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Li F, Tan Z, Chen H, Gao Y, Xia J, Huang T, Liang L, Zhang J, Zhang X, Shi X, Chen Q, Shu Q, Yu L. Integrative analysis of bulk and single-cell RNA sequencing reveals the gene expression profile and the critical signaling pathways of type II CPAM. Cell Biosci 2024; 14:94. [PMID: 39026356 PMCID: PMC11264590 DOI: 10.1186/s13578-024-01276-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUD Type II congenital pulmonary airway malformation (CPAM) is a rare pulmonary microcystic developmental malformation. Surgical excision is the primary treatment for CPAM, although maternal steroids and betamethasone have proven effective in reducing microcystic CPAM. Disturbed intercellular communication may contribute to the development of CPAM. This study aims to investigate the expression profile and analyze intercellular communication networks to identify genes potentially associated with type II CPAM pathogenesis and therapeutic targets. METHODS RNA sequencing (RNA-seq) was performed on samples extracted from both the cystic area and the adjacent normal tissue post-surgery in CPAM patients. Iterative weighted gene correlation network analysis (iWGCNA) was used to identify genes specifically expressed in type II CPAM. Single-cell RNA-seq (scRNA-seq) was integrated to unveil the heterogeneity in cell populations and analyze the communication and interaction within epithelial cell sub-populations. RESULTS A total of 2,618 differentially expressed genes were identified, primarily enriched in cilium-related biological process and inflammatory response process. Key genes such as EDN1, GPR17, FPR2, and CHRM1, involved in the G protein-coupled receptor (GPCR) signaling pathway and playing roles in cell differentiation, apoptosis, calcium homeostasis, and the immune response, were highlighted based on the protein-protein interaction network. Type II CPAM-associated modules, including ciliary function-related genes, were identified using iWGCNA. By integrating scRNA-seq data, AGR3 (related to calcium homeostasis) and SLC11A1 (immune related) were identified as the only two differently expressed genes in epithelial cells of CPAM. Cell communication analysis revealed that alveolar type 1 (AT1) and alveolar type 2 (AT2) cells were the predominant communication cells for outgoing and incoming signals in epithelial cells. The ligands and receptors between epithelial cell subtypes included COLLAGEN genes enriched in PI3K-AKT singaling and involved in epithelial to mesenchymal transition. CONCLUSIONS In summary, by integrating bulk RNA-seq data of type II CPAM with scRNA-seq data, the gene expression profile and critical signaling pathways such as GPCR signaling and PI3K-AKT signaling pathways were revealed. Abnormally expressed genes in these pathways may disrupt epithelial-mesenchymal transition and contribute to the development of CPAM. Given the effectiveness of prenatal treatments of microcystic CPAM using maternal steroids and maternal betamethasone administration, targeting the genes and signaling pathways involved in the development of CPAM presents a promising therapeutic strategy.
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Affiliation(s)
- Fengxia Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Zheng Tan
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Hongyu Chen
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yue Gao
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jie Xia
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Ting Huang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Liang Liang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jian Zhang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xianghong Zhang
- Department of Cardiac Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xucong Shi
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Qiang Chen
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Jiangxi, China.
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Lan Yu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
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2
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Xu G, Pan T, Li S, Guo J, Zhang Y, Xu Q, Chen R, Ma Y, Li Y. Mapping Single-Cell Transcriptomes of Endometrium Reveals Potential Biomarkers in Endometrial Cancer. Immunotargets Ther 2024; 13:349-366. [PMID: 39050484 PMCID: PMC11268782 DOI: 10.2147/itt.s470994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Background The heterogeneity and dynamic changes of endometrial cells have a significant impact on health as they determine the normal function of the endometrium during the menstrual cycle. Dysfunction of the endometrium can lead to the occurrence of various gynecological diseases. Therefore, deconvolution of immune microenvironment that drives transcriptional programs throughout the menstrual cycle is key to understand regulatory biology of endometrium. Methods Herein, we comprehensively analyzed single-cell transcriptome of 59,397 cells across ten human endometrium samples and revealed the dynamic cellular heterogeneity throughout the menstrual cycle. Results We identified two perivascular cell subtypes, four epithelial subtypes and four fibroblast cell types in endometrium. Moreover, we inferred the cell type-specific transcription factor (TF) activities and linked critical TFs to transcriptional output of diverse immune cell types, highlighting the importance of transcriptional regulation in endometrium. Dynamic interactions between various types of cells in endometrium contribute to a range of biological pathways regulating differentiation of secretory. Integration of the molecular biomarkers identified in endometrium and bulk transcriptome of 535 endometrial cancers (EC), we revealed five RNA-based molecular subtypes of EC with highly intratumoral heterogeneity and different clinical manifestations. Mechanism analysis uncovered clinically relevant pathways for pathogenesis of EC. Conclusion In summary, our results revealed the dynamic immune microenvironment of endometrium and provided novel insights into future development of RNA-based treatments for endometriosis and endometrial carcinoma.
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Affiliation(s)
- Gang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China, Harbin, 150081, People’s Republic of China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Tao Pan
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Si Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang, 150081, People’s Republic of China
| | - Jing Guo
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Ya Zhang
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Qi Xu
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Renwei Chen
- Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
| | - Yongsheng Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Reproductive Medical Center, National Center for International Research, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 571199, People’s Republic of China
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, Heilongjiang, 150081, People’s Republic of China
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3
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Boisteau E, Posseme C, Di Modugno F, Edeline J, Coulouarn C, Hrstka R, Martisova A, Delom F, Treton X, Eriksson LA, Chevet E, Lièvre A, Ogier-Denis E. Anterior gradient proteins in gastrointestinal cancers: from cell biology to pathophysiology. Oncogene 2022; 41:4673-4685. [PMID: 36068336 DOI: 10.1038/s41388-022-02452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/03/2022] [Accepted: 08/23/2022] [Indexed: 11/09/2022]
Abstract
Most of the organs of the digestive tract comprise secretory epithelia that require specialized molecular machines to achieve their functions. As such anterior gradient (AGR) proteins, which comprise AGR1, AGR2, and AGR3, belong to the protein disulfide isomerase family, and are involved in secretory and transmembrane protein biogenesis in the endoplasmic reticulum. They are generally expressed in epithelial cells with high levels in most of the digestive tract epithelia. To date, the vast majority of the reports concern AGR2, which has been shown to exhibit various subcellular localizations and exert pro-oncogenic functions. AGR2 overexpression has recently been associated with a poor prognosis in digestive cancers. AGR2 is also involved in epithelial homeostasis. Its deletion in mice results in severe diffuse gut inflammation, whereas in inflammatory bowel diseases, the secretion of AGR2 in the extracellular milieu participates in the reshaping of the cellular microenvironment. AGR2 thus plays a key role in inflammation and oncogenesis and may represent a therapeutic target of interest. In this review, we summarize the already known roles and mechanisms of action of the AGR family proteins in digestive diseases, their expression in the healthy digestive tract, and in digestive oncology. At last, we discuss the potential diagnostic and therapeutic implications underlying the biology of AGR proteins.
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Affiliation(s)
- Emeric Boisteau
- INSERM U1242, University of Rennes, Rennes, France.,Department of Gastroenterology, University Hospital Pontchaillou, University of Rennes, Rennes, France
| | - Céline Posseme
- INSERM U1242, University of Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Federico Di Modugno
- INSERM U1242, University of Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Julien Edeline
- INSERM U1242, University of Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | | | - Roman Hrstka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Andrea Martisova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Xavier Treton
- Assistance Publique-Hôpitaux de Paris, University of Paris, Clichy, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France. .,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
| | - Astrid Lièvre
- INSERM U1242, University of Rennes, Rennes, France. .,Department of Gastroenterology, University Hospital Pontchaillou, University of Rennes, Rennes, France.
| | - Eric Ogier-Denis
- INSERM U1242, University of Rennes, Rennes, France. .,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
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4
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Bertoli-Avella A, Hotakainen R, Al Shehhi M, Urzi A, Pareira C, Marais A, Al Shidhani K, Aloraimi S, Morales-Torres G, Fisher S, Demuth L, Moteleb Selim LA, Al Menabawy N, Busehail M, AlShaikh M, Gilani N, Chalabi DN, Alharbi NS, Alfadhel M, Abdelrahman M, Venselaar H, Anjum N, Saeed A, Alghamdi MA, Aljaedi H, Arabi H, Karageorgou V, Khan S, Hajjari Z, Radefeldt M, Al-Ali R, Tripolszki K, Jamhawi A, Paknia O, Cozma C, Cheema H, Ameziane N, Al-Muhsen S, Bauer P. A disorder clinically resembling cystic fibrosis caused by biallelic variants in the AGR2 gene. J Med Genet 2021; 59:993-1001. [PMID: 34952832 PMCID: PMC9554030 DOI: 10.1136/jmedgenet-2021-108150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/10/2021] [Indexed: 11/08/2022]
Abstract
Purpose We sought to describe a disorder clinically mimicking cystic fibrosis (CF) and to elucidate its genetic cause. Methods Exome/genome sequencing and human phenotype ontology data of nearly 40 000 patients from our Bio/Databank were analysed. RNA sequencing of samples from the nasal mucosa from patients, carriers and controls followed by transcriptome analysis was performed. Results We identified 13 patients from 9 families with a CF-like phenotype consisting of recurrent lower respiratory infections (13/13), failure to thrive (13/13) and chronic diarrhoea (8/13), with high morbidity and mortality. All patients had biallelic variants in AGR2, (1) two splice-site variants, (2) gene deletion and (3) three missense variants. We confirmed aberrant AGR2 transcripts caused by an intronic variant and complete absence of AGR2 transcripts caused by the large gene deletion, resulting in loss of function (LoF). Furthermore, transcriptome analysis identified significant downregulation of components of the mucociliary machinery (intraciliary transport, cilium organisation), as well as upregulation of immune processes. Conclusion We describe a previously unrecognised autosomal recessive disorder caused by AGR2 variants. AGR2-related disease should be considered as a differential diagnosis in patients presenting a CF-like phenotype. This has implications for the molecular diagnosis and management of these patients. AGR2 LoF is likely the disease mechanism, with consequent impairment of the mucociliary defence machinery. Future studies should aim to establish a better understanding of the disease pathophysiology and to identify potential drug targets.
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Affiliation(s)
| | - Ronja Hotakainen
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | | | - Alice Urzi
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Catarina Pareira
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Anett Marais
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | | | | | | | - Steffen Fisher
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Laura Demuth
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | | | - Nihal Al Menabawy
- Pediatric Neurology and Metabolic division, Cairo University Childrens Hospital, Cairo, Egypt
| | - Maryam Busehail
- Department of Pediatrics, Salmaniya Medical Complex, Manama, Bahrain
| | - Mohammed AlShaikh
- Department of Pediatrics, Salmaniya Medical Complex, Manama, Bahrain
| | | | | | - Nasser S Alharbi
- Pulmonology Unit, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomic Research department, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- Genetics and Precision Medicine department (GPM), King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Mohammed Abdelrahman
- Immunology Research laboratory, Department of Pediatrics, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboudumc, Radboud Institute for Molecular Life Sciences, Nijmegen, Gelderland, Netherlands
| | - Nadeem Anjum
- Department of Pediatric Gastroenterology, Children's Hospital of Lahore, Lahore, Pakistan
| | - Anjum Saeed
- Department of Pediatric Gastroenterology, Children's Hospital of Lahore, Lahore, Pakistan
| | - Malak Ali Alghamdi
- Medical Genetics Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hamad Aljaedi
- Department of Pathology, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hisham Arabi
- Department of Pediatrics, King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | | | - Suliman Khan
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Zahra Hajjari
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Mandy Radefeldt
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Ruslan Al-Ali
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | | | - Amer Jamhawi
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Omid Paknia
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Claudia Cozma
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Huma Cheema
- Department of Pediatric Gastroenterology, Children's Hospital of Lahore, Lahore, Pakistan
| | - Najim Ameziane
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
| | - Saleh Al-Muhsen
- Immunology Research laboratory, Department of Pediatrics, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Peter Bauer
- Medical Reporting & Genomic Research, Centogene GmbH, Rostock, Germany
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5
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Mun DG, Vanderboom PM, Madugundu AK, Garapati K, Chavan S, Peterson JA, Saraswat M, Pandey A. DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. J Proteome Res 2021; 20:4165-4175. [PMID: 34292740 PMCID: PMC8315246 DOI: 10.1021/acs.jproteome.1c00506] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Indexed: 12/15/2022]
Abstract
Since the recent outbreak of COVID-19, there have been intense efforts to understand viral pathogenesis and host immune response to combat SARS-CoV-2. It has become evident that different host alterations can be identified in SARS-CoV-2 infection based on whether infected cells, animal models or clinical samples are studied. Although nasopharyngeal swabs are routinely collected for SARS-CoV-2 detection by RT-PCR testing, host alterations in the nasopharynx at the proteomic level have not been systematically investigated. Thus, we sought to characterize the host response through global proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry (TIMS) and high-resolution QTOF mass spectrometer with parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of pooled nasopharyngeal swab samples was performed in the PASEF enabled DDA mode, which identified 7723 proteins that were then used to generate a spectral library. This approach provided peptide level evidence of five missing proteins for which MS/MS spectrum and mobilograms were validated with synthetic peptides. Subsequently, quantitative proteomic profiling was carried out for 90 individual nasopharyngeal swab samples (45 positive and 45 negative) in DIA combined with PASEF, termed as diaPASEF mode, which resulted in a total of 5023 protein identifications. Of these, 577 proteins were found to be upregulated in SARS-CoV-2 positive samples. Functional analysis of these upregulated proteins revealed alterations in several biological processes including innate immune response, viral protein assembly, and exocytosis. To the best of our knowledge, this study is the first to deploy diaPASEF for quantitative proteomic profiling of clinical samples and shows the feasibility of adopting such an approach to understand mechanisms and pathways altered in diseases.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
| | - Patrick M. Vanderboom
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
| | - Anil K. Madugundu
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
- Center for Molecular Medicine, National
Institute of Mental Health and Neurosciences, Hosur Road, Bangalore,
560029, Karnataka India
- Institute of Bioinformatics, International
Technology Park, Bangalore, 560066, Karnataka
India
- Manipal Academy of Higher
Education, Manipal, 576104, Karnataka India
| | - Kishore Garapati
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
- Institute of Bioinformatics, International
Technology Park, Bangalore, 560066, Karnataka
India
- Manipal Academy of Higher
Education, Manipal, 576104, Karnataka India
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
| | - Jane A. Peterson
- Proteomics Core, Medical Genome Facility,
Mayo Clinic, Rochester, Minnesota 55905, United
States
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
- Institute of Bioinformatics, International
Technology Park, Bangalore, 560066, Karnataka
India
- Manipal Academy of Higher
Education, Manipal, 576104, Karnataka India
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology,
Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota
55905, United States
- Center for Molecular Medicine, National
Institute of Mental Health and Neurosciences, Hosur Road, Bangalore,
560029, Karnataka India
- Center for Individualized Medicine, Mayo
Clinic, Rochester, Minnesota 55905, United States
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6
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Identification of Toxocara canis Antigen-Interacting Partners by Yeast Two-Hybrid Assay and a Putative Mechanism of These Host-Parasite Interactions. Pathogens 2021; 10:pathogens10080949. [PMID: 34451413 PMCID: PMC8398310 DOI: 10.3390/pathogens10080949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 01/11/2023] Open
Abstract
Toxocara canis is a zoonotic roundworm that infects humans and dogs all over the world. Upon infection, larvae migrate to various tissues leading to different clinical syndromes. The host–parasite interactions underlying the process of infection remain poorly understood. Here, we describe the application of a yeast two-hybrid assay to screen a human cDNA library and analyse the interactome of T. canis larval molecules. Our data identifies 16 human proteins that putatively interact with the parasite. These molecules were associated with major biological processes, such as protein processing, transport, cellular component organisation, immune response and cell signalling. Some of these identified interactions are associated with the development of a Th2 response, neutrophil activity and signalling in immune cells. Other interactions may be linked to neurodegenerative processes observed during neurotoxocariasis, and some are associated with lung pathology found in infected hosts. Our results should open new areas of research and provide further data to enable a better understanding of this complex and underestimated disease.
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7
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Ye R, Wang C, Sun P, Bai S, Zhao L. AGR3 Regulates Airway Epithelial Junctions in Patients with Frequent Exacerbations of COPD. Front Pharmacol 2021; 12:669403. [PMID: 34177583 PMCID: PMC8232749 DOI: 10.3389/fphar.2021.669403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/01/2021] [Indexed: 01/07/2023] Open
Abstract
Background: The mechanisms underlying differences in the susceptibility to chronic obstructive pulmonary disease (COPD) exacerbations between patients are not well understood. Recent studies have shown that the patients with frequent COPD exacerbations is related to specific protein expression in lung tissue. Anterior gradient 3 (AGR3) is expressed in airway epithelial cells in the lung and proteomic analysis revealed that its expression is decreased in patients with frequent COPD exacerbations. Moreover, the loss of epithelial integrity might facilitate trans-epithelial permeability of pathogens in such patients. This study was performed to determine that AGR3 protein play a role in COPD frequency exacerbators. Methods: Human lung tissues were collected from current-smoking patients (Control; n = 15) as well as patients with infrequent COPD exacerbations (IFCOPD; n = 18) and frequent COPD exacerbations (FCOPD; n = 8). While AGR3 protein expression was measured by immunohistochemistry and western blotting, AGR mRNA expression was determined by real time quantitative polymerase chain reaction (RT-qPCR). Furthermore, adherent junctions (AJs) and tight junctions (TJs) protein expression in human lung tissues were measured by immunohistochemistry. The effects of cigarette smoke extract (CSE) on AJ and TJ protein and mRNA expression in BEAS-2B cells were assessed by western blotting and RT-qPCR. In addition, the effect of AGR3 overexpression and knockdown on AJ and TJ protein expression was determined. Results: AGR3 was mainly expressed in the airway epithelium and AGR3-positive products were localized in the cytoplasm. Western blotting and RT-qPCR results showed that AGR3 protein (p = 0.009) and mRNA (p = 0.04) expression in the FCOPD group was significantly lower than that in the IFCOPD group. Moreover, E-cadherin, occludin, and zonula occludens-1 (ZO-1) expression was lower in the FCOPD group than in the IFCOPD group. The protein and mRNA expression of E-cadherin, occludin, and ZO-1 was decreased within 24 h post-CSE exposure. AGR3 overexpression rescued CSE-induced downregulation of E-cadherin, occludin, and ZO-1. Conclusion: Difference in AGR3 expression in the lung tissue might be correlated with increased susceptibility to COPD exacerbation. AGR3 can prevent CSE-induced downregulation of E-cadherin, occludin, and ZO-1 in airway epithelial cells. Loss of AGR3 might promote viral and bacterial infection and induce immune inflammation to increase COPD exacerbation.
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Affiliation(s)
- Rui Ye
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cuihong Wang
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Pengbo Sun
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Bai
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Li Zhao
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
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8
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Nakada EM, Sun R, Fujii U, Martin JG. The Impact of Endoplasmic Reticulum-Associated Protein Modifications, Folding and Degradation on Lung Structure and Function. Front Physiol 2021; 12:665622. [PMID: 34122136 PMCID: PMC8188853 DOI: 10.3389/fphys.2021.665622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022] Open
Abstract
The accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and induces the unfolded protein response (UPR) and other mechanisms to restore ER homeostasis, including translational shutdown, increased targeting of mRNAs for degradation by the IRE1-dependent decay pathway, selective translation of proteins that contribute to the protein folding capacity of the ER, and activation of the ER-associated degradation machinery. When ER stress is excessive or prolonged and these mechanisms fail to restore proteostasis, the UPR triggers the cell to undergo apoptosis. This review also examines the overlooked role of post-translational modifications and their roles in protein processing and effects on ER stress and the UPR. Finally, these effects are examined in the context of lung structure, function, and disease.
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Affiliation(s)
- Emily M. Nakada
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre (RI-MUHC), McGill University, Montreal, QC, Canada
- McGill University, Montreal, QC, Canada
| | - Rui Sun
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre (RI-MUHC), McGill University, Montreal, QC, Canada
- McGill University, Montreal, QC, Canada
| | - Utako Fujii
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre (RI-MUHC), McGill University, Montreal, QC, Canada
- McGill University, Montreal, QC, Canada
| | - James G. Martin
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre (RI-MUHC), McGill University, Montreal, QC, Canada
- McGill University, Montreal, QC, Canada
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9
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Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition. Nat Med 2021; 27:806-814. [PMID: 33958799 PMCID: PMC9009537 DOI: 10.1038/s41591-021-01332-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
Cystic fibrosis (CF) is a lethal autosomal recessive disorder that afflicts more than 70,000 people. People with CF experience multi-organ dysfunction resulting from aberrant electrolyte transport across polarized epithelia due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CF-related lung disease is by far the most important determinant of morbidity and mortality. Here we report results from a multi-institute consortium in which single-cell transcriptomics were applied to define disease-related changes by comparing the proximal airway of CF donors (n = 19) undergoing transplantation for end-stage lung disease with that of previously healthy lung donors (n = 19). Disease-dependent differences observed include an overabundance of epithelial cells transitioning to specialized ciliated and secretory cell subsets coupled with an unexpected decrease in cycling basal cells. Our study yields a molecular atlas of the proximal airway epithelium that will provide insights for the development of new targeted therapies for CF airway disease.
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10
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Mohieldin AM, Pala R, Beuttler R, Moresco JJ, Yates JR, Nauli SM. Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles. J Extracell Vesicles 2021; 10:e12086. [PMID: 33936569 PMCID: PMC8077156 DOI: 10.1002/jev2.12086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 12/28/2022] Open
Abstract
Extracellular vesicles (EVs) are cell‐derived membrane vesicles that are released into the extracellular space. EVs encapsulate key proteins and mediate intercellular signalling pathways. Recently, primary cilia have been shown to release EVs under fluid‐shear flow, but many proteins encapsulated in these vesicles have never been identified. Primary cilia are ubiquitous mechanosensory organelles that protrude from the apical surface of almost all human cells. Primary cilia also serve as compartments for signalling pathways, and their defects have been associated with a wide range of human genetic diseases called ciliopathies. To better understand the mechanism of ciliopathies, it is imperative to know the distinctive protein profiles of the differently sourced EVs (cilia vs cytosol). Here, we isolated EVs from ciliated wild‐type (WT) and non‐ciliated IFT88 knockout (KO) mouse endothelial cells using fluid‐shear flow followed by a conventional method of EV isolation. EVs isolated from WT and KO exhibited distinctive sizes. Differences in EV protein contents were studied using liquid chromatography with tandem mass spectrometry (LC‐MS‐MS) and proteomic comparative analysis, which allowed us to classify proteins between ciliary EVs and cytosolic EVs derived from WT and KO, respectively. A total of 79 proteins were exclusively expressed in WT EVs, 145 solely in KO EVs, and 524 in both EVs. Our bioinformatics analyses revealed 29% distinct protein classes and 75% distinct signalling pathways between WT and KO EVs. Based on our statistical analyses and in vitro studies, we identified NADPH‐cytochrome P450 reductase (POR), and CD166 antigen (CD166) as potential biomarkers for ciliary and cytosolic EVs, respectively. Our protein‐protein interaction network analysis revealed that POR, but not CD166, interacted with either established or strong ciliopathy gene candidates. This report shows the unique differences between EVs secreted from cilia and the cytosol. These results will be important in advancing our understanding of human genetic diseases.
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Affiliation(s)
- Ashraf M Mohieldin
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA.,Department of Medicine University of California Irvine Irvine California USA
| | - Rajasekharreddy Pala
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA
| | - Richard Beuttler
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA
| | - James J Moresco
- Department of Molecular Medicine The Scripps Research Institute La Jolla California USA
| | - John R Yates
- Department of Molecular Medicine The Scripps Research Institute La Jolla California USA
| | - Surya M Nauli
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA.,Department of Medicine University of California Irvine Irvine California USA
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11
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Tempest N, Batchelor E, Hill CJ, Al-Lamee H, Drury J, Drakeley AJ, Hapangama DK. Anterior Gradient Protein 3 and S100 Calcium-Binding Protein P Levels in Different Endometrial Epithelial Compartments May Play an Important Role in Recurrent Pregnancy Failure. Int J Mol Sci 2021; 22:ijms22083835. [PMID: 33917163 PMCID: PMC8067849 DOI: 10.3390/ijms22083835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/31/2021] [Accepted: 04/04/2021] [Indexed: 01/31/2023] Open
Abstract
Recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL) are distressing conditions without effective treatments. The luminal epithelium (LE) is integral in determining receptivity of the endometrium, whereas functionalis glands and stroma aid in nurturing early embryo development. Calcium signalling pathways are known to be of vital importance to embryo implantation and pregnancy establishment, and anterior gradient protein 3 (AGR3) and S100 calcium-binding protein P (S100P) are involved with these pathways. We initially examined 20 full-thickness endometrial biopsies from premenopausal women across the menstrual cycle to characterize levels of AGR3 protein in each endometrial sub-region at the cellular level. A further 53 endometrial pipelle biopsies collected in the window of implantation were subsequently assessed to determine differential endometrial AGR3 and S100P levels relevant to RIF (n = 13) and RPL (n = 10) in comparison with parous women (n = 30) using immunohistochemistry. Significantly higher AGR3 and S100P immunostaining was observed in ciliated cells of the LE of women with recurrent reproductive failure compared with parous women, suggesting aberrant subcellular location-associated pathophysiology for these conditions. The nuclear localisation of S100P may allow transcriptional regulatory function, which is necessary for implantation of a viable pregnancy. Further work is thus warranted to assess their utility as diagnostic/therapeutic targets.
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Affiliation(s)
- Nicola Tempest
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (E.B.); (C.J.H.); (H.A.-L.); (J.D.); (D.K.H.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK
- Hewitt Centre for Reproductive Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK;
- Correspondence:
| | - Elizabeth Batchelor
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (E.B.); (C.J.H.); (H.A.-L.); (J.D.); (D.K.H.)
| | - Christopher J. Hill
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (E.B.); (C.J.H.); (H.A.-L.); (J.D.); (D.K.H.)
| | - Hannan Al-Lamee
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (E.B.); (C.J.H.); (H.A.-L.); (J.D.); (D.K.H.)
- Hewitt Centre for Reproductive Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK;
| | - Josephine Drury
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (E.B.); (C.J.H.); (H.A.-L.); (J.D.); (D.K.H.)
| | - Andrew J. Drakeley
- Hewitt Centre for Reproductive Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK;
| | - Dharani K. Hapangama
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (E.B.); (C.J.H.); (H.A.-L.); (J.D.); (D.K.H.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK
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12
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Lee L, Ostrowski LE. Motile cilia genetics and cell biology: big results from little mice. Cell Mol Life Sci 2020; 78:769-797. [PMID: 32915243 DOI: 10.1007/s00018-020-03633-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]
Abstract
Our understanding of motile cilia and their role in disease has increased tremendously over the last two decades, with critical information and insight coming from the analysis of mouse models. Motile cilia form on specific epithelial cell types and typically beat in a coordinated, whip-like manner to facilitate the flow and clearance of fluids along the cell surface. Defects in formation and function of motile cilia result in primary ciliary dyskinesia (PCD), a genetically heterogeneous disorder with a well-characterized phenotype but no effective treatment. A number of model systems, ranging from unicellular eukaryotes to mammals, have provided information about the genetics, biochemistry, and structure of motile cilia. However, with remarkable resources available for genetic manipulation and developmental, pathological, and physiological analysis of phenotype, the mouse has risen to the forefront of understanding mammalian motile cilia and modeling PCD. This is evidenced by a large number of relevant mouse lines and an extensive body of genetic and phenotypic data. More recently, application of innovative cell biological techniques to these models has enabled substantial advancement in elucidating the molecular and cellular mechanisms underlying the biogenesis and function of mammalian motile cilia. In this article, we will review genetic and cell biological studies of motile cilia in mouse models and their contributions to our understanding of motile cilia and PCD pathogenesis.
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Affiliation(s)
- Lance Lee
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA. .,Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, USA.
| | - Lawrence E Ostrowski
- Marsico Lung Institute/Cystic Fibrosis Center and Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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13
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Obacz J, Sommerova L, Sicari D, Durech M, Avril T, Iuliano F, Pastorekova S, Hrstka R, Chevet E, Delom F, Fessart D. Extracellular AGR3 regulates breast cancer cells migration via Src signaling. Oncol Lett 2019; 18:4449-4456. [PMID: 31611954 PMCID: PMC6781763 DOI: 10.3892/ol.2019.10849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
Human anterior gradient proteins AGR2 and AGR3 are overexpressed in a variety of adenocarcinomas and are often secreted in cancer patients' specimens, which suggests a role for AGR proteins in intra and extracellular compartments. Although these proteins exhibit high sequence homology, AGR2 is predominantly described as a pro-oncogene and a potential prognostic biomarker. However, little is known about the function of AGR3. Therefore, the aim of the present study was to investigate the role of AGR3 in breast cancer. The results demonstrated that breast cancer cells secrete AGR3. Furthermore, it was revealed that extracellular AGR3 (eAGR3) regulates tumor cell adhesion and migration. The current study indicated that the pharmacological and genetic perturbation of Src kinase signaling, through treatment with Dasatinib (protein kinase inhibitor) or investigating cells that express a dominant-negative form of Src, significantly abrogated eAGR3-mediated breast cancer cell migration. Therefore, the results indicated that eAGR3 may control tumor cell migration via activation of Src kinases. The results of the present study indicated that eAGR3 may serve as a microenvironmental signaling molecule in tumor-associated processes.
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Affiliation(s)
- Joanna Obacz
- INSERM U1242, 'Chemistry, Oncogenesis Stress Signaling', University of Rennes Campus 1, F-35000 Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, F-35000 Rennes, France.,Masaryk Memorial Cancer Institute, RECAMO, 656 53 Brno, Czech Republic.,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic
| | - Lucia Sommerova
- Masaryk Memorial Cancer Institute, RECAMO, 656 53 Brno, Czech Republic
| | - Daria Sicari
- INSERM U1242, 'Chemistry, Oncogenesis Stress Signaling', University of Rennes Campus 1, F-35000 Rennes, France
| | - Michal Durech
- Masaryk Memorial Cancer Institute, RECAMO, 656 53 Brno, Czech Republic
| | - Tony Avril
- INSERM U1242, 'Chemistry, Oncogenesis Stress Signaling', University of Rennes Campus 1, F-35000 Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, F-35000 Rennes, France
| | - Filippo Iuliano
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic
| | - Silvia Pastorekova
- Masaryk Memorial Cancer Institute, RECAMO, 656 53 Brno, Czech Republic.,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic
| | - Roman Hrstka
- Masaryk Memorial Cancer Institute, RECAMO, 656 53 Brno, Czech Republic
| | - Eric Chevet
- INSERM U1242, 'Chemistry, Oncogenesis Stress Signaling', University of Rennes Campus 1, F-35000 Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, F-35000 Rennes, France
| | - Frederic Delom
- University of Bordeaux, ACTION, F-33000 Bordeaux, France.,INSERM U1218, F-33000 Bordeaux, France.,Bergonie Cancer Institute, F-33000 Bordeaux, France
| | - Delphine Fessart
- INSERM U1242, 'Chemistry, Oncogenesis Stress Signaling', University of Rennes Campus 1, F-35000 Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, F-35000 Rennes, France.,University of Bordeaux, ACTION, F-33000 Bordeaux, France.,INSERM U1218, F-33000 Bordeaux, France
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14
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Delom F, Nazaraliyev A, Fessart D. The role of protein disulphide isomerase AGR2 in the tumour niche. Biol Cell 2018; 110:271-282. [DOI: 10.1111/boc.201800024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/21/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Frederic Delom
- University of Bordeaux; INSERM U1218; Bordeaux F-33000 France
- Institut Bergonié, Comprehensive Cancer Centre; Bordeaux F-33076 France
| | - Amal Nazaraliyev
- University of Bordeaux; INSERM U1218; Bordeaux F-33000 France
- Institut Bergonié, Comprehensive Cancer Centre; Bordeaux F-33076 France
| | - Delphine Fessart
- INSERM U1242; “Chemistry, Oncogenesis, Stress, Signaling”; Université; de Rennes 1; Rennes France
- Centre de Lutte Contre le Cancer Eugène Marquis; Rennes France
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15
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Nguyen VD, Biterova E, Salin M, Wierenga RK, Ruddock LW. Crystal structure of human anterior gradient protein 3. Acta Crystallogr F Struct Biol Commun 2018; 74:425-430. [PMID: 29969106 DOI: 10.1107/s2053230x18009093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
Oxidative protein folding in the endoplasmic reticulum is catalyzed by the protein disulfide isomerase family of proteins. Of the 20 recognized human family members, the structures of eight have been deposited in the PDB along with domains from six more. Three members of this family, ERp18, anterior gradient protein 2 (AGR2) and anterior gradient protein 3 (AGR3), are single-domain proteins which share sequence similarity. While ERp18 has a canonical active-site motif and is involved in native disulfide-bond formation, AGR2 and AGR3 lack elements of the active-site motif found in other family members and may both interact with mucins. In order to better define its function, the structure of AGR3 is required. Here, the recombinant expression, purification, crystallization and crystal structure of human AGR3 are described.
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Affiliation(s)
- Van Dat Nguyen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Ekaterina Biterova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Mikko Salin
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
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16
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Abstract
PURPOSE OF REVIEW Research on the biology of cilia, complex hair-like cellular organelles, has greatly informed our understanding of its crucial role in respiratory health and the pathogenesis of primary ciliary dyskinesia (PCD), including the genetics behind this condition. This review will summarize the current state of the art in the field highlighting its clinical implications. RECENT FINDINGS The genetics of PCD have exploded over the past few years as knowledge acquired from model systems has permitted the identification of genes that are key components of the ciliary apparatus and its function. In addition, clinical criteria and diagnostic tools have emerged that permit more clear identification of affected individuals. SUMMARY The rate of progress in the field continues to accelerate through international collaborative efforts and standardization of methods. Although the genetics behind PCD are complex, given the large number of genes associated with disease, as well as the large number of possible mutations even at the individual gene level, this knowledge is rapidly translating in improved diagnostics and hopefully in the near future in the identification of potential therapeutics.
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Affiliation(s)
- Carlos E. Milla
- The Stanford Cystic Fibrosis Center, Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, 770 Welch Rd., Ste. 350, Palo Alto, CA 94304, P. +1-650-736-9824, F. +1-650-723-5201,
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17
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Brychtova V, Mohtar A, Vojtesek B, Hupp TR. Mechanisms of anterior gradient-2 regulation and function in cancer. Semin Cancer Biol 2015; 33:16-24. [PMID: 25937245 DOI: 10.1016/j.semcancer.2015.04.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 04/10/2015] [Accepted: 04/21/2015] [Indexed: 01/12/2023]
Abstract
Proteins targeted to secretory pathway enter the endoplasmic reticulum where they undergo post-translational modification and subsequent quality control executed by exquisite catalysts of protein folding, protein disulphide isomerases (PDIs). These enzymes can often provide strict conformational protein folding solutions to highly cysteine-rich cargo as they facilitate disulphide rearrangement in the endoplasmic reticulum. Under conditions when PDI substrates are not isomerised properly, secreted proteins can accumulate in the endoplasmic reticulum leading to endoplasmic reticulum stress initiation with implications for human disease development. Anterior Gradient-2 (AGR2) is an endoplasmic reticulum-resident PDI superfamily member that has emerged as a dominant effector of basic biological properties in vertebrates including blastoderm formation and limb regeneration. AGR2 perturbation in mammals influences disease processes including cancer progression and drug resistance, asthma, and inflammatory bowel disease. This review will focus on the molecular characteristics, function, and regulation of AGR2, views on its emerging biological functions and misappropriation in disease, and prospects for therapeutic intervention into endoplasmic reticulum-resident protein folding pathways for improving the treatment of human disease.
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Affiliation(s)
- Veronika Brychtova
- Masaryk Memorial Cancer Institute, RECAMO, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Aiman Mohtar
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre Cell Signalling Unit, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Borivoj Vojtesek
- Masaryk Memorial Cancer Institute, RECAMO, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Ted R Hupp
- Masaryk Memorial Cancer Institute, RECAMO, Zluty kopec 7, 65653 Brno, Czech Republic; Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre Cell Signalling Unit, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK.
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