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Avila-Ponce de León U, Vázquez-Jiménez A, Padilla-Longoria P, Resendis-Antonio O. Uncoding the interdependency of tumor microenvironment and macrophage polarization: insights from a continuous network approach. Front Immunol 2023; 14:1150890. [PMID: 37283734 PMCID: PMC10240616 DOI: 10.3389/fimmu.2023.1150890] [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: 01/26/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
The balance between pro- and anti-inflammatory immune system responses is crucial to preventing complex diseases like cancer. Macrophages are essential immune cells that contribute to this balance constrained by the local signaling profile of the tumor microenvironment. To understand how pro- and anti-inflammatory unbalance emerges in cancer, we developed a theoretical analysis of macrophage differentiation that is derived from activated monocytes circulating in the blood. Once recruited to the site of inflammation, monocytes can be polarized based on the specific interleukins and chemokines in the microenvironment. To quantify this process, we used a previous regulatory network reconstructed by our group and transformed Boolean Network attractors of macrophage polarization to an ODE scheme, it enables us to quantify the activation of their genes in a continuous fashion. The transformation was developed using the interaction rules with a fuzzy logic approach. By implementing this approach, we analyzed different aspects that cannot be visualized in the Boolean setting. For example, this approach allows us to explore the dynamic behavior at different concentrations of cytokines and transcription factors in the microenvironment. One important aspect to assess is the evaluation of the transitions between phenotypes, some of them characterized by an abrupt or a gradual transition depending on specific concentrations of exogenous cytokines in the tumor microenvironment. For instance, IL-10 can induce a hybrid state that transits between an M2c and an M2b macrophage. Interferon- γ can induce a hybrid between M1 and M1a macrophage. We further demonstrated the plasticity of macrophages based on a combination of cytokines and the existence of hybrid phenotypes or partial polarization. This mathematical model allows us to unravel the patterns of macrophage differentiation based on the competition of expression of transcriptional factors. Finally, we survey how macrophages may respond to a continuously changing immunological response in a tumor microenvironment.
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Affiliation(s)
- Ugo Avila-Ponce de León
- Programa de Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de Mexico, Mexico
| | - Aarón Vázquez-Jiménez
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de Mexico, Mexico
| | - Pablo Padilla-Longoria
- Institute for Applied Mathematics (IIMAS), Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de Mexico, Mexico
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
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Wang Y, Zhu CL, Li P, Liu Q, Li HR, Yu CM, Deng XM, Wang JF. The role of G protein-coupled receptor in neutrophil dysfunction during sepsis-induced acute respiratory distress syndrome. Front Immunol 2023; 14:1112196. [PMID: 36891309 PMCID: PMC9986442 DOI: 10.3389/fimmu.2023.1112196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
Sepsis is defined as a life-threatening dysfunction due to a dysregulated host response to infection. It is a common and complex syndrome and is the leading cause of death in intensive care units. The lungs are most vulnerable to the challenge of sepsis, and the incidence of respiratory dysfunction has been reported to be up to 70%, in which neutrophils play a major role. Neutrophils are the first line of defense against infection, and they are regarded as the most responsive cells in sepsis. Normally, neutrophils recognize chemokines including the bacterial product N-formyl-methionyl-leucyl-phenylalanine (fMLP), complement 5a (C5a), and lipid molecules Leukotriene B4 (LTB4) and C-X-C motif chemokine ligand 8 (CXCL8), and enter the site of infection through mobilization, rolling, adhesion, migration, and chemotaxis. However, numerous studies have confirmed that despite the high levels of chemokines in septic patients and mice at the site of infection, the neutrophils cannot migrate to the proper target location, but instead they accumulate in the lungs, releasing histones, DNA, and proteases that mediate tissue damage and induce acute respiratory distress syndrome (ARDS). This is closely related to impaired neutrophil migration in sepsis, but the mechanism involved is still unclear. Many studies have shown that chemokine receptor dysregulation is an important cause of impaired neutrophil migration, and the vast majority of these chemokine receptors belong to the G protein-coupled receptors (GPCRs). In this review, we summarize the signaling pathways by which neutrophil GPCR regulates chemotaxis and the mechanisms by which abnormal GPCR function in sepsis leads to impaired neutrophil chemotaxis, which can further cause ARDS. Several potential targets for intervention are proposed to improve neutrophil chemotaxis, and we hope that this review may provide insights for clinical practitioners.
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Affiliation(s)
- Yi Wang
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Cheng-long Zhu
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Peng Li
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Qiang Liu
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hui-ru Li
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Faculty of Anesthesiology, Weifang Medical University, Weifang, Shandong, China
| | - Chang-meng Yu
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao-ming Deng
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Faculty of Anesthesiology, Weifang Medical University, Weifang, Shandong, China
| | - Jia-feng Wang
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
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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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Hidalgo A, Chilvers ER, Summers C, Koenderman L. The Neutrophil Life Cycle. Trends Immunol 2019; 40:584-597. [PMID: 31153737 DOI: 10.1016/j.it.2019.04.013] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/25/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
Abstract
Neutrophils are recognized as an essential part of the innate immune response, but an active debate still exists regarding the life cycle of these cells. Neutrophils first differentiate in the bone marrow through progenitor intermediaries before entering the blood, in a process that gauges the extramedullary pool size. Once believed to be directly eliminated in the marrow, liver, and spleen, neutrophils, after circulating for less than 1 day, are now known to redistribute into multiple tissues with poorly understood kinetics. In this review, we provide an update on the dynamic distribution of neutrophils across tissues in health and disease, and emphasize differences between humans and model organisms. We further highlight issues to be addressed to exploit the unique features of neutrophils in the clinic.
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Affiliation(s)
- Andrés Hidalgo
- Area of Developmental and Cell Biology, Centro Nacional de Investigaciones, Cardiovasculares Carlos III (CNIC), Madrid, Spain; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany.
| | - Edwin R Chilvers
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Charlotte Summers
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Leo Koenderman
- Laboratory of Translational Immunology, Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands.
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Rodríguez A, Naveja JJ, Torres L, García de Teresa B, Juárez-Figueroa U, Ayala-Zambrano C, Azpeitia E, Mendoza L, Frías S. WIP1 Contributes to the Adaptation of Fanconi Anemia Cells to DNA Damage as Determined by the Regulatory Network of the Fanconi Anemia and Checkpoint Recovery Pathways. Front Genet 2019; 10:411. [PMID: 31130988 PMCID: PMC6509935 DOI: 10.3389/fgene.2019.00411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/15/2019] [Indexed: 02/01/2023] Open
Abstract
DNA damage adaptation (DDA) allows the division of cells with unrepaired DNA damage. DNA repair deficient cells might take advantage of DDA to survive. The Fanconi anemia (FA) pathway repairs DNA interstrand crosslinks (ICLs), and deficiencies in this pathway cause a fraction of breast and ovarian cancers as well as FA, a chromosome instability syndrome characterized by bone marrow failure and cancer predisposition. FA cells are hypersensitive to ICLs; however, DDA might promote their survival. We present the FA-CHKREC Boolean Network Model, which explores how FA cells might use DDA. The model integrates the FA pathway with the G2 checkpoint and the checkpoint recovery (CHKREC) processes. The G2 checkpoint mediates cell-cycle arrest (CCA) and the CHKREC activates cell-cycle progression (CCP) after resolution of DNA damage. Analysis of the FA-CHKREC network indicates that CHKREC drives DDA in FA cells, ignoring the presence of unrepaired DNA damage and allowing their division. Experimental inhibition of WIP1, a CHKREC component, in FA lymphoblast and cancer cell lines prevented division of FA cells, in agreement with the prediction of the model.
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Affiliation(s)
- Alfredo Rodríguez
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - J Jesús Naveja
- PECEM, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leda Torres
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Benilde García de Teresa
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Ulises Juárez-Figueroa
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cecilia Ayala-Zambrano
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Eugenio Azpeitia
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sara Frías
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Gutiérrez-Jiménez C, Hysenaj L, Alfaro-Alarcón A, Mora-Cartín R, Arce-Gorvel V, Moreno E, Gorvel JP, Barquero-Calvo E. Persistence of Brucella abortus in the Bone Marrow of Infected Mice. J Immunol Res 2018; 2018:5370414. [PMID: 30622977 PMCID: PMC6304906 DOI: 10.1155/2018/5370414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/28/2018] [Accepted: 09/17/2018] [Indexed: 01/10/2023] Open
Abstract
Brucellosis is a zoonotic bacterial infection that may persist for long periods causing relapses in antibiotic-treated patients. The ability of Brucella to develop chronic infections is linked to their capacity to invade and replicate within the mononuclear phagocyte system, including the bone marrow (BM). Persistence of Brucella in the BM has been associated with hematological complications such as neutropenia, thrombocytopenia, anemia, and pancytopenia in human patients. In the mouse model, we observed that the number of Brucella abortus in the BM remained constant for up to 168 days of postinfection. This persistence was associated with histopathological changes, accompanied by augmented numbers of BM myeloid GMP progenitors, PMNs, and CD4+ lymphocytes during the acute phase (eight days) of the infection in the BM. Monocytes, PMNs, and GMP cells were identified as the cells harboring Brucella in the BM. We propose that the BM is an essential niche for the bacterium to establish long-lasting infections and that infected PMNs may serve as vehicles for dispersion of Brucella organisms, following the Trojan horse hypothesis. Monocytes are solid candidates for Brucella reservoirs in the BM.
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Affiliation(s)
- Cristina Gutiérrez-Jiménez
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Lisiena Hysenaj
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France
| | - Alejandro Alfaro-Alarcón
- Pathology Department, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Ricardo Mora-Cartín
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | | | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | | | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
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Liquitaya-Montiel AJ, Mendoza L. Dynamical Analysis of the Regulatory Network Controlling Natural Killer Cells Differentiation. Front Physiol 2018; 9:1029. [PMID: 30116200 PMCID: PMC6082967 DOI: 10.3389/fphys.2018.01029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022] Open
Abstract
Many disease fighting strategies have focused on the generation of NK cells, since they constitute the main immune barrier against cancer and intracellular pathogens such as viruses. Therefore, a predictive model for the development of NK cells would constitute a useful tool to test several hypotheses regarding the production of these cells during both physiological and pathological conditions. Here, we present a boolean network model that reproduces experimental results reported on the literature regarding the progressive stages of the development of NK cells in wild-type and mutant backgrounds. The model allows for the simulation of different conditions, including extracellular micro-environment as well as the simulation of genetic alterations. It also describes how NK cell differentiation depends on a molecular regulatory network that controls the specification of lymphoid lineages, such as T and B cells, which share a common progenitor with NKs. Furthermore, the study shows that the structure of the regulatory network strongly determines the stability of the expression patterns against perturbations.
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Affiliation(s)
- Adhemar J. Liquitaya-Montiel
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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