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Juaiti M, Feng Y, Tang Y, Liang B, Zha L, Yu Z. Integrated bioinformatics analysis and experimental animal models identify a robust biomarker and its correlation with the immune microenvironment in pulmonary arterial hypertension. Heliyon 2024; 10:e29587. [PMID: 38660271 PMCID: PMC11040037 DOI: 10.1016/j.heliyon.2024.e29587] [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: 03/17/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Background Pulmonary arterial hypertension (PAH) represents a substantial global risk to human health. This study aims to identify diagnostic biomarkers for PAH and assess their association with the immune microenvironment through the utilization of sophisticated bioinformatics techniques. Methods Based on two microarray datasets, differentially expressed genes (DEGs) were detected, and hub genes underwent a sequence of machine learning analyses. After pathways associated with PAH were assessed by gene enrichment analysis, the identified genes were validated using external datasets and confirmed in a monocrotaline (MCT)-induced rat model. In addition, three algorithms were employed to estimate the proportions of various immune cell types, and the link between hub genes and immune cells was substantiated. Results Using SVM, LASSO, and WGCNA, we identified seven hub genes, including (BPIFA1, HBA2, HBB, LOC441081, PI15, S100A9, and WIF1), of which only BPIFA1 remained stable in the external datasets and was validated in an MCT-induced rat model. Furthermore, the results of the functional enrichment analysis established a link between PAH and both metabolism and the immune system. Correlation assessment showed that BPIFA1 expression in the MCP-counter algorithm was negatively associated with various immune cell types, positively correlated with macrophages in the ssGSEA algorithm, and correlated with M1 and M2 macrophages in the CIBERSORT algorithm. Conclusion BPIFA1 serves as a modulator of PAH, with the potential to impact the immune microenvironment and disease progression, possibly through its regulatory influence on both M1 and M2 macrophages.
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Affiliation(s)
- Mukamengjiang Juaiti
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Yilu Feng
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Yiyang Tang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Benhui Liang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Lihuang Zha
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Zaixin Yu
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
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2
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Santos MF, Silva MC, Freitas TMS, Dias JM, Moura MI, Juliano RS, Fioravanti CS, Carmo AS. Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds. Trop Anim Health Prod 2024; 56:92. [PMID: 38430430 DOI: 10.1007/s11250-024-03933-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: 03/17/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024]
Abstract
This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.
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Affiliation(s)
- M F Santos
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - M C Silva
- Federal University of Grande Dourados, Grande Dourados, Dourados, MS, Brazil
| | - T M S Freitas
- Brasilia University Center of Goiás, São Luís dos Montes Belos, GO, Brazil
- Goiás State University - West Campus, São Luís de Montes Belos, GO, Brazil
| | - J M Dias
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - M I Moura
- Veterinary Medicine Department, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil
| | - R S Juliano
- EMBRAPA - Brazilian Agricultural Research Corporation, Pantanal, MS, Brazil
| | - C S Fioravanti
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - A S Carmo
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil.
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3
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Li Q, Wang Y, Ji L, He J, Liu H, Xue W, Yue H, Dong R, Liu X, Wang D, Zhang H. Cellular and molecular mechanisms of fibrosis and resolution in bleomycin-induced pulmonary fibrosis mouse model revealed by spatial transcriptome analysis. Heliyon 2023; 9:e22461. [PMID: 38125541 PMCID: PMC10730595 DOI: 10.1016/j.heliyon.2023.e22461] [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: 05/27/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
The bleomycin-induced pulmonary fibrosis mouse model is commonly used in idiopathic pulmonary fibrosis research, but its cellular and molecular changes and efficiency as a model at the molecular level are not fully understood. In this study, we used spatial transcriptome technology to investigate the cellular and molecular changes in the lungs of bleomycin-induced pulmonary fibrosis mouse models. Our analyses revealed cell dynamics during fibrosis in epithelial cells, mesenchymal cells, immunocytes, and erythrocytes with their spatial distribution available. We confirmed the differentiation of the alveolar type II (AT2) cell type expressing Krt8, and we inferred their trajectories from both the AT2 cells and club cells. In addition to the fibrosis process, we also noticed evidence of self-resolving, especially to identify possible self-resolving related genes, including Prkca. Our findings provide insights into the cellular and molecular mechanisms underlying fibrosis resolution and represent the first spatiotemporal transcriptome dataset of the bleomycin-induced fibrosis mouse model.
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Affiliation(s)
| | - Yue Wang
- BGI-Beijing, Beijing 102601, China
| | - Liu Ji
- Dalian Maternal and Child Health Hospital of Liaoning Province, Dalian 116033, China
| | - Jianhan He
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | | | | | - Huihui Yue
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Ruihan Dong
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xin Liu
- BGI-Beijing, Beijing 102601, China
| | - Daqing Wang
- Dalian Maternal and Child Health Hospital of Liaoning Province, Dalian 116033, China
| | - Huilan Zhang
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
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4
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Habet V, Li N, Qi J, Peng G, Charkoftaki G, Vasiliou V, Sharma L, Pober JS, Dela Cruz C, Yan X, Pierce RW. Integrated Analysis of Tracheobronchial Fluid from Before and After Cardiopulmonary Bypass Reveals Activation of the Integrated Stress Response and Altered Pulmonary Microvascular Permeability. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:23-42. [PMID: 37009190 PMCID: PMC10052603 DOI: 10.59249/kfyz8002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Objective: We aim to comprehensively describe the transcriptional activity and signaling of pulmonary parenchymal and immune cells before and after cardiopulmonary bypass (CPB) by using a multi-omic approach coupled with functional cellular assays. We hypothesize that key signaling pathways from specific cells within the lung alter pulmonary endothelial cell function resulting in worsening or improving disease. Methods: We collected serial tracheobronchial lavage samples from intubated patients less than 2-years-old undergoing surgery with CPB. Samples were immediately processed for single cell RNA sequencing (10x Genomics). Cell clustering, cell-type annotation, and visualization were performed, and differentially expressed genes (DEG) between serial samples were identified. Metabolomic and proteomic analyses were performed on the supernatant using mass spectrometry and a multiplex assay (SomaScan) respectively. Functional assays were done using electric cell-substrate impedance sensing to measure resistance across human pulmonary microvascular endothelial cells (HPMECs). Results: Analysis of eight patients showed a heterogeneous mixture of pulmonary parenchymal and immune cells. Cell clustering demonstrated time-dependent changes in the transcriptomic signature indicating altered cellular phenotypes after CPB. DEG analysis was represented by genes involved in host defense, innate immunity, and the mitochondrial respiratory transport chain. Ingenuity pathway analysis showed upregulation of the integrated stress response across all cell types after CPB. Metabolomic analysis demonstrated upregulation of ascorbate and aldarate metabolism. Unbiased proteomic analysis revealed upregulation of proteins involved in cytokine and chemokine pathways. Post-CPB patient supernatant improved HMPEC barrier function, suggesting a protective cellular response to CPB. Conclusion: Children who undergo CPB for cardiac surgery have distinct cell populations, transcriptional activity, and metabolism that change over time. The response to ischemia-reperfusion injury in the lower airway of children appears to be protective, with the need to identify potential targets through future investigations.
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Affiliation(s)
- Victoria Habet
- Department of Pediatrics, Section of Critical Care
Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public
Health, New Haven, CT, USA
| | - Ji Qi
- Department of Biostatistics, Yale School of Public
Health, New Haven, CT, USA
| | - Gang Peng
- Department of Biostatistics, Yale School of Public
Health, New Haven, CT, USA
| | - Georgia Charkoftaki
- Department of Epidemiology, Yale School of Public
Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Epidemiology, Yale School of Public
Health, New Haven, CT, USA
| | - Lokesh Sharma
- Department of Internal Medicine, Center for Pulmonary
Personalized Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine,
Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
| | - Jordan S. Pober
- Department of Immunobiology, Yale School of Medicine,
New Haven, CT, USA
| | - Charles Dela Cruz
- Department of Internal Medicine, Center for Pulmonary
Personalized Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine,
Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public
Health, New Haven, CT, USA
- Department of Internal Medicine, Center for Pulmonary
Personalized Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine,
Yale School of Medicine, New Haven, CT, USA
| | - Richard W. Pierce
- Department of Pediatrics, Section of Critical Care
Medicine, Yale School of Medicine, New Haven, CT, USA
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5
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Ahmad HI, Khan FA, Khan MA, Imran S, Akhtar RW, Pandupuspitasari NS, Negara W, Chen J. Molecular Evolution of the Bactericidal/Permeability-Increasing Protein (BPIFA1) Regulating the Innate Immune Responses in Mammals. Genes (Basel) 2022; 14:genes14010015. [PMID: 36672756 PMCID: PMC9858190 DOI: 10.3390/genes14010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bactericidal/permeability-increasing protein, a primary factor of the innate immune system of mammals, participates in natural immune protection against invading bacteria. BPIFA1 actively contributes to host defense via multiple mechanisms, such as antibacterial, surfactant, airway surface liquid control, and immunomodulatory activities. However, the evolutionary history and selection forces on the BPIFA1 gene in mammals during adaptive evolution are poorly understood. This study examined the BPIFA1 gene of humans compared with that of other mammalian species to estimate the selective pressure derived by adaptive evolution. To assess whether or not positive selection occurred, we employed several different possibility tests (M1 vs. M2 and M7 vs. M8). The proportions of positively selected sites were significant, with a likelihood log value of 93.63 for the BPIFA1 protein. The Selecton server was used on the same dataset to reconfirm positive selection for specific sites by employing the Mechanistic-Empirical Combination model, thus providing additional evidence supporting the findings of positive selection. There was convincing evidence for positive selection signals in the BPIFA1 genes of mammalian species, which was more significant for selection signs and creating signals. We performed probability tests comparing various models based on dN/dS ratios to recognize specific codons under positive selection pressure. We identified positively selected sites in the LBP-BPI domain of BPIFA1 proteins in the mammalian genome, including a lipid-binding domain with a very high degree of selectivity for DPPC. BPIFA1 activates the upper airway's innate immune system in response to numerous genetic signals in the mammalian genome. These findings highlight evolutionary advancements in immunoregulatory effects that play a significant role in the antibacterial and antiviral defenses of mammalian species.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Correspondence: (H.I.A.); (J.C.)
| | - Faheem Ahmed Khan
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore 54000, Pakistan
- Research Center for Animal Husbandry, National Research and Innovation Agency, South Tangerang 15314, Indonesia
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Safdar Imran
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Rana Waseem Akhtar
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang 50275, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, South Tangerang 15314, Indonesia
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
- Correspondence: (H.I.A.); (J.C.)
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6
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Clark GC, Elfsmark L, Armstrong S, Essex-Lopresti A, Gustafsson Å, Ryan Y, Moore K, Paszkiewicz K, Green AC, Hiscox JA, David J, Jonasson S. From "crisis to recovery": A complete insight into the mechanisms of chlorine injury in the lung. Life Sci 2022; 312:121252. [PMID: 36460096 DOI: 10.1016/j.lfs.2022.121252] [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: 09/05/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
Chlorine (Cl2) gas is a toxic industrial chemical (TIC) that poses a hazard to human health following accidental and/or intentional (e.g. terrorist) release. By using a murine model of sub-lethal Cl2 exposure we have examined the airway hyper responsiveness, cellular infiltrates, transcriptomic and proteomic responses of the lung. In the "crisis" phase at 2 h and 6 h there is a significant decreases in leukocytes within bronchoalveolar lavage fluid accompanied by an upregulation within the proteome of immune pathways ultimately resulting in neutrophil influx at 24 h. A flip towards "repair" in the transcriptome and proteome occurs at 24 h, neutrophil influx and an associated drop in the lung function persisting until 14 d post-exposure and subsequent "recovery" after 28 days. Collectively, this research provides new insights into the mechanisms of damage, early global responses and processes of repair induced in the lung following the inhalation of Cl2.
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Affiliation(s)
- Graeme C Clark
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK; Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK.
| | - Linda Elfsmark
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK
| | - Angela Essex-Lopresti
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Åsa Gustafsson
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
| | - Yan Ryan
- Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK
| | - Karen Moore
- University of Exeter, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Konrad Paszkiewicz
- University of Exeter, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - A Christopher Green
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK
| | - Jonathan David
- Chemical, Biological and Radiological Division, DSTL Porton Down, Salisbury SP4 0JQ, UK
| | - Sofia Jonasson
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden.
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7
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Hu N, Mo XM, Xu SN, Tang HN, Zhou YH, Li L, Zhou HD. A novel antimicrobial peptide derived from human BPIFA1 protein protects against Candida albicans infection. Innate Immun 2022; 28:67-78. [PMID: 35201913 PMCID: PMC9058375 DOI: 10.1177/17534259221080543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/19/2022] [Accepted: 01/30/2022] [Indexed: 11/15/2022] Open
Abstract
Bactericidal/permeability-increasing fold containing family A, member 1 (BPIFA1) is an innate immunity defense protein. Our previous studies proved its antibacterial and antiviral effects, but its role in fungi remains unknown. The study aimed to identify antifungal peptides (AFP) derived from BPIFA1, and three antimicrobial peptides (AMP1-3) were designed. The antifungal effects were proved by growth inhibition assay. AMP3 activity was confirmed by germ tube growth experiment and XTT assay. Its effects on cell wall and membrane of Candida albicans were assessed by tannic acid and Annexin V-FITC/PI double staining, respectively. Additionally, scanning electron microscope (SEM) and transmission electron microscopy (TEM) were used for morphological and ultrastructural observation. The expression of ALS1, EAP1, and SUN41 was tested by qPCR. Ultimately, three AMPs could fight against C. albicans in vitro, and AMP3 was highly effective. It functioned by destroying the integrity of cell wall and normal structure of cell membrane. It also inhibited biofilm formation of C. albicans. In addition, AMP3 down-regulated the expression of ALS1, EAP1, and SUN41, those are known to be involved in virulence of C. albicans. Altogether, the study reported successful development of a novel AFP, which could be used as a new strategy for antifungal therapy.
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Affiliation(s)
- Nan Hu
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
- Nan Hu and Xi-Ming Mo contribute equally to the paper
| | - Xi-Ming Mo
- Department of clinical laboratory medicine, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
- Nan Hu and Xi-Ming Mo contribute equally to the paper
| | - Shi-Na Xu
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Hao-Neng Tang
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
- Department of clinical laboratory medicine, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Ying-Hui Zhou
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Long Li
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Hou-De Zhou
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
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8
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Bannier-Hélaouët M, Post Y, Korving J, Trani Bustos M, Gehart H, Begthel H, Bar-Ephraim YE, van der Vaart J, Kalmann R, Imhoff SM, Clevers H. Exploring the human lacrimal gland using organoids and single-cell sequencing. Cell Stem Cell 2021; 28:1221-1232.e7. [PMID: 33730555 DOI: 10.1016/j.stem.2021.02.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/11/2021] [Accepted: 02/18/2021] [Indexed: 12/28/2022]
Abstract
The lacrimal gland is essential for lubrication and protection of the eye. Disruption of lacrimal fluid production, composition, or release results in dry eye, causing discomfort and damage to the ocular surface. Here, we describe the establishment of long-term 3D organoid culture conditions for mouse and human lacrimal gland. Organoids can be expanded over multiple months and recapitulate morphological and transcriptional features of lacrimal ducts. CRISPR-Cas9-mediated genome editing reveals the master regulator for eye development Pax6 to be required for differentiation of adult lacrimal gland cells. We address cellular heterogeneity of the lacrimal gland by providing a single-cell atlas of human lacrimal gland tissue and organoids. Finally, human lacrimal gland organoids phenocopy the process of tear secretion in response to neurotransmitters and can engraft and produce mature tear products upon orthotopic transplantation in mouse. Together, this study provides an experimental platform to study the (patho-)physiology of the lacrimal gland.
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Affiliation(s)
- Marie Bannier-Hélaouët
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Yorick Post
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Marc Trani Bustos
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Helmuth Gehart
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Institute for Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Yotam E Bar-Ephraim
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Jelte van der Vaart
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Rachel Kalmann
- Department of Ophthalmology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Saskia M Imhoff
- Department of Ophthalmology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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9
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Zheng WB, Zou Y, He JJ, Elsheikha HM, Liu GH, Hu MH, Wang SL, Zhu XQ. Global profiling of lncRNAs-miRNAs-mRNAs reveals differential expression of coding genes and non-coding RNAs in the lung of beagle dogs at different stages of Toxocara canis infection. Int J Parasitol 2020; 51:49-61. [PMID: 32991917 DOI: 10.1016/j.ijpara.2020.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022]
Abstract
The roundworm Toxocara canis causes toxocariasis in dogs and larval migrans in humans. Better understanding of the lung response to T. canis infection could explain why T. canis must migrate to and undergoes part of its development inside the lung of the definitive host. In this study, we profiled the expression patterns of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in the lungs of Beagle dogs infected by T. canis, using high throughput RNA sequencing. At 24 h p.i., 1,012 lncRNAs, 393 mRNAs and 10 miRNAs were differentially expressed (DE). We also identified 883 DElncRNAs, 264 DEmRNAs and 20 DEmiRNAs at 96 h p.i., and 996 DElncRNAs, 342 DEmRNAs and eight DEmiRNAs at 36 days p.i., between infected and control dogs. Significant changes in the levels of expression of transcripts related to immune response and inflammation were associated with the antiparasitic response of the lung to T. canis. The remarkable increase in the expression of scgb1a1 at all time points after infection suggests the need for consistent moderation of the excessive inflammatory response. Also, upregulation of foxj1 at 24 h p.i., and downregulation of IL-1β and IL-21 at 96 h p.i., suggest an attenuation of the humoral immunity of infected dogs. These results indicate that T. canis pathogenesis in the lung is mediated through contributions from both pro-inflammatory and anti-inflammatory mechanisms. Competing endogenous RNA (ceRNA) network analysis revealed significant interactions between DElncRNAs, DEmiRNAs and DEmRNAs, and improved our understanding of the ceRNA regulatory mechanisms in the context of T. canis infection. These data provide comprehensive understanding of the regulatory networks that govern the lung response to T. canis infection and reveal new mechanistic insights into the interaction between the host and parasite during the course of T. canis infection in the canine.
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Affiliation(s)
- Wen-Bin Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, China; Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Yang Zou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, China
| | - Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, China.
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Min-Hua Hu
- National Canine Laboratory Animal Resource Center, Guangzhou General Pharmaceutical Research Institute Co., Ltd, Guangzhou, Guangdong Province 510240, China
| | - Shui-Lian Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, China; College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province 030801, China.
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Zhang R, Trower J, Wu T. Degradation of bacterial permeability family member A1 (BPIFA1) by house dust mite (HDM) cysteine protease Der p 1 abrogates immune modulator function. Int J Biol Macromol 2020; 164:4022-4031. [PMID: 32890564 PMCID: PMC7467078 DOI: 10.1016/j.ijbiomac.2020.08.214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 01/01/2023]
Abstract
Bacterial permeability family member A1 (BPIFA1) is one of the most abundant proteins present in normal airway surface liquid (ASL). It is known to be diminished in asthmatic patients' sputum, which causes airway hyperresponsiveness (AHR). What is currently unclear is how environmental factors, such as allergens' impact on BPIFA1's abundance and functions in the context of allergic asthma. House dust mite (HDM) is a predominant domestic source of aeroallergens. The group of proteases found in HDM is thought to cleave multiple cellular protective mechanisms, and therefore foster the development of allergic asthma. Here, we show that BPIFA1 is cleaved by HDM proteases in a time-, dose-, and temperature-dependent manner. We have also shown the main component in HDM that is responsible for BPIFA1's degradation is Der p1. Fragmented BPIFA1 failed to bind E. coli lipopolysaccharide (LPS), and hence elevated TNFα and IL-6 secretion in human whole blood. BPIFA1 degradation is also observed in vivo in bronchoalveolar fluid (BALF) of mice which are intranasally instilled with HDM. These data suggest that proteases associated with environmental allergens such as HDM cleave BPIFA1 and therefore impair its immune modulator function.
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Affiliation(s)
- Rui Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, PR China
| | - Jessika Trower
- Department of Pharmaceutical Sciences, 302 East Lawson Street, North Carolina Central University, Durham, NC 27707, USA
| | - Tongde Wu
- Department of Pharmaceutical Sciences, 302 East Lawson Street, North Carolina Central University, Durham, NC 27707, USA; Biomanufacturing Research Institute & Technology Enterprise (BRITE), 302 East Lawson Street, North Carolina Central University, Durham, NC 27707, USA.
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