patients with IgA nephropathy (IgAN) with unclear clinical relevance. Autoantibody (autoAb) biomarkers to detect and track progression of IgAN are an unmet clinical need. The objective of the study was to identify IgA-specific autoAbs specific to IgAN. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS High-density protein microarrays were evaluated IgG autoAbs in the serum of IgAN patients (n = 22) and controls (n = 10). Clinical parameters, including annual GFR and urine protein measurements, were collected on all patients over 5 years. Bioinformatic data analysis was performed to select targets for further validation by immunohistochemistry (IHC). RESULTS One hundred seventeen (1.4%) specific antibodies were increased in IgAN. Among the most significant were the autoAb to the Ig family of proteins. IgAN-specific autoAbs (approximately 50%) were mounted against proteins predominantly expressed in glomeruli and tubules, and selected candidates were verified by IHC. Receiver operating characteristic analysis of our study demonstrated that IgG autoAb levels (matriline 2, ubiquitin-conjugating enzyme E2W, DEAD box protein, and protein kinase D1) might be used in combination with 24-hour proteinuria to improve prediction of the progression of IgAN (area under the curve = 0.86, P = 0.02). CONCLUSIONS IgAN is associated with elevated IgG autoAbs to multiple proteins in the kidney. This first analysis of the repertoire of autoAbs in IgAN identifies novel, immunogenic protein targets that are highly expressed in the kidney glomerulus and tubules that may bear relevance in the pathogenesis and progression of IgAN.
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Affiliation(s)
- Tara K Sigdel
- Departments of Pediatrics-Nephrology, Stanford University School of Medicine, Stanford, CA 94304, USA
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Cheng J, Zhang XM, Shen ZY, Chen WH, Cai WJ, Ying J, Hu GR, Liu RH. [Immunoregulatory mechanisms of an optimal Chinese herbal monomer compound in mice with allergic rhinitis]. ACTA ACUST UNITED AC 2011; 9:1360-6. [PMID: 22152776 DOI: 10.3736/jcim20111213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To study the immunoregulatory effect of an optimal Chinese herbal monomer compound, which consists of three monomers, namely, icariin, baicalin and Astragalus saponin I, in a mouse model of allergic rhinitis. METHODS A mouse model of allergic rhinitis was established by intraperitoneal injection of ovalbumin and aluminum hydroxide gel suspension. The splenic lymphocytes of the mice were separated, cultured in 96-well plates and divided into three groups: control group, concanavalin A group and compound group. Splenic lymphocyte proliferation was detected by cell counting kit-8 method at different time points. Cell cycle distribution was observed by flow cytometry (FCM) also at different time points. The changes of intracellular calcium concentration of splenic lymphocytes were measured by fluorescence microplate reader after the cells were incubated with fluorescence probe Fluo-3/AM. RESULTS The Chinese herbal monomer compound could inhibit cell proliferation induced by concanavalin A (P<0.01). And the inhibition presented a time-effect relationship. With extending of the action time, the inhibition rate gradually increased and reached peak at the 48th hour. FCM test revealed the fact that concanavalin A could promote cells to enter into the mitosis by reducing the percentage of cells in G0/G1 phases while increasing the percentage of cells in S and G(2)/M phases. Compared with the concanavalin A, the compound could increase the percentage of cells in G(0)/G(1) phases and at the same time reduce the percentage of cells in S and G(2)/M phases at different time points, with the effect most significant at the 24th hour (P<0.05 or P<0.01). The results of the test taken by the fluorescence microplate reader revealed that the fluorescence value of the concanavalin A group increased with time in the previous 24 h while the compound could reduce this trend obviously, thus reduce the intracellular calcium concentration (P<0.01). CONCLUSION The Chinese herbal monomer compound can inhibit the proliferation of cultured splenic lymphocytes of mice with allergic rhinitis. The effects of the compound of lowering intracellular calcium concentration and arresting cell cycle at G(0)/G(1) phases from entering into S and G(2)/M phases are responsible for its antiproliferation activity.
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Affiliation(s)
- Jian Cheng
- Institute of Integrative Medicine, Fudan University, Shanghai, China
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Proteomic Analysis for Malonylastragaloside I in U937 Leukemia Cells by Modified Label-free Quantitative Strategy with LC Chip Q-TOF MS/MS. Chin J Nat Med 2011. [DOI: 10.1016/s1875-5364(11)60068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Berger M, Krebs P, Crozat K, Li X, Croker BA, Siggs OM, Popkin D, Du X, Lawson BR, Theofilopoulos AN, Xia Y, Khovananth K, Moresco EM, Satoh T, Takeuchi O, Akira S, Beutler B. An Slfn2 mutation causes lymphoid and myeloid immunodeficiency due to loss of immune cell quiescence. Nat Immunol 2010; 11:335-43. [PMID: 20190759 PMCID: PMC2861894 DOI: 10.1038/ni.1847] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 01/25/2010] [Indexed: 12/13/2022]
Abstract
We describe a new form of inherited immunodeficiency revealed by an N-ethyl-N-nitrosourea (ENU)-induced mutation called elektra. Homozygotes showed enhanced susceptibility to bacterial and viral infections, and diminished numbers of T cells and inflammatory monocytes that failed to proliferate upon infection and died via the intrinsic apoptotic pathway in response to diverse proliferative stimuli. Elektra mice exhibited an increased proportion of T cells poised to replicate DNA and their T cells expressed a subset of activation markers, suggestive of a semi-activated state. The elektra phenotype was positionally ascribed to a mutation in the gene encoding Schlafen-2 (Slfn2). Our findings reveal a physiological role for Slfn2 in the defense against pathogens through regulation of quiescence in T cells and monocytes.
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Affiliation(s)
- Michael Berger
- Department of Genetics, The Scripps Research Institute, La Jolla, California, USA
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