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Barrera-Lopez JF, Cumplido-Laso G, Olivera-Gomez M, Garrido-Jimenez S, Diaz-Chamorro S, Mateos-Quiros CM, Benitez DA, Centeno F, Mulero-Navarro S, Roman AC, Carvajal-Gonzalez JM. Early Atf4 activity drives airway club and goblet cell differentiation. Life Sci Alliance 2024; 7:e202302284. [PMID: 38176727 PMCID: PMC10766780 DOI: 10.26508/lsa.202302284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
Activating transcription factor 4 (Atf4), which is modulated by the protein kinase RNA-like ER kinase (PERK), is a stress-induced transcription factor responsible for controlling the expression of a wide range of adaptive genes, enabling cells to withstand stressful conditions. However, the impact of the Atf4 signaling pathway on airway regeneration remains poorly understood. In this study, we used mouse airway epithelial cell culture models to investigate the role of PERK/Atf4 in respiratory tract differentiation. Through pharmacological inhibition and silencing of ATF4, we uncovered the crucial involvement of PERK/Atf4 in the differentiation of basal stem cells, leading to a reduction in the number of secretory cells. ChIP-seq analysis revealed direct binding of ATF4 to regulatory elements of genes associated with osteoblast differentiation and secretory cell function. Our findings provide valuable insights into the role of ATF4 in airway epithelial differentiation and its potential involvement in innate immune responses and cellular adaptation to stress.
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Affiliation(s)
- Juan F Barrera-Lopez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Guadalupe Cumplido-Laso
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Marcos Olivera-Gomez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Sergio Garrido-Jimenez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Selene Diaz-Chamorro
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Clara M Mateos-Quiros
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Dixan A Benitez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Francisco Centeno
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Sonia Mulero-Navarro
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Angel C Roman
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Jose M Carvajal-Gonzalez
- https://ror.org/0174shg90 Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
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2
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Lu X, Yin P, Li H, Gao W, Jia H, Ma W. Transcriptome Analysis of Key Genes Involved in the Initiation of Spermatogonial Stem Cell Differentiation. Genes (Basel) 2024; 15:141. [PMID: 38397131 PMCID: PMC10888189 DOI: 10.3390/genes15020141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
PURPOSE The purpose of this study was to screen the genes and pathways that are involved in spermatogonia stem cell (SSC) differentiation regulation during the transition from Aundiff to A1. Methods: RNA sequencing was performed to screen differentially expressed genes at 1 d and 2 d after SSC differentiation culture. KEGG pathway enrichment and GO function analysis were performed to reveal the genes and pathways related to the initiation of early SSC differentiation. RESULTS The GO analysis showed that Rpl21, which regulates cell differentiation initiation, significantly increased after 1 day of SSC differentiation. The expressions of Fn1, Cd9, Fgf2, Itgb1, Epha2, Ctgf, Cttn, Timp2 and Fgfr1, which are related to promoting differentiation, were up-regulated after 2 days of SSC differentiation. The analysis of the KEGG pathway revealed that RNA transport is the most enriched pathway 1 day after SSC differentiation. Hspa2, which promotes the differentiation of male reproductive cells, and Cdkn2a, which participates in the cell cycle, were significantly up-regulated. The p53 pathway and MAPK pathway were the most enriched pathways 2 days after SSC differentiation. Cdkn1a, Hmga2, Thbs1 and Cdkn2a, microRNAs that promote cell differentiation, were also significantly up-regulated. CONCLUSIONS RNA transport, the MAPK pathway and the p53 pathway may play vital roles in early SSC differentiation, and Rpl21, Fn1, Cd9, Fgf2, Itgb1, Epha2, Ctgf, Cttn, Timp2, Fgfr1, Hspa2, Cdkn2a, Cdkn1a, Hmga2 and Thbs1 are involved in the initiation of SSC differentiation. The findings of this study provide a reference for further revelations of the regulatory mechanism of SSC differentiation.
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Affiliation(s)
| | | | | | | | | | - Wenzhi Ma
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Key Laboratory of Reproduction and Genetics of Ningxia Hui Autonomous Region, School of Basic Medical Science, Ningxia Medical University, Yinchuan 750004, China; (X.L.); (P.Y.); (H.L.); (W.G.); (H.J.)
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3
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Bravo M, Diaz-Chamorro S, Garrido-Jiménez S, Blanco J, Simón I, García W, Montero MJ, Gonçalves P, Martínez C, Cumplido-Laso G, Benítez DA, Mulero-Navarro S, Centeno F, Román ÁC, Fernández-Llario P, Cerrato R, Carvajal-González JM. Immunomodulatory effects of inactivated Ligilactobacillus salivarius CECT 9609 on respiratory epithelial cells. Vet Res 2023; 54:91. [PMID: 37845774 PMCID: PMC10580541 DOI: 10.1186/s13567-023-01228-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/07/2023] [Indexed: 10/18/2023] Open
Abstract
The microbiota in humans and animals play crucial roles in defense against pathogens and offer a promising natural source for immunomodulatory products. However, the development of physiologically relevant model systems and protocols for testing such products remains challenging. In this study, we present an experimental condition where various natural products derived from the registered lactic acid bacteria Ligilactobacillus salivarius CECT 9609, known for their immunomodulatory activity, were tested. These products included live and inactivated bacteria, as well as fermentation products at different concentrations and culture times. Using our established model system, we observed no morphological changes in the airway epithelium upon exposure to Pasteurella multocida, a common respiratory pathogen. However, early molecular changes associated with the innate immune response were detected through transcript analysis. By employing diverse methodologies ranging from microscopy to next-generation sequencing (NGS), we characterized the interaction of these natural products with the airway epithelium and their potential beneficial effects in the presence of P. multocida infection. In particular, our discovery highlights that among all Ligilactobacillus salivarius CECT 9609 products tested, only inactivated cells preserve the conformation and morphology of respiratory epithelial cells, while also reversing or altering the natural immune responses triggered by Pasteurella multocida. These findings lay the groundwork for further exploration into the protective role of these bacteria and their derivatives.
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Affiliation(s)
| | - Selene Diaz-Chamorro
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | - Sergio Garrido-Jiménez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | | | | | | | | | | | | | - Guadalupe Cumplido-Laso
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | - Dixan Agustín Benítez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | - Sonia Mulero-Navarro
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | - Francisco Centeno
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | - Ángel Carlos Román
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain
| | | | | | - José María Carvajal-González
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071, Badajoz, Spain.
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4
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Gautam LK, Harriott NC, Caceres AM, Ryan AL. Basic Science Perspective on Engineering and Modeling the Large Airways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1413:73-106. [PMID: 37195527 DOI: 10.1007/978-3-031-26625-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The airway epithelium provides a physical and biochemical barrier playing a key role in protecting the lung from infiltration of pathogens and irritants and is, therefore, crucial in maintaining tissue homeostasis and regulating innate immunity. Due to continual inspiration and expiration of air during breathing, the epithelium is exposed to a plethora of environmental insults. When severe or persistent, these insults lead to inflammation and infection. The effectiveness of the epithelium as a barrier is reliant upon its capacity for mucociliary clearance, immune surveillance, and regeneration upon injury. These functions are accomplished by the cells that comprise the airway epithelium and the niche in which they reside. Engineering of new physiological and pathological models of the proximal airways requires the generation of complex structures comprising the surface airway epithelium, submucosal gland epithelium, extracellular matrix, and niche cells, including smooth muscle cells, fibroblasts, and immune cells. This chapter focuses on the structure-function relationships in the airways and the challenges of developing complex engineered models of the human airway.
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Affiliation(s)
- Lalit K Gautam
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Noa C Harriott
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Adrian M Caceres
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Amy L Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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5
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Gupta A, Sasse SK, Berman R, Gruca MA, Dowell RD, Chu HW, Downey GP, Gerber AN. Integrated genomics approaches identify transcriptional mediators and epigenetic responses to Afghan desert particulate matter in small airway epithelial cells. Physiol Genomics 2022; 54:389-401. [PMID: 36062885 PMCID: PMC9550581 DOI: 10.1152/physiolgenomics.00063.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/15/2022] [Accepted: 08/29/2022] [Indexed: 01/14/2023] Open
Abstract
Military Deployment to Southwest Asia and Afghanistan and exposure to toxic airborne particulates have been associated with an increased risk of developing respiratory disease, collectively termed deployment-related respiratory diseases (DRRDs). Our knowledge about how particulates mediate respiratory disease is limited, precluding the appropriate recognition or management. Central to this limitation is the lack of understanding of how exposures translate into dysregulated cell identity with dysregulated transcriptional programs. The small airway epithelium is involved in both the pathobiology of DRRD and fine particulate matter deposition. To characterize small airway epithelial cell epigenetic and transcriptional responses to Afghan desert particulate matter (APM) and investigate the functional interactions of transcription factors that mediate these responses, we applied two genomics assays, the assay for transposase accessible chromatin with sequencing (ATAC-seq) and Precision Run-on sequencing (PRO-seq). We identified activity changes in a series of transcriptional pathways as candidate regulators of susceptibility to subsequent insults, including signal-dependent pathways, such as loss of cytochrome P450 or P53/P63, and lineage-determining transcription factors, such as GRHL2 loss or TEAD3 activation. We further demonstrated that TEAD3 activation was unique to APM exposure despite similar inflammatory responses when compared with wood smoke particle exposure and that P53/P63 program loss was uniquely positioned at the intersection of signal-dependent and lineage-determining transcriptional programs. Our results establish the utility of an integrated genomics approach in characterizing responses to exposures and identifying genomic targets for the advanced investigation of the pathogenesis of DRRD.
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Affiliation(s)
- Arnav Gupta
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Reena Berman
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Margaret A Gruca
- Biofrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Robin D Dowell
- Biofrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hong Wei Chu
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Gregory P Downey
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado
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6
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Wang S, Li X, Ma Q, Wang Q, Wu J, Yu H, Li K, Li Y, Wang J, Zhang Q, Wang Y, Wu Q, Chen H. Glutamine Metabolism Is Required for Alveolar Regeneration during Lung Injury. Biomolecules 2022; 12:biom12050728. [PMID: 35625656 PMCID: PMC9138637 DOI: 10.3390/biom12050728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
(1) Background: Abnormal repair after alveolar epithelial injury drives the progression of idiopathic pulmonary fibrosis (IPF). The maintenance of epithelial integrity is based on the self-renewal and differentiation of alveolar type 2 (AT2) cells, which require sufficient energy. However, the role of glutamine metabolism in the maintenance of the alveolar epithelium remains unclear. In this study, we investigated the role of glutamine metabolism in AT2 cells of patients with IPF and in mice with bleomycin-induced fibrosis. (2) Methods: Single-cell RNA sequencing (scRNA-seq), transcriptome, and metabolomics analyses were conducted to investigate the changes in the glutamine metabolic pathway during pulmonary fibrosis. Metabolic inhibitors were used to stimulate AT2 cells to block glutamine metabolism. Regeneration of AT2 cells was detected using bleomycin-induced mouse lung fibrosis and organoid models. (3) Results: Single-cell analysis showed that the expression levels of catalytic enzymes responsible for glutamine catabolism were downregulated (p < 0.001) in AT2 cells of patients with IPF, suggesting the accumulation of unusable glutamine. Combined analysis of the transcriptome (p < 0.05) and metabolome (p < 0.001) revealed similar changes in glutamine metabolism in bleomycin-induced pulmonary fibrosis in mice. Mechanistically, inhibition of the key enzymes involved in glucose metabolism, glutaminase-1 (GLS1) and glutamic-pyruvate transaminase-2 (GPT2) leads to reduced proliferation (p < 0.01) and differentiation (p < 0.01) of AT2 cells. (4) Conclusions: Glutamine metabolism is required for alveolar epithelial regeneration during lung injury.
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Affiliation(s)
- Sisi Wang
- Department of Basic Medicine, Haihe Clinical School, Tianjin Medical University, Tianjin 300350, China; (S.W.); (Q.M.)
| | - Xue Li
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
| | - Qingwen Ma
- Department of Basic Medicine, Haihe Clinical School, Tianjin Medical University, Tianjin 300350, China; (S.W.); (Q.M.)
| | - Qi Wang
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
| | - Junping Wu
- Department of Tuberculosis, Haihe Hospital, Tianjin University, Tianjin 300350, China; (J.W.); (H.Y.)
| | - Hongzhi Yu
- Department of Tuberculosis, Haihe Hospital, Tianjin University, Tianjin 300350, China; (J.W.); (H.Y.)
| | - Kuan Li
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
| | - Yu Li
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
| | - Jianhai Wang
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
| | - Qiuyang Zhang
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
| | - Youwei Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
- Correspondence: (Y.W.); (Q.W.); (H.C.)
| | - Qi Wu
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin 300350, China
- Correspondence: (Y.W.); (Q.W.); (H.C.)
| | - Huaiyong Chen
- Department of Basic Medicine, Haihe Clinical School, Tianjin Medical University, Tianjin 300350, China; (S.W.); (Q.M.)
- Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin 300350, China; (X.L.); (Q.W.); (K.L.); (Y.L.); (J.W.); (Q.Z.)
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin 300350, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Tianjin 300350, China
- Correspondence: (Y.W.); (Q.W.); (H.C.)
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7
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Wu M, Zhang X, Lin Y, Zeng Y. Roles of airway basal stem cells in lung homeostasis and regenerative medicine. Respir Res 2022; 23:122. [PMID: 35562719 PMCID: PMC9102684 DOI: 10.1186/s12931-022-02042-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/01/2022] [Indexed: 11/10/2022] Open
Abstract
Airway basal stem cells (BSCs) in the proximal airways are recognized as resident stem cells capable of self-renewing and differentiating to virtually every pseudostratified epithelium cell type under steady-state and after acute injury. In homeostasis, BSCs typically maintain a quiescent state. However, when exposed to acute injuries by either physical insults, chemical damage, or pathogen infection, the remaining BSCs increase their proliferation rate apace within the first 24 h and differentiate to restore lung homeostasis. Given the progenitor property of airway BSCs, it is attractive to research their biological characteristics and how they maintain homeostatic airway structure and respond to injury. In this review, we focus on the roles of BSCs in lung homeostasis and regeneration, detail the research progress in the characteristics of airway BSCs, the cellular and molecular signaling communications involved in BSCs-related airway repair and regeneration, and further discuss the in vitro models for airway BSC propagation and their applications in lung regenerative medicine therapy.
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Affiliation(s)
- Meirong Wu
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China
| | - Xiaojing Zhang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China
| | - Yijian Lin
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China.,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China
| | - Yiming Zeng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China. .,Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China. .,Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, People's Republic of China.
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