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Nikolopoulos D, Loukogiannaki C, Sentis G, Garantziotis P, Manolakou T, Kapsala N, Nikoloudaki M, Pieta A, Flouda S, Parodis I, Bertsias G, Fanouriakis A, Filia A, Boumpas DT. Disentangling the riddle of systemic lupus erythematosus with antiphospholipid syndrome: blood transcriptome analysis reveals a less-pronounced IFN-signature and distinct molecular profiles in venous versus arterial events. Ann Rheum Dis 2024:ard-2024-225664. [PMID: 38609158 DOI: 10.1136/ard-2024-225664] [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: 02/12/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
INTRODUCTION Systemic lupus erythematosus with antiphospholipid syndrome (SLE-APS) represents a challenging SLE endotype whose molecular basis remains unknown. METHODS We analysed whole-blood RNA-sequencing data from 299 patients with SLE (108 SLE-antiphospholipid antibodies (aPL)-positive, including 67 SLE-APS; 191 SLE-aPL-negative) and 72 matched healthy controls (HC). Pathway enrichment analysis, unsupervised weighted gene coexpression network analysis and machine learning were applied to distinguish disease endotypes. RESULTS Patients with SLE-APS demonstrated upregulated type I and II interferon (IFN) pathways compared with HC. Using a 100-gene random forests model, we achieved a cross-validated accuracy of 75.6% in distinguishing these two states. Additionally, the comparison between SLE-APS and SLE-aPL-negative revealed 227 differentially expressed genes, indicating downregulation of IFN-α and IFN-γ signatures, coupled with dysregulation of the complement cascade, B-cell activation and neutrophil degranulation. Unsupervised analysis of SLE transcriptome identified 21 gene modules, with SLE-APS strongly linked to upregulation of the 'neutrophilic/myeloid' module. Within SLE-APS, venous thromboses positively correlated with 'neutrophilic/myeloid' and 'B cell' modules, while arterial thromboses were associated with dysregulation of 'DNA damage response (DDR)' and 'metabolism' modules. Anticardiolipin and anti-β2GPI positivity-irrespective of APS status-were associated with the 'neutrophilic/myeloid' and 'protein-binding' module, respectively. CONCLUSIONS There is a hierarchical upregulation and-likely-dependence on IFN in SLE with the highest IFN signature observed in SLE-aPL-negative patients. Venous thrombotic events are associated with neutrophils and B cells while arterial events with DDR and impaired metabolism. This may account for their differential requirements for anticoagulation and provide rationale for the potential use of mTOR inhibitors such as sirolimus and the direct fIIa inhibitor dabigatran in SLE-APS.
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Affiliation(s)
- Dionysis Nikolopoulos
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Loukogiannaki
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, AG Groningen, Τhe Netherlands
| | - George Sentis
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Panagiotis Garantziotis
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Department of Internal Medicine 3-Rheumatology and Immunology, Friedrich Alexander University Erlangen-Nuremberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Theodora Manolakou
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Noemin Kapsala
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Myrto Nikoloudaki
- Rheumatology, University of Crete School of Medicine, Iraklio, Crete, Greece
| | - Antigone Pieta
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Sofia Flouda
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Parodis
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - George Bertsias
- Rheumatology, University of Crete School of Medicine, Iraklio, Crete, Greece
- Laboratory of Autoimmunity-Inflammation, Institute of Molecular Biology and Biotechnology, Heraklion, Crete, Greece
| | - Antonis Fanouriakis
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasia Filia
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dimitrios T Boumpas
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Stergioti EM, Manolakou T, Sentis G, Samiotaki M, Kapsala N, Fanouriakis A, Boumpas DT, Banos A. Transcriptomic and proteomic profiling reveals distinct pathogenic features of peripheral non-classical monocytes in systemic lupus erythematosus. Clin Immunol 2023; 255:109765. [PMID: 37678715 DOI: 10.1016/j.clim.2023.109765] [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: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Peripheral blood monocytes propagate inflammation in systemic lupus erythematosus (SLE). Three major populations of monocytes have been recognized namely classical (CM), intermediate (IM) and non-classical monocytes (NCM). Herein, we performed a comprehensive transcriptomic, proteomic and functional characterization of the three peripheral monocytic subsets from active SLE patients and healthy individuals. Our data demonstrate extensive molecular disruptions in circulating SLE NCM, characterized by enhanced inflammatory features such as deregulated DNA repair, cell cycle and heightened IFN signaling combined with differentiation and developmental cues. Enhanced DNA damage, elevated expression of p53, G0 arrest of cell cycle and increased autophagy stress the differentiation potential of NCM in SLE. This immunogenic profile is associated with an activated macrophage phenotype of NCM exhibiting M1 characteristics in the circulation, fueling the inflammatory response. Together, these findings identify circulating SLE NCM as a pathogenic cell type in the disease that could represent an additional therapeutic target.
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Affiliation(s)
- Eirini Maria Stergioti
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 115 27, Greece; 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens 124 62, Greece.
| | - Theodora Manolakou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 115 27, Greece
| | - George Sentis
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 115 27, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Vari, Athens 166 72, Greece
| | - Noemin Kapsala
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens 124 62, Greece
| | - Antonis Fanouriakis
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens 124 62, Greece
| | - Dimitrios T Boumpas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 115 27, Greece.
| | - Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 115 27, Greece.
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Stergioti EM, Manolakou T, Boumpas DT, Banos A. Antiviral Innate Immune Responses in Autoimmunity: Receptors, Pathways, and Therapeutic Targeting. Biomedicines 2022; 10:2820. [PMID: 36359340 PMCID: PMC9687478 DOI: 10.3390/biomedicines10112820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 09/28/2023] Open
Abstract
Innate immune receptors sense nucleic acids derived from viral pathogens or self-constituents and initiate an immune response, which involves, among other things, the secretion of cytokines including interferon (IFN) and the activation of IFN-stimulated genes (ISGs). This robust and well-coordinated immune response is mediated by the innate immune cells and is critical to preserving and restoring homeostasis. Like an antiviral response, during an autoimmune disease, aberrations of immune tolerance promote inflammatory responses to self-components, such as nucleic acids and immune complexes (ICs), leading to the secretion of cytokines, inflammation, and tissue damage. The aberrant immune response within the inflammatory milieu of the autoimmune diseases may lead to defective viral responses, predispose to autoimmunity, or precipitate a flare of an existing autoimmune disease. Herein, we review the literature on the crosstalk between innate antiviral immune responses and autoimmune responses and discuss the pitfalls and challenges regarding the therapeutic targeting of the mechanisms involved.
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Affiliation(s)
- Eirini Maria Stergioti
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, 115 27 Athens, Greece
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Theodora Manolakou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, 115 27 Athens, Greece
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, 115 27 Athens, Greece
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, 124 62 Athens, Greece
| | - Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, 115 27 Athens, Greece
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Manolakou T, Nikolopoulos D, Gkikas D, Filia A, Samiotaki M, Stamatakis G, Fanouriakis A, Politis P, Banos A, Alissafi T, Verginis P, Boumpas DT. ATR-mediated DNA damage responses underlie aberrant B cell activity in systemic lupus erythematosus. SCIENCE ADVANCES 2022; 8:eabo5840. [PMID: 36306362 PMCID: PMC9616496 DOI: 10.1126/sciadv.abo5840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
B cells orchestrate autoimmune responses in patients with systemic lupus erythematosus (SLE), but broad-based B cell-directed therapies show only modest efficacy while blunting humoral immune responses to vaccines and inducing immunosuppression. Development of more effective therapies targeting pathogenic clones is a currently unmet need. Here, we demonstrate enhanced activation of the ATR/Chk1 pathway of the DNA damage response (DDR) in B cells of patients with active SLE disease. Treatment of B cells with type I IFN, a key driver of immunity in SLE, induced expression of ATR via binding of interferon regulatory factor 1 to its gene promoter. Pharmacologic targeting of ATR in B cells, via a specific inhibitor (VE-822), attenuated their immunogenic profile, including proinflammatory cytokine secretion, plasmablast formation, and antibody production. Together, these findings identify the ATR-mediated DDR axis as the orchestrator of the type I IFN-mediated B cell responses in SLE and as a potential novel therapeutic target.
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Affiliation(s)
- Theodora Manolakou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Corresponding author. (T.M.); (P.V.); (D.T.B.)
| | - Dionysis Nikolopoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Dimitrios Gkikas
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 115 27, Athens, Greece
| | - Anastasia Filia
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Vari, Attica, Greece
- Centre of New Biotechnologies and Precision Medicine (CNBPM) School of Medicine, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - George Stamatakis
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Vari, Attica, Greece
- Centre of New Biotechnologies and Precision Medicine (CNBPM) School of Medicine, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | | | - Panagiotis Politis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 115 27, Athens, Greece
- School of Medicine, European University Cyprus, 1516, Nicosia, Cyprus
| | - Aggelos Banos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Themis Alissafi
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 115 27, Athens, Greece
- Laboratory of Biology, National and Kapodistrian University of Athens Medical School, 124 62 Athens, Greece
| | - Panayotis Verginis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 700 13 Heraklion, Greece
- Laboratory of Immune Regulation and Tolerance, Division of Basic Sciences, University of Crete Medical School, 700 13 Heraklion, Greece
- Corresponding author. (T.M.); (P.V.); (D.T.B.)
| | - Dimitrios T. Boumpas
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Joint Rheumatology Program, 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, 124 62 Athens, Greece
- Corresponding author. (T.M.); (P.V.); (D.T.B.)
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Schilz JR, Dashner-Titus EJ, Simmons KA, Erdei E, Bolt AM, MacKenzie DA, Hudson LG. The immunotoxicity of natural and depleted uranium: From cells to people. Toxicol Appl Pharmacol 2022; 454:116252. [PMID: 36152676 PMCID: PMC10044422 DOI: 10.1016/j.taap.2022.116252] [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: 06/13/2022] [Revised: 08/30/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022]
Abstract
Uranium is a naturally occurring element found in the environment as a mixture of isotopes with differing radioactive properties. Enrichment of mined material results in depleted uranium waste with substantially reduced radioactivity but retains the capacity for chemical toxicity. Uranium mine and milling waste are dispersed by wind and rain leading to environmental exposures through soil, air, and water contamination. Uranium exposure is associated with numerous adverse health outcomes in humans, yet there is limited understanding of the effects of depleted uranium on the immune system. The purpose of this review is to summarize findings on uranium immunotoxicity obtained from cell, rodent and human population studies. We also highlight how each model contributes to an understanding of mechanisms that lead to immunotoxicity and limitations inherent within each system. Information from population, animal, and laboratory studies will be needed to significantly expand our knowledge of the contributions of depleted uranium to immune dysregulation, which may then inform prevention or intervention measures for exposed communities.
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Affiliation(s)
- Jodi R Schilz
- Division of Physical Therapy, School of Medicine, University of New Mexico, Albuquerque, NM, United States of America.
| | - Erica J Dashner-Titus
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Karen A Simmons
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Esther Erdei
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Alicia M Bolt
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Debra A MacKenzie
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
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Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy. Front Immunol 2021; 12:797880. [PMID: 34970273 PMCID: PMC8712645 DOI: 10.3389/fimmu.2021.797880] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
The DNA damage response (DDR) is an organized network of multiple interwoven components evolved to repair damaged DNA and maintain genome fidelity. Conceptually the DDR includes damage sensors, transducer kinases, and effectors to maintain genomic stability and accurate transmission of genetic information. We have recently gained a substantially improved molecular and mechanistic understanding of how DDR components are interconnected to inflammatory and immune responses to stress. DDR shapes both innate and adaptive immune pathways: (i) in the context of innate immunity, DDR components mainly enhance cytosolic DNA sensing and its downstream STimulator of INterferon Genes (STING)-dependent signaling; (ii) in the context of adaptive immunity, the DDR is needed for the assembly and diversification of antigen receptor genes that is requisite for T and B lymphocyte development. Imbalances between DNA damage and repair impair tissue homeostasis and lead to replication and transcription stress, mutation accumulation, and even cell death. These impacts from DDR defects can then drive tumorigenesis, secretion of inflammatory cytokines, and aberrant immune responses. Yet, DDR deficiency or inhibition can also directly enhance innate immune responses. Furthermore, DDR defects plus the higher mutation load in tumor cells synergistically produce primarily tumor-specific neoantigens, which are powerfully targeted in cancer immunotherapy by employing immune checkpoint inhibitors to amplify immune responses. Thus, elucidating DDR-immune response interplay may provide critical connections for harnessing immunomodulatory effects plus targeted inhibition to improve efficacy of radiation and chemotherapies, of immune checkpoint blockade, and of combined therapeutic strategies.
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Affiliation(s)
- Zu Ye
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yin Shi
- Department of Immunology, Zhejiang University School of Medicine, Hangzhou, China
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - John A. Tainer
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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