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Wang L, Mao L, Xiao W, Chen P. Natural killer cells immunosenescence and the impact of lifestyle management. Biochem Biophys Res Commun 2023; 689:149216. [PMID: 37976836 DOI: 10.1016/j.bbrc.2023.149216] [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: 09/03/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Natural killer cells (NKs) are lymphocytes of the innate immune system that quickly respond to viruses, infections, and tumors during their short cell life cycle. However, it was recently found that NKs undergo quantitative, distributional, structural, and functional phenotypic changes during aging that suppress immune responses, which is known as immunosenescence. The aging host environment, cytokine regulation, cytomegalovirus status, and hypothalamic‒pituitary‒adrenal axis have significant effects on NK function. Different lifestyle management interventions modulate the number and cytotoxic activity of NKs, which are essential for rebuilding the immune barrier against pathogens in elderly individuals. Based on recent studies, we review the phenotypic changes of and potential threats of NKs during aging and explore the underlying mechanisms. By summarizing the effects of lifestyle management on NKs and their application prospects, we aim to provide evidence for enhancing immune system function against immune diseases in elderly individuals.
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Affiliation(s)
- Lian Wang
- The Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai, 200438, China.
| | - Liwei Mao
- The Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai, 200438, China.
| | - Weihua Xiao
- The Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai, 200438, China.
| | - Peijie Chen
- The Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai, 200438, China.
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CD4+ T Cell Regulatory Network Underlies the Decrease in Th1 and the Increase in Anergic and Th17 Subsets in Severe COVID-19. Pathogens 2022; 12:pathogens12010018. [PMID: 36678366 PMCID: PMC9865341 DOI: 10.3390/pathogens12010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In this model we use a dynamic and multistable Boolean regulatory network to provide a mechanistic explanation of the lymphopenia and dysregulation of CD4+ T cell subsets in COVID-19 and provide therapeutic targets. Using a previous model, the cytokine micro-environments found in mild, moderate, and severe COVID-19 with and without TGF-β and IL-10 was we simulated. It shows that as the severity of the disease increases, the number of antiviral Th1 cells decreases, while the the number of Th1-like regulatory and exhausted cells and the proportion between Th1 and Th1R cells increases. The addition of the regulatory cytokines TFG-β and IL-10 makes the Th1 attractor unstable and favors the Th17 and regulatory subsets. This is associated with the contradictory signals in the micro-environment that activate SOCS proteins that block the signaling pathways. Furthermore, it determined four possible therapeutic targets that increase the Th1 compartment in severe COVID-19: the activation of the IFN-γ pathway, or the inhibition of TGF-β or IL-10 pathways or SOCS1 protein; from these, inhibiting SOCS1 has the lowest number of predicted collateral effects. Finally, a tool is provided that allows simulations of specific cytokine environments and predictions of CD4 T cell subsets and possible interventions, as well as associated secondary effects.
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Müssel C, Ikonomi N, Werle SD, Weidner FM, Maucher M, Schwab JD, Kestler HA. CANTATA - prediction of missing links in Boolean networks using genetic programming. Bioinformatics 2022; 38:4893-4900. [PMID: 36094334 PMCID: PMC9620829 DOI: 10.1093/bioinformatics/btac623] [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: 03/02/2022] [Revised: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 11/27/2022] Open
Abstract
Motivation Biological processes are complex systems with distinct behaviour. Despite the growing amount of available data, knowledge is sparse and often insufficient to investigate the complex regulatory behaviour of these systems. Moreover, different cellular phenotypes are possible under varying conditions. Mathematical models attempt to unravel these mechanisms by investigating the dynamics of regulatory networks. Therefore, a major challenge is to combine regulations and phenotypical information as well as the underlying mechanisms. To predict regulatory links in these models, we established an approach called CANTATA to support the integration of information into regulatory networks and retrieve potential underlying regulations. This is achieved by optimizing both static and dynamic properties of these networks. Results Initial results show that the algorithm predicts missing interactions by recapitulating the known phenotypes while preserving the original topology and optimizing the robustness of the model. The resulting models allow for hypothesizing about the biological impact of certain regulatory dependencies. Availability and implementation Source code of the application, example files and results are available at https://github.com/sysbio-bioinf/Cantata. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christoph Müssel
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
| | - Nensi Ikonomi
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
| | - Silke D Werle
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
| | - Felix M Weidner
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
| | - Markus Maucher
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
| | - Julian D Schwab
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Baden-Wuerttemberg, Germany
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Interleukin 15 in Cell-Based Cancer Immunotherapy. Int J Mol Sci 2022; 23:ijms23137311. [PMID: 35806311 PMCID: PMC9266896 DOI: 10.3390/ijms23137311] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023] Open
Abstract
Cell-based cancer immunotherapy, such as chimeric antigen receptor (CAR) engineered T and natural killer (NK) cell therapies, has become a revolutionary new pillar in cancer treatment. Interleukin 15 (IL-15), a potent immunostimulatory cytokine that potentiates T and NK cell immune responses, has demonstrated the reliability and potency to potentially improve the therapeutic efficacy of current cell therapy. Structurally similar to interleukin 2 (IL-2), IL-15 supports the persistence of CD8+ memory T cells while inhibiting IL-2-induced T cell death that better maintains long-term anti-tumor immunity. In this review, we describe the biology of IL-15, studies on administrating IL-15 and/or its derivatives as immunotherapeutic agents, and IL-15-armored immune cells in adoptive cell therapy. We also discuss the advantages and challenges of incorporating IL-15 in cell-based immunotherapy and provide directions for future investigation.
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Ordaz-Arias MA, Díaz-Alvarez L, Zúñiga J, Martinez-Sánchez ME, Balderas-Martínez YI. Cyclic Attractors Are Critical for Macrophage Differentiation, Heterogeneity, and Plasticity. Front Mol Biosci 2022; 9:807228. [PMID: 35480895 PMCID: PMC9035596 DOI: 10.3389/fmolb.2022.807228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/11/2022] [Indexed: 01/27/2023] Open
Abstract
Adaptability, heterogeneity, and plasticity are the hallmarks of macrophages. How these complex properties emerge from the molecular interactions is an open question. Thus, in this study we propose an actualized regulatory network of cytokines, signaling pathways, and transcription factors to survey the differentiation, heterogeneity, and plasticity of macrophages. The network recovers attractors, which in regulatory networks correspond to cell types, that correspond to M0, M1, M2a, M2b, M2c, M2d, M2-like, and IL-6 producing cells, including multiple cyclic attractors that are stable to perturbations. These cyclic attractors reproduce experimental observations and show that oscillations result from the structure of the network. We also study the effect of the environment in the differentiation and plasticity of macrophages, showing that the observed heterogeneity in macrophage populations is a result of the regulatory network and its interaction with the micro-environment. The macrophage regulatory network gives a mechanistic explanation to the heterogeneity and plasticity of macrophages seen in vivo and in vitro, and offers insights into the mechanism that allows the immune system to react to a complex dynamic environment.
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Affiliation(s)
- Manuel Azaid Ordaz-Arias
- Laboratorio de Biopatología Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- Licenciatura en Ciencias Genómicas, UNAM, Cuernavaca, Mexico
| | - Laura Díaz-Alvarez
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, UNAM, Mexico City, Mexico
| | - Joaquín Zúñiga
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias Biomédicas, Mexico City, Mexico
| | - Mariana Esther Martinez-Sánchez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- *Correspondence: Mariana Esther Martinez-Sánchez, ; Yalbi Itzel Balderas-Martínez,
| | - Yalbi Itzel Balderas-Martínez
- Laboratorio de Biopatología Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- *Correspondence: Mariana Esther Martinez-Sánchez, ; Yalbi Itzel Balderas-Martínez,
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Enciso J, Mendoza L, Álvarez-Buylla ER, Pelayo R. Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies. PeerJ 2020; 8:e9902. [PMID: 33062419 PMCID: PMC7531334 DOI: 10.7717/peerj.9902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background The blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system. Methods By reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages. Results While the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our mutant models revealed an abnormal delay in the BCR assembly upon NFkB activation, concomitant to sustained Flt3 signaling, down-regulation of Ebf1, Irf4 and Pax5 genes transcription, and reduced Ig recombination, pointing to a potential lineage commitment blockage. Discussion For the first time, an inducible CXCR7hi B cell precursor endowed with the potential capability of shifting central lymphoid niches, is inferred by computational modeling. Its phenotype is compatible with that of leukemia-initiating cells and might be the foundation that bridges inflammation with blockage-related malignancies and a wide range of immunological diseases. Besides the predicted differentiation impairment, inflammation-inducible phenotypes open the possibility of newly formed niches colonized by the reported precursor. Thus, emergent bone marrow ecosystems are predicted following a pro-inflammatory induction, that may lead to hematopoietic instability associated to blockage pathologies.
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Affiliation(s)
- Jennifer Enciso
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Metepec, Puebla, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, México.,Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, México
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México
| | | | - Rosana Pelayo
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Metepec, Puebla, Mexico
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Transcriptional Regulation of Natural Killer Cell Development and Functions. Cancers (Basel) 2020; 12:cancers12061591. [PMID: 32560225 PMCID: PMC7352776 DOI: 10.3390/cancers12061591] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are the major lymphocyte subset of the innate immune system. Their ability to mediate anti-tumor cytotoxicity and produce cytokines is well-established. However, the molecular mechanisms associated with the development of human or murine NK cells are not fully understood. Knowledge is being gained about the environmental cues, the receptors that sense the cues, signaling pathways, and the transcriptional programs responsible for the development of NK cells. Specifically, a complex network of transcription factors (TFs) following microenvironmental stimuli coordinate the development and maturation of NK cells. Multiple TFs are involved in the development of NK cells in a stage-specific manner. In this review, we summarize the recent advances in the understandings of TFs involved in the regulation of NK cell development, maturation, and effector function, in the aspects of their mechanisms, potential targets, and functions.
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Vashishtha S, Broderick G, Craddock TJA, Barnes ZM, Collado F, Balbin EG, Fletcher MA, Klimas NG. Leveraging Prior Knowledge to Recover Characteristic Immune Regulatory Motifs in Gulf War Illness. Front Physiol 2020; 11:358. [PMID: 32411011 PMCID: PMC7198798 DOI: 10.3389/fphys.2020.00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Potentially linked to the basic physiology of stress response, Gulf War Illness (GWI) is a debilitating condition presenting with complex immune, endocrine and neurological symptoms. Here we interrogate the immune response to physiological stress by measuring 16 blood-borne immune markers at 8 time points before, during and after maximum exercise challenge in n = 12 GWI veterans and n = 11 healthy veteran controls deployed to the same theater. Immune markers were combined into functional sets and the dynamics of their joint expression described as classical rate equations. These empirical networks were further informed structurally by projection onto prior knowledge networks mined from the literature. Of the 49 literature-informed immune signaling interactions, 21 were found active in the combined exercise response data. However, only 4 signals were common to both subject groups while 7 were uniquely active in GWI and 10 uniquely active in healthy veterans. Feedforward mediation of IL-23 and IL-17 by IL-6 and IL-10 emerged as distinguishing control elements that were characteristically active in GWI versus healthy subjects. Simulated restructuring of the regulatory circuitry in GWI as a result of applying an IL-6 receptor antagonist in combination with either a Th1 (IL-2, IFNγ, and TNFα) or IL-23 receptor antagonist predicted a partial rescue of immune response elements previously associated with illness severity. Overall, results suggest that pharmacologically altering the topology of the immune response circuitry identified as active in GWI can inform on strategies that while not curative, may nonetheless deliver a reduction in symptom burden. A lasting and more complete remission in GWI may therefore require manipulation of a broader physiology, namely one that includes endocrine oversight of immune function.
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Affiliation(s)
- Saurabh Vashishtha
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States.,Department of Biomedical Engineering, Kate Gleason College of Engineering, Rochester Institute of Technology, Rochester, NY, United States
| | - Travis J A Craddock
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Departments of Psychology & Neuroscience, Computer Science and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Zachary M Barnes
- Diabetes Research Institute, University of Miami, Miami, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Fanny Collado
- Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Elizabeth G Balbin
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Mary Ann Fletcher
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Departments of Psychology & Neuroscience, Computer Science and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
| | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States.,Departments of Psychology & Neuroscience, Computer Science and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States.,Miami Veterans Affairs Medical Center, Miami, FL, United States
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Enciso J, Pelayo R, Villarreal C. From Discrete to Continuous Modeling of Lymphocyte Development and Plasticity in Chronic Diseases. Front Immunol 2019; 10:1927. [PMID: 31481957 PMCID: PMC6710364 DOI: 10.3389/fimmu.2019.01927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
The molecular events leading to differentiation, development, and plasticity of lymphoid cells have been subject of intense research due to their key roles in multiple pathologies, such as lymphoproliferative disorders, tumor growth maintenance and chronic diseases. The emergent roles of lymphoid cells and the use of high-throughput technologies have led to an extensive accumulation of experimental data allowing the reconstruction of gene regulatory networks (GRN) by integrating biochemical signals provided by the microenvironment with transcriptional modules of lineage-specific genes. Computational modeling of GRN has been useful for the identification of molecular switches involved in lymphoid specification, prediction of microenvironment-dependent cell plasticity, and analyses of signaling events occurring downstream the activation of antigen recognition receptors. Among most common modeling strategies to analyze the dynamical behavior of GRN, discrete dynamic models are widely used for their capacity to capture molecular interactions when a limited knowledge of kinetic parameters is present. However, they are less powerful when modeling complex systems sensitive to biochemical gradients. To compensate it, discrete models may be transformed into regulatory networks that includes state variables and parameters varying within a continuous range. This approach is based on a system of differential equations dynamics with regulatory interactions described by fuzzy logic propositions. Here, we discuss the applicability of this method on modeling of development and plasticity processes of adaptive lymphocytes, and its potential implications in the study of pathological landscapes associated to chronic diseases.
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Affiliation(s)
- Jennifer Enciso
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosana Pelayo
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Carlos Villarreal
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Física Cuántica y Fotónica, Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico
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