1
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Shields MA, Metropulos AE, Spaulding C, Alzahrani KA, Hirose T, Ohno S, Pham TND, Munshi HG. BET Inhibition Rescues Acinar-Ductal-Metaplasia and Ciliogenesis and Ameliorates Chronic Pancreatitis-Driven Changes in Mice with Loss of the Polarity Protein Par3. Cell Mol Gastroenterol Hepatol 2024; 18:101389. [PMID: 39128653 PMCID: PMC11437875 DOI: 10.1016/j.jcmgh.2024.101389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND & AIMS The apical-basal polarity of pancreatic acinar cells is essential for maintaining tissue architecture. However, the mechanisms by which polarity proteins regulate acinar pancreas injury and regeneration are poorly understood. METHODS Cerulein-induced pancreatitis was induced in mice with conditional deletion of the polarity protein Par3 in the pancreas. The impact of Par3 loss on pancreas injury and regeneration was assessed by histologic analyses and transcriptional profiling by RNA sequencing. Mice were pretreated with the bromodomain and extraterminal domain (BET) inhibitor JQ1 before cotreatment with cerulein to determine the effect of BET inhibition on pancreas injury and regeneration. RESULTS Initially, we show that Par3 is increased in acinar-ductal metaplasia (ADM) lesions present in human and mouse chronic pancreatitis specimens. Although Par3 loss disrupts tight junctions, Par3 is dispensable for pancreatogenesis. However, with aging, Par3 loss results in low-grade inflammation, acinar degeneration, and pancreatic lipomatosis. Par3 loss exacerbates acute pancreatitis-induced injury and chronic pancreatitis-induced acinar cell loss, promotes pancreatic lipomatosis, and prevents regeneration. Par3 loss also results in suppression of chronic pancreatitis-induced ADM and primary ciliogenesis. Notably, targeting BET proteins attenuates chronic pancreatitis-induced loss of primary cilia and promotes ADM in mice lacking pancreatic Par3. Targeting BET proteins also attenuates cerulein-induced acinar cell loss and enhances recovery of acinar cell mass and body weight of mice lacking pancreatic Par3. CONCLUSIONS Combined, this study demonstrates how Par3 restrains chronic pancreatitis-induced changes in the pancreas and identifies a potential role for BET inhibitors to attenuate pancreas injury and facilitate regeneration.
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Affiliation(s)
- Mario A Shields
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; The Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois.
| | - Anastasia E Metropulos
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Jesse Brown VA Medical Center, Chicago, Illinois
| | - Christina Spaulding
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Jesse Brown VA Medical Center, Chicago, Illinois
| | - Khulood A Alzahrani
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shigeo Ohno
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Thao N D Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; The Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
| | - Hidayatullah G Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; The Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois; Jesse Brown VA Medical Center, Chicago, Illinois.
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2
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Gilbert E, Craggs J, Modepalli V. Gene Regulatory Network that Shaped the Evolution of Larval Apical Organ in Cnidaria. Mol Biol Evol 2024; 41:msad285. [PMID: 38152864 PMCID: PMC10781443 DOI: 10.1093/molbev/msad285] [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: 09/25/2023] [Revised: 11/24/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023] Open
Abstract
Among non-bilaterian animals, a larval apical sensory organ with integrated neurons is only found in cnidarians. Within cnidarians, an apical organ with a ciliary tuft is mainly found in Actiniaria. Whether this apical tuft has evolved independently in Actiniaria or alternatively originated in the common ancestor of Cnidaria and Bilateria and was lost in specific groups is uncertain. To test this hypothesis, we generated transcriptomes of the apical domain during the planula stage of four species representing three key groups of cnidarians: Aurelia aurita (Scyphozoa), Nematostella vectensis (Actiniaria), and Acropora millepora and Acropora tenuis (Scleractinia). We showed that the canonical genes implicated in patterning the apical domain of N. vectensis are largely absent in A. aurita. In contrast, the apical domain of the scleractinian planula shares gene expression pattern with N. vectensis. By comparing the larval single-cell transcriptomes, we revealed the apical organ cell type of Scleractinia and confirmed its homology to Actiniaria. However, Fgfa2, a vital regulator of the regionalization of the N. vectensis apical organ, is absent in the scleractinian genome. Likewise, we found that FoxJ1 and 245 genes associated with cilia are exclusively expressed in the N. vectensis apical domain, which is in line with the presence of ciliary apical tuft in Actiniaria and its absence in Scleractinia and Scyphozoa. Our findings suggest that the common ancestor of cnidarians lacked a ciliary apical tuft, and it could have evolved independently in the Actiniaria.
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Affiliation(s)
- Eleanor Gilbert
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Jamie Craggs
- Horniman Museum and Gardens, London SE23 3PQ, UK
| | - Vengamanaidu Modepalli
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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3
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Lyu Q, Li Q, Zhou J, Zhao H. Formation and function of multiciliated cells. J Cell Biol 2024; 223:e202307150. [PMID: 38032388 PMCID: PMC10689204 DOI: 10.1083/jcb.202307150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/29/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
In vertebrates, multiciliated cells (MCCs) are terminally differentiated cells that line the airway tracts, brain ventricles, and reproductive ducts. Each MCC contains dozens to hundreds of motile cilia that beat in a synchronized manner to drive fluid flow across epithelia, the dysfunction of which is associated with a group of human diseases referred to as motile ciliopathies, such as primary cilia dyskinesia. Given the dynamic and complex process of multiciliogenesis, the biological events essential for forming multiple motile cilia are comparatively unelucidated. Thanks to advancements in genetic tools, omics technologies, and structural biology, significant progress has been achieved in the past decade in understanding the molecular mechanism underlying the regulation of multiple motile cilia formation. In this review, we discuss recent studies with ex vivo culture MCC and animal models, summarize current knowledge of multiciliogenesis, and particularly highlight recent advances and their implications.
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Affiliation(s)
- Qian Lyu
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Qingchao Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Huijie Zhao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
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4
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Wang H, Zuo S, Zheng J, Peng Z, Yao X, Wang J, Weber HC, Qin X, Xiang Y, Liu C, Ji M, Liu H, Pan L, Qu X. Knockout of the BRAP homolog in mice leads to abnormal tracheal cilia. FEBS Lett 2023; 597:2626-2642. [PMID: 37715941 DOI: 10.1002/1873-3468.14734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/29/2023] [Accepted: 07/08/2023] [Indexed: 09/18/2023]
Abstract
Both bombesin receptor-activated protein (BRAP) and its mouse homolog have been found to be expressed in bronchial epithelia but with unclear functions. Using electron microscopy combined with histological assays, we found that BRAP homolog deficiency in mice led to abnormal tracheal cilia. Rab-3A-interacting protein (Rabin8), a protein that might play a role in cilia development, was screened by yeast two-hybrid and further verified to have interaction with human BRAP by co-immunoprecipitation and pulldown assays. The expression levels of Rabin8, together with acetylated α-tubulin, a marker of cilia, were either downregulated by knockdown of BRAP or upregulated by overexpression of BRAP in cultured immortalized human bronchial epithelial cells. These results reveal a role for BRAP in airway cilia formation.
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Affiliation(s)
- Hui Wang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Suhui Zuo
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jiaoyun Zheng
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Peng
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xueping Yao
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
- Functional Center, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Jie Wang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Horst Christian Weber
- Section of Gastroenterology, and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, MA, USA
| | - Xiaoqun Qin
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Yang Xiang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Chi Liu
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Ming Ji
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Huijun Liu
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Lang Pan
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xiangping Qu
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
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5
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Cumplido-Laso G, Benitez DA, Mulero-Navarro S, Carvajal-Gonzalez JM. Transcriptional Regulation of Airway Epithelial Cell Differentiation: Insights into the Notch Pathway and Beyond. Int J Mol Sci 2023; 24:14789. [PMID: 37834236 PMCID: PMC10573127 DOI: 10.3390/ijms241914789] [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: 07/12/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The airway epithelium is a critical component of the respiratory system, serving as a barrier against inhaled pathogens and toxins. It is composed of various cell types, each with specific functions essential to proper airway function. Chronic respiratory diseases can disrupt the cellular composition of the airway epithelium, leading to a decrease in multiciliated cells (MCCs) and an increase in secretory cells (SCs). Basal cells (BCs) have been identified as the primary stem cells in the airway epithelium, capable of self-renewal and differentiation into MCCs and SCs. This review emphasizes the role of transcription factors in the differentiation process from BCs to MCCs and SCs. Recent advancements in single-cell RNA sequencing (scRNAseq) techniques have provided insights into the cellular composition of the airway epithelium, revealing specialized and rare cell types, including neuroendocrine cells, tuft cells, and ionocytes. Understanding the cellular composition and differentiation processes within the airway epithelium is crucial for developing targeted therapies for respiratory diseases. Additionally, the maintenance of BC populations and the involvement of Notch signaling in BC self-renewal and differentiation are discussed. Further research in these areas could provide valuable insights into the mechanisms underlying airway epithelial homeostasis and disease pathogenesis.
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Affiliation(s)
- Guadalupe Cumplido-Laso
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain; (D.A.B.); (S.M.-N.)
| | | | | | - Jose Maria Carvajal-Gonzalez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain; (D.A.B.); (S.M.-N.)
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Shields MA, Metropulos AE, Spaulding C, Hirose T, Ohno S, Pham TN, Munshi HG. BET inhibition rescues ciliogenesis and ameliorates pancreatitis-driven phenotypic changes in mice with Par3 loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557654. [PMID: 37745543 PMCID: PMC10515915 DOI: 10.1101/2023.09.14.557654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The apical-basal polarity of pancreatic acinar cells is essential for maintaining tissue architecture. However, the mechanisms by which polarity proteins regulate acinar pancreas tissue homeostasis are poorly understood. Here, we evaluate the role of Par3 in acinar pancreas injury and homeostasis. While Par3 loss in the mouse pancreas disrupts tight junctions, Par3 loss is dispensable for pancreatogenesis. However, with aging, Par3 loss results in low-grade inflammation, acinar degeneration, and pancreatic lipomatosis. Par3 loss also exacerbates pancreatitis-induced acinar cell loss, resulting in pronounced pancreatic lipomatosis and failure to regenerate. Moreover, Par3 loss in mice harboring mutant Kras causes extensive pancreatic intraepithelial neoplastic (PanIN) lesions and large pancreatic cysts. We also show that Par3 loss restricts injury-induced primary ciliogenesis. Significantly, targeting BET proteins enhances primary ciliogenesis during pancreatitis-induced injury and, in mice with Par3 loss, limits pancreatitis-induced acinar loss and facilitates acinar cell regeneration. Combined, this study demonstrates how Par3 restrains pancreatitis- and Kras-induced changes in the pancreas and identifies a potential role for BET inhibitors to attenuate pancreas injury and facilitate pancreas tissue regeneration.
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Affiliation(s)
- Mario A. Shields
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Anastasia E. Metropulos
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Christina Spaulding
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shigeo Ohno
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Thao N.D. Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Hidayatullah G. Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
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7
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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Zhang D, Zhang C, Zhu Y, Xie H, Yue C, Li M, Wei W, Peng Y, Yin G, Guo Y, Guan Y. Recruitment of transcription factor ETS1 to activated accessible regions promotes the transcriptional program of cilia genes. Nucleic Acids Res 2023:gkad506. [PMID: 37326025 PMCID: PMC10359609 DOI: 10.1093/nar/gkad506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Defects in cilia genes, which are critical for cilia formation and function, can cause complicated ciliopathy syndromes involving multiple organs and tissues; however, the underlying regulatory mechanisms of the networks of cilia genes in ciliopathies remain enigmatic. Herein, we have uncovered the genome-wide redistribution of accessible chromatin regions and extensive alterations of expression of cilia genes during Ellis-van Creveld syndrome (EVC) ciliopathy pathogenesis. Mechanistically, the distinct EVC ciliopathy-activated accessible regions (CAAs) are shown to positively regulate robust changes in flanking cilia genes, which are a key requirement for cilia transcription in response to developmental signals. Moreover, a single transcription factor, ETS1, can be recruited to CAAs, leading to prominent chromatin accessibility reconstruction in EVC ciliopathy patients. In zebrafish, the collapse of CAAs driven by ets1 suppression subsequently causes defective cilia proteins, resulting in body curvature and pericardial oedema. Our results depict a dynamic landscape of chromatin accessibility in EVC ciliopathy patients, and uncover an insightful role for ETS1 in controlling the global transcriptional program of cilia genes by reprogramming the widespread chromatin state.
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Affiliation(s)
- Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Chong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yanmei Zhu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Haixia Xie
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Caifeng Yue
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
- Department of Laboratory Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Mingfeng Li
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Wenlu Wei
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yu Peng
- Pediatric Intensive Care Unit Central, People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Guibin Yin
- Department of Orthopedics, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yunmiao Guo
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yiting Guan
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
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9
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Kim DY, Sub YJ, Kim HY, Cho KJ, Choi WI, Choi YJ, Lee MG, Hildebrandt F, Gee HY. LRRC6 regulates biogenesis of motile cilia by aiding FOXJ1 translocation into the nucleus. Cell Commun Signal 2023; 21:142. [PMID: 37328841 PMCID: PMC10273532 DOI: 10.1186/s12964-023-01135-y] [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: 12/26/2022] [Accepted: 04/22/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND LRRC6 is an assembly factor for dynein arms in the cytoplasm of motile ciliated cells, and when mutated, dynein arm components remained in the cytoplasm. Here, we demonstrate the role of LRRC6 in the active nuclear translocation of FOXJ1, a master regulator for cilia-associated gene transcription. METHODS We generated Lrrc6 knockout (KO) mice, and we investigated the role of LRRC6 on ciliopathy development by using proteomic, transcriptomic, and immunofluorescence analysis. Experiments on mouse basal cell organoids confirmed the biological relevance of our findings. RESULTS The absence of LRRC6 in multi-ciliated cells hinders the assembly of ODA and IDA components of cilia; in this study, we showed that the overall expression of proteins related to cilia decreased as well. Expression of cilia-related transcripts, specifically ODA and IDA components, dynein axonemal assembly factors, radial spokes, and central apparatus was lower in Lrrc6 KO mice than in wild-type mice. We demonstrated that FOXJ1 was present in the cytoplasm and translocated into the nucleus when LRRC6 was expressed and that this process was blocked by INI-43, an importin α inhibitor. CONCLUSIONS Taken together, these results hinted at the LRRC6 transcriptional regulation of cilia-related genes via the nuclear translocation of FOXJ1. Video Abstract.
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Affiliation(s)
- Dong Yun Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Division of Gastroenterology, Department of Internal Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Yu Jin Sub
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hye-Youn Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyeong Jee Cho
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Won Il Choi
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Yo Jun Choi
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Heon Yung Gee
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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10
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Arora S, Rana M, Sachdev A, D’Souza JS. Appearing and disappearing acts of cilia. J Biosci 2023. [DOI: 10.1007/s12038-023-00326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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11
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Zhou S, Liu Y, Yang Y, Huang H, Qiu Q. Shorter Cilia Length and Aberrant Ciliated Marker DNAI1 in Allergic Rhinitis. J Inflamm Res 2023; 16:373-380. [PMID: 36741287 PMCID: PMC9896970 DOI: 10.2147/jir.s393025] [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: 10/11/2022] [Accepted: 11/26/2022] [Indexed: 02/02/2023] Open
Abstract
Purpose This study aimed to investigate whether the impaired ciliary length and aberrant ciliary ultrastructure marker, dynein axonemal intermediate chain 1 (DNAI1), are important pathological characteristics in nasal mucosa from patients with allergic rhinitis (AR). Patients and Methods Biopsies were taken from the inferior turbinate (IT) of controls (n = 20) and patients with AR (n = 20). The ciliary length and the DNAI1 location patterns were assessed by using immunofluorescent staining. Three patterns of DNAI1 localization were defined using a semi-quantitative scoring system: normal (N), partial (P) and absence (A). Every individual section was assigned a score between 0 and 2 in each high-power field (5 fields per sample). The score of 0 = pattern N >70%; 1 = patterns N + P >70%; and 2 = pattern A ≥30%. The receiver operating characteristic (ROC) curve was used to evaluate the predicted value of DNAI1 score for AR. Results The ciliary length was reduced by 33.3% in patients with AR compared with controls (P < 0.0001). The higher DNAI1 score was found in the AR group, with a median (first and third quartile) of 0.9 (0.4 and 1.08), which was 0.1 (0 and 0.76) in the control group (P = 0.0071). The ROC of DNAI1 was calculated based on the area under the curve of 0.74 (P = 0.0094). The cutoff value of ROC was 0.5833, with a sensitivity and specificity of 70%. Conclusion These results suggested that the shorter ciliary length and aberrant localization of DNAI1 are potentially important pathological characteristics of the allergic nasal mucosa. The aberrant localization of DNAI1 may provide a novel candidate target for clinical management of AR.
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Affiliation(s)
- Suizi Zhou
- Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People’s Republic of China,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yitong Liu
- Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People’s Republic of China,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yueying Yang
- Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People’s Republic of China
| | - Hongming Huang
- Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People’s Republic of China
| | - Qianhui Qiu
- Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People’s Republic of China,Correspondence: Qianhui Qiu, Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People’s Republic of China, Email
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12
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Arora S, Rana M, Sachdev A, D'Souza JS. Appearing and disappearing acts of cilia. J Biosci 2023; 48:8. [PMID: 36924208 PMCID: PMC10005925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The past few decades have seen a rise in research on vertebrate cilia and ciliopathy, with interesting collaborations between basic and clinical scientists. This work includes studies on ciliary architecture, composition, evolution, and organelle generation and its biological role. The human body has cells that harbour any of the following four types of cilia: 9+0 motile, 9+0 immotile, 9+2 motile, and 9+2 immotile. Depending on the type, cilia play an important role in cell/fluid movement, mating, sensory perception, and development. Defects in cilia are associated with a wide range of human diseases afflicting the brain, heart, kidneys, respiratory tract, and reproductive system. These are commonly known as ciliopathies and affect millions of people worldwide. Due to their complex genetic etiology, diagnosis and therapy have remained elusive. Although model organisms like Chlamydomonas reinhardtii have been a useful source for ciliary research, reports of a fascinating and rewarding translation of this research into mammalian systems, especially humans, are seen. The current review peeks into one of the complex features of this organelle, namely its birth, the common denominators across the formation of both 9+0 and 9+2 ciliary types, the molecules involved in ciliogenesis, and the steps that go towards regulating their assembly and disassembly.
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Affiliation(s)
- Shashank Arora
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (E), Mumbai 400098, India
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13
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Czerny CC, Borschel A, Cai M, Otto M, Hoyer-Fender S. FOXA1 is a transcriptional activator of Odf2/Cenexin and regulates primary ciliation. Sci Rep 2022; 12:21468. [PMID: 36509813 PMCID: PMC9744847 DOI: 10.1038/s41598-022-25966-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Primary cilia are sensory organelles essential for embryonic and postnatal development, and tissue homeostasis in adulthood. They are generated in a cell cycle-dependent manner and found on most cells of the body. Although cilia formation is intensively investigated virtually nothing is known about the transcriptional regulation of primary ciliation. We used here Odf2/Cenexin, encoding a protein of the mother centriole and the basal body that is mandatory for primary cilia formation, as the target gene for the identification of transcriptional activators. We identified a consensus binding site for Fox transcription factors (TFs) in its promoter region and focused here on the Fox family. We found transcriptional activation of Odf2 neither by FOXO TFs nor by the core TF for multiciliation, FOXJ1. However, we identified FOXA1 as a transcriptional activator of Odf2 by reporter gene assays and qRT-PCR, and showed by qWB that Foxa1 knockdown caused a decrease in ODF2 and CP110 proteins. We verified the binding sequence of FOXA1 in the Odf2 promoter by ChIP. Finally, we demonstrated that knockdown of FOXA1 affected primary cilia formation. We, thus, showed for the first time, that FOXA1 regulates primary ciliation by transcriptional activation of ciliary genes.
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Affiliation(s)
- Christian Carl Czerny
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Anett Borschel
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Mingfang Cai
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Madeline Otto
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany ,grid.424957.90000 0004 0624 9165Present Address: Thermo Fisher Scientific GENEART, Regensburg, Germany
| | - Sigrid Hoyer-Fender
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
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14
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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15
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Hulme L, Hochstetler A, Schwerk C, Schroten H, Ishikawa H, Tung CY, Perrin B, Blazer-Yost B. Characterization of TRPV4-mediated signaling pathways in an optimized human choroid plexus epithelial cell line. Am J Physiol Cell Physiol 2022; 323:C1823-C1842. [PMID: 35938676 PMCID: PMC9744646 DOI: 10.1152/ajpcell.00193.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022]
Abstract
The objectives of these studies were twofold: 1) to characterize the human choroid plexus papilloma (HIBCPP) cell line as a model of the blood-cerebrospinal fluid barrier (BCSFB) via morphology, tightness, and polarization of transporters in choroid plexus epithelia (CPe), and 2) to utilize Ussing-style electrophysiology to elucidate signaling pathways associated with the activation of the transient receptor potential vanilloid 4 (TRPV4) channel involved in cerebrospinal fluid (CSF) secretion. RT-PCR was implemented to determine gene expression of cell fate markers, junctional complex proteins, and transporters of interest. Scanning electron microscopy and confocal three-dimensional renderings of cultures grown on permeable supports were utilized to delineate the morphology of the brush border, junctional complexes, and polarization of key transporters. Electrophysiology was used to understand and explore TRPV4-mediated signaling in the HIBCPP cell line, considering both short-circuit current (Isc) and conductance responses. HIBCPP cells grown under optimized culture conditions exhibited minimal multilayering, developed an intermediate resistance monolayer, retained differentiation properties, and expressed, and correctly localized, junctional proteins and native transporters. We found that activation of TRPV4 resulted in a robust, multiphasic change in electrogenic ion flux and increase in conductance accompanied by substantial fluid secretion. This response appears to be modulated by a number of different effectors, implicating phospholipase C (PLC), protein kinase C (PKC), and phosphoinositide 3-kinase (PI3K) in TRPV4-mediated ion flux. The HIBCPP cell line is a representative model of the human BCSFB, which can be utilized for studies of transporter function, intracellular signaling, and regulation of CSF production.
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Affiliation(s)
- Louise Hulme
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Alexandra Hochstetler
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Christian Schwerk
- Department of Pediatrics, Pediatric Infectious Diseases, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Horst Schroten
- Department of Pediatrics, Pediatric Infectious Diseases, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hiroshi Ishikawa
- Department of Neurosurgery, Laboratory of Clinical Regenerative Medicine, University of Tsukuba, Ibaraki, Japan
| | - Chun-Yu Tung
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Benjamin Perrin
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Bonnie Blazer-Yost
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
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16
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Ignatenko O, Malinen S, Rybas S, Vihinen H, Nikkanen J, Kononov A, Jokitalo ES, Ince-Dunn G, Suomalainen A. Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes. J Biophys Biochem Cytol 2022; 222:213692. [PMID: 36383135 PMCID: PMC9674092 DOI: 10.1083/jcb.202203019] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/19/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Astrocytes, often considered as secondary responders to neurodegeneration, are emerging as primary drivers of brain disease. Here we show that mitochondrial DNA depletion in astrocytes affects their primary cilium, the signaling organelle of a cell. The progressive oxidative phosphorylation deficiency in astrocytes induces FOXJ1 and RFX transcription factors, known as master regulators of motile ciliogenesis. Consequently, a robust gene expression program involving motile cilia components and multiciliated cell differentiation factors are induced. While the affected astrocytes still retain a single cilium, these organelles elongate and become remarkably distorted. The data suggest that chronic activation of the mitochondrial integrated stress response (ISRmt) in astrocytes drives anabolic metabolism and promotes ciliary elongation. Collectively, our evidence indicates that an active signaling axis involving mitochondria and primary cilia exists and that ciliary signaling is part of ISRmt in astrocytes. We propose that metabolic ciliopathy is a novel pathomechanism for mitochondria-related neurodegenerative diseases.
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Affiliation(s)
- Olesia Ignatenko
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Satu Malinen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sofiia Rybas
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Joni Nikkanen
- Cardiovascular Research Institute, University of California, San Francisco, CA
| | | | - Eija S. Jokitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gulayse Ince-Dunn
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Suomalainen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,HUS Diagnostics, Helsinki University Hospital, Helsinki, Finland
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17
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Pandit R, Singh I, Ansari A, Raval J, Patel Z, Dixit R, Shah P, Upadhyay K, Chauhan N, Desai K, Shah M, Modi B, Joshi M, Joshi C. First report on genome wide association study in western Indian population reveals host genetic factors for COVID-19 severity and outcome. Genomics 2022; 114:110399. [PMID: 35680011 PMCID: PMC9169419 DOI: 10.1016/j.ygeno.2022.110399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023]
Abstract
Different human races across the globe responded in a different way to the SARS-CoV-2 infection leading to different disease severity. Therefore, it is anticipated that host genetic factors have a straight association with the COVID-19. We identified a total 6, 7, and 6 genomic loci for deceased-recovered, asymptomatic-recovered, and deceased-asymptomatic group comparison, respectively. Unfavourable alleles of the markers nearby the genes which are associated with lung and heart diseases such as Tumor necrosis factor superfamily (TNFSF4&18), showed noteworthy association with the disease severity and outcome for the COVID-19 patients in the western Indian population. The markers found with significant association with disease prognosis or recovery are of value in determining the individual's response to SARS-CoV-2 infection and can be used for the risk prediction in COVID-19. Besides, GWAS study in other populations from India may help to strengthen the outcome of this study.
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Affiliation(s)
- Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Indra Singh
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Raghav Dixit
- Commissionerate of Health Medical Services and Medical Education Gandhinagar, Gujarat 382010, India
| | - Pranay Shah
- Department of Microbiology, B.J. Medical College and Civil hospital, Institute of Medical Post-Graduate Studies and Research, Ahmedabad, Gujarat 380016, India
| | - Kamlesh Upadhyay
- Department of Medicine, B.J. Medical College and Civil hospital, Institute of Medical Post-Graduate Studies and Research, Ahmedabad, Gujarat 380016, India
| | - Naresh Chauhan
- Department of Community Medicine, Government Medical College, Surat, Gujarat 395001, India
| | - Kairavi Desai
- Department of Microbiology, Government Medical College, Bhavnagar, Gujarat 364001, India
| | - Meenakshi Shah
- Department of General Medicine, GMERS Medical College & Hospital, Gotri, Vadodara, Gujarat 390021, India
| | - Bhavesh Modi
- Department of Community Medicine, GMERS Medical College, Gandhinagar, Gujarat 382012, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India.
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18
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Paranjapye A, Leir SH, Huang F, Kerschner JL, Harris A. Cell function and identity revealed by comparative scRNA-seq analysis in human nasal, bronchial and epididymis epithelia. Eur J Cell Biol 2022; 101:151231. [PMID: 35597096 PMCID: PMC9357053 DOI: 10.1016/j.ejcb.2022.151231] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/19/2022] [Accepted: 04/30/2022] [Indexed: 11/07/2022] Open
Abstract
The evolutionary relationship of cells within tissues having a similar function but located in different anatomical sites is of considerable biological interest. The development of single-cell RNA sequencing (scRNA-seq) protocols has greatly enhanced opportunities to address this topic. Here we focus on cells in the epithelium which lines two regions of the human respiratory tract and the male genital ducts to delineate the shared, differentiated functions of the different cell populations. Transcriptomic data were used to assess the gene expression profiles of human bronchial, nasal, and epididymal epithelium (HBE, HNE, and HEE). Bulk RNA-seq showed many shared genes expressed in cells from the nasal and bronchial epithelium and highlighted their divergence from the epididymal epithelium. ScRNA-seq in HBE and HNE cells demonstrated overlapping gene expression patterns within basal and secretory cell populations. Moreover, the distribution of cell types was altered in HNE cells derived from donors with cystic fibrosis (CF) when compared to cells from healthy donors. Next, the HBE and HNE datasets were merged and confirmed intersection of cell type gene expression profiles from the two sites. However, secretory and ciliated cells were the most abundant types in the HBE samples, while more basal cells were seen in the HNE populations. We then merged single-cell data from the epididymis to determine if overlapping functions of these cells corresponded to those in the airway. Of note, only the pulmonary ionocytes/epididymis clear cells showed a strongly conserved identity, which was confirmed by imputation in bulk RNA-seq datasets from the same cells.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Felix Huang
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jenny L Kerschner
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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19
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Leon A, Subirana L, Magre K, Cases I, Tena JJ, Irimia M, Gomez-Skarmeta JL, Escriva H, Bertrand S. Gene regulatory networks of epidermal and neural fate choice in a chordate. Mol Biol Evol 2022; 39:6547258. [PMID: 35276009 PMCID: PMC9004418 DOI: 10.1093/molbev/msac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Neurons are a highly specialized cell type only found in metazoans. They can be scattered throughout the body or grouped together, forming ganglia or nerve cords. During embryogenesis, centralized nervous systems develop from the ectoderm, which also forms the epidermis. How pluripotent ectodermal cells are directed toward neural or epidermal fates, and to which extent this process is shared among different animal lineages, are still open questions. Here, by using micromere explants, we were able to define in silico the putative gene regulatory networks (GRNs) underlying the first steps of the epidermis and the central nervous system formation in the cephalochordate amphioxus. We propose that although the signal triggering neural induction in amphioxus (i.e., Nodal) is different from vertebrates, the main transcription factors implicated in this process are conserved. Moreover, our data reveal that transcription factors of the neural program seem to not only activate neural genes but also to potentially have direct inputs into the epidermal GRN, suggesting that the Nodal signal might also contribute to neural fate commitment by repressing the epidermal program. Our functional data on whole embryos support this result and highlight the complex interactions among the transcription factors activated by the signaling pathways that drive ectodermal cell fate choice in chordates.
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Affiliation(s)
- Anthony Leon
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Kevin Magre
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
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20
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Kuruş M, Akbari S, Eskier D, Bursalı A, Ergin K, Erdal E, Karakülah G. Transcriptome Dynamics of Human Neuronal Differentiation From iPSC. Front Cell Dev Biol 2022; 9:727747. [PMID: 34970540 PMCID: PMC8712770 DOI: 10.3389/fcell.2021.727747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
The generation and use of induced pluripotent stem cells (iPSCs) in order to obtain all differentiated adult cell morphologies without requiring embryonic stem cells is one of the most important discoveries in molecular biology. Among the uses of iPSCs is the generation of neuron cells and organoids to study the biological cues underlying neuronal and brain development, in addition to neurological diseases. These iPSC-derived neuronal differentiation models allow us to examine the gene regulatory factors involved in such processes. Among these regulatory factors are long non-coding RNAs (lncRNAs), genes that are transcribed from the genome and have key biological functions in establishing phenotypes, but are frequently not included in studies focusing on protein coding genes. Here, we provide a comprehensive analysis and overview of the coding and non-coding transcriptome during multiple stages of the iPSC-derived neuronal differentiation process using RNA-seq. We identify previously unannotated lncRNAs via genome-guided de novo transcriptome assembly, and the distinct characteristics of the transcriptome during each stage, including differentially expressed and stage specific genes. We further identify key genes of the human neuronal differentiation network, representing novel candidates likely to have critical roles in neurogenesis using coexpression network analysis. Our findings provide a valuable resource for future studies on neuronal differentiation.
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Affiliation(s)
- Meltem Kuruş
- Department of Histology and Embryology, Faculty of Medicine, Izmir Katip Çelebi University, Izmir, Turkey
| | | | - Doğa Eskier
- İzmir Biomedicine and Genome Center, İzmir, Turkey.,İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | | | - Kemal Ergin
- Department of Histology and Embryology, Faculty of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Esra Erdal
- İzmir Biomedicine and Genome Center, İzmir, Turkey.,Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Gökhan Karakülah
- İzmir Biomedicine and Genome Center, İzmir, Turkey.,İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
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21
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Zhang C, Li C, Yang L, Leng L, Jovic D, Wang J, Fang F, Li G, Zhao D, Li X, Lin L, Luo Y, Bolund L, Huang J, Lin G, Xu F. The Dynamic Changes of Transcription Factors During the Development Processes of Human Biparental and Uniparental Embryos. Front Cell Dev Biol 2021; 9:709498. [PMID: 34604214 PMCID: PMC8484909 DOI: 10.3389/fcell.2021.709498] [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: 05/14/2021] [Accepted: 08/24/2021] [Indexed: 12/20/2022] Open
Abstract
Previous studies have revealed that transcription factors (TFs) play important roles in biparental (BI) early human embryogenesis. However, the contribution of TFs during early uniparental embryo development is still largely unknown. Here we systematically studied the expression profiles of transcription factors in early embryonic development and revealed the dynamic changes of TFs in human biparental and uniparental embryogenesis by single-cell RNA sequencing (scRNA-seq). In general, the TF expression model of uniparental embryos showed a high degree of conformity with biparental embryos. The detailed network analysis of three different types of embryos identified that 10 out of 17 hub TFs were shared or specifically owned, such as ZNF480, ZNF581, PHB, and POU5F1, were four shared TFs, ZFN534, GTF3A, ZNF771, TEAD4, and LIN28A, were androgenic (AG) specific TFs, and ZFP42 was the only one parthenogenetic (PG) specific TF. All the four shared TFs were validated using human embryonic stem cell (hESC) differentiation experiments; most of their target genes are responsible for stem cell maintenance and differentiation. We also found that Zf-C2H2, HMG, and MYB were three dominant transcription factor families that appeared in early embryogenesis. Altogether, our work provides a comprehensive regulatory framework and better understanding of TF function in human biparental and uniparental embryogenesis.
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Affiliation(s)
- Chenxi Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Conghui Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ling Yang
- BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Lizhi Leng
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Dragomirka Jovic
- BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Jun Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Fang Fang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Guibo Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xuemei Li
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Yonglun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Bolund
- BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ge Lin
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Fengping Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI Cell, BGI-Shenzhen, Shenzhen, China
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22
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Baldi P, Alhassen W, Chen S, Nguyen H, Khoudari M, Alachkar A. Large-scale analysis reveals spatiotemporal circadian patterns of cilia transcriptomes in the primate brain. J Neurosci Res 2021; 99:2610-2624. [PMID: 34310750 PMCID: PMC11391745 DOI: 10.1002/jnr.24919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 01/13/2023]
Abstract
Cilia are dynamic subcellular systems, with core structural and functional components operating in a highly coordinated manner. Since many environmental stimuli sensed by cilia are circadian in nature, it is reasonable to speculate that genes encoding cilia structural and functional components follow rhythmic circadian patterns of expression. Using computational methods and the largest spatiotemporal gene expression atlas of primates, we identified and analyzed the circadian rhythmic expression of cilia genes across 22 primate brain areas. We found that around 73% of cilia transcripts exhibited circadian rhythmicity across at least one of 22 brain regions. In 12 brain regions, cilia transcriptomes were significantly enriched with circadian oscillating transcripts, as compared to the rest of the transcriptome. The phase of the cilia circadian transcripts deviated from the phase of the majority of the background circadian transcripts, and transcripts coding for cilia basal body components accounted for the majority of cilia circadian transcripts. In addition, adjacent or functionally connected brain nuclei had large overlapping complements of circadian cilia genes. Most remarkably, cilia circadian transcripts shared across the basal ganglia nuclei and the prefrontal cortex peaked in these structures in sequential fashion that is similar to the sequential order of activation of the basal ganglia-cortical circuitry in connection with movement coordination, albeit on completely different timescales. These findings support a role for the circadian spatiotemporal orchestration of cilia gene expression in the normal physiology of the basal ganglia-cortical circuit and motor control. Studying orchestrated cilia rhythmicity in the basal ganglia-cortical circuits and other brain circuits may help develop better functional models, and shed light on the causal effects cilia functions have on these circuits and on the regulation of movement and other behaviors.
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Affiliation(s)
- Pierre Baldi
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
| | - Wedad Alhassen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Siwei Chen
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
| | - Henry Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Mohammad Khoudari
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Amal Alachkar
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
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23
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Yaqub N, Wayne G, Birchall M, Song W. Recent advances in human respiratory epithelium models for drug discovery. Biotechnol Adv 2021; 54:107832. [PMID: 34481894 DOI: 10.1016/j.biotechadv.2021.107832] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/08/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
The respiratory epithelium is intimately associated with the pathophysiologies of highly infectious viral contagions and chronic illnesses such as chronic obstructive pulmonary disorder, presently the third leading cause of death worldwide with a projected economic burden of £1.7 trillion by 2030. Preclinical studies of respiratory physiology have almost exclusively utilised non-humanised animal models, alongside reductionistic cell line-based models, and primary epithelial cell models cultured at an air-liquid interface (ALI). Despite their utility, these model systems have been limited by their poor correlation to the human condition. This has undermined the ability to identify novel therapeutics, evidenced by a 15% chance of success for medicinal respiratory compounds entering clinical trials in 2018. Consequently, preclinical studies require new translational efficacy models to address the problem of respiratory drug attrition. This review describes the utility of the current in vivo (rodent), ex vivo (isolated perfused lungs and precision cut lung slices), two-dimensional in vitro cell-line (A549, BEAS-2B, Calu-3) and three-dimensional in vitro ALI (gold-standard and co-culture) and organoid respiratory epithelium models. The limitations to the application of these model systems in drug discovery research are discussed, in addition to perspectives of the future innovations required to facilitate the next generation of human-relevant respiratory models.
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Affiliation(s)
- Naheem Yaqub
- UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, Department of Surgical Biotechnology, Division of Surgery & Interventional Science, University College London, London NW3 2PF, UK
| | - Gareth Wayne
- Novel Human Genetics, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Martin Birchall
- The Ear Institute, Faculty of Brain Sciences, University College London, London WC1X 8EE, UK.
| | - Wenhui Song
- UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, Department of Surgical Biotechnology, Division of Surgery & Interventional Science, University College London, London NW3 2PF, UK.
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24
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Matossian MD, Elliott S, Van Hoang T, Burks HE, Wright MK, Alzoubi MS, Yan T, Chang T, Wathieu H, Windsor GO, Hartono AB, Lee S, Zuercher WJ, Drewry DH, Wells C, Kapadia N, Buechlein A, Fang F, Nephew KP, Collins-Burow BM, Burow ME. NEK5 activity regulates the mesenchymal and migratory phenotype in breast cancer cells. Breast Cancer Res Treat 2021; 189:49-61. [PMID: 34196902 DOI: 10.1007/s10549-021-06295-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/13/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE Breast cancer remains a prominent global disease affecting women worldwide despite the emergence of novel therapeutic regimens. Metastasis is responsible for most cancer-related deaths, and acquisition of a mesenchymal and migratory cancer cell phenotypes contributes to this devastating disease. The utilization of kinase targets in drug discovery have revolutionized the field of cancer research but despite impressive advancements in kinase-targeting drugs, a large portion of the human kinome remains understudied in cancer. NEK5, a member of the Never-in-mitosis kinase family, is an example of such an understudied kinase. Here, we characterized the function of NEK5 in breast cancer. METHODS Stably overexpressing NEK5 cell lines (MCF7) and shRNA knockdown cell lines (MDA-MB-231, TU-BcX-4IC) were utilized. Cell morphology changes were evaluated using immunofluorescence and quantification of cytoskeletal components. Cell proliferation was assessed by Ki-67 staining and transwell migration assays tested cell migration capabilities. In vivo experiments with murine models were necessary to demonstrate NEK5 function in breast cancer tumor growth and metastasis. RESULTS NEK5 activation altered breast cancer cell morphology and promoted cell migration independent of effects on cell proliferation. NEK5 overexpression or knockdown does not alter tumor growth kinetics but promotes or suppresses metastatic potential in a cell type-specific manner, respectively. CONCLUSION While NEK5 activity modulated cytoskeletal changes and cell motility, NEK5 activity affected cell seeding capabilities but not metastatic colonization or proliferation in vivo. Here we characterized NEK5 function in breast cancer systems and we implicate NEK5 in regulating specific steps of metastatic progression.
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Affiliation(s)
| | - Steven Elliott
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - T Van Hoang
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Hope E Burks
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Maryl K Wright
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Madlin S Alzoubi
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Thomas Yan
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Tiffany Chang
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Henri Wathieu
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Gabrielle O Windsor
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Alifiani Bo Hartono
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sean Lee
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nirav Kapadia
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aaron Buechlein
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
| | - Fang Fang
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
| | - Kenneth P Nephew
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| | | | - Matthew E Burow
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
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25
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Loukas I, Skamnelou M, Tsaridou S, Bournaka S, Grigoriadis S, Taraviras S, Lygerou Z, Arbi M. Fine-tuning multiciliated cell differentiation at the post-transcriptional level: contribution of miR-34/449 family members. Biol Rev Camb Philos Soc 2021; 96:2321-2332. [PMID: 34132477 DOI: 10.1111/brv.12755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 01/28/2023]
Abstract
Cell differentiation is a process that must be precisely regulated for the maintenance of tissue homeostasis. Differentiation towards a multiciliated cell fate is characterized by well-defined stages, where a transcriptional cascade is activated leading to the formation of multiple centrioles and cilia. Centrioles migrate and dock to the apical cell surface and, acting as basal bodies, give rise to multiple motile cilia. The concerted movement of cilia ensures directional fluid flow across epithelia and defects either in their number or structure can lead to disease phenotypes. Micro-RNAs (miRNAs; miRs) are small, non-coding RNA molecules that play an important role in post-transcriptional regulation of gene expression. miR-34b/c and miR-449a/b/c specifically function throughout the differentiation of multiciliated cells, fine-tuning the expression of many different centriole- and cilia-related genes. They strictly regulate the expression levels of genes that are required both for commitment towards the multiciliated cell fate (e.g. Notch) and for the establishment and maintenance of this fate by regulating the expression of transcription factors and structural components of the pathway. Herein we review miR-34 and miR-449 spatiotemporal regulation along with their roles during the different stages of multiciliogenesis.
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Affiliation(s)
- Ioannis Loukas
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Margarita Skamnelou
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Stavroula Tsaridou
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Spyridoula Bournaka
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Sokratis Grigoriadis
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Stavros Taraviras
- Laboratory of Physiology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
| | - Marina Arbi
- Laboratory of Biology, School of Medicine, University of Patras, Rio, Patras, 26504, Greece
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26
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Wu YJ, Liu Y, Hu YQ, Wang L, Bai FR, Xu C, Wu JW. Control of multiciliogenesis by miR-34/449 in the male reproductive tract through enforcing cell cycle exit. J Cell Sci 2021; 134:261955. [PMID: 33973639 PMCID: PMC8182409 DOI: 10.1242/jcs.253450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Multiciliated cells (MCCs) are terminally differentiated postmitotic cells that possess hundreds of motile cilia on their apical surface. Defects in cilia formation are associated with ciliopathies that affect many organs. In this study, we tested the role and mechanism of the miR-34/449 family in the regulation of multiciliogenesis in EDs using an miR-34b/c−/−; miR-449−/− double knockout (dKO) mouse model. MiR-34b/c and miR-449 depletion led to a reduced number of MCCs and abnormal cilia structure in the EDs starting from postnatal day (P)14. However, abnormal MCC differentiation in the dKO EDs could be observed as early as P7. RNA-seq analyses revealed that the aberrant development of MCCs in the EDs of dKO mice was associated with the upregulation of genes involved in cell cycle control. Using a cyclin-dependent kinase inhibitor to force cell cycle exit promoted MCC differentiation, and partially rescued the defective multiciliogenesis in the EDs of dKO mice. Taken together, our results suggest that miR-34b/c and miR-449 play an essential role in multiciliogenesis in EDs by regulating cell cycle exit. Summary: Mutagenic, expression and histological analyses reveal an essential role for miR-34b/c and miR-449 in multiciliogenesis in efferent ductules of the male reproductive tract by regulating cell cycle exit.
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Affiliation(s)
- Yu-Jie Wu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Yue Liu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Yan-Qin Hu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Li Wang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Fu-Rong Bai
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Chen Xu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Jing-Wen Wu
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
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27
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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: 92] [Impact Index Per Article: 30.7] [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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28
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Yusifov E, Dumoulin A, Stoeckli ET. Investigating Primary Cilia during Peripheral Nervous System Formation. Int J Mol Sci 2021; 22:3176. [PMID: 33804711 PMCID: PMC8003989 DOI: 10.3390/ijms22063176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 12/22/2022] Open
Abstract
The primary cilium plays a pivotal role during the embryonic development of vertebrates. It acts as a somatic signaling hub for specific pathways, such as Sonic Hedgehog signaling. In humans, mutations in genes that cause dysregulation of ciliogenesis or ciliary function lead to severe developmental disorders called ciliopathies. Beyond its role in early morphogenesis, growing evidence points towards an essential function of the primary cilium in neural circuit formation in the central nervous system. However, very little is known about a potential role in the formation of the peripheral nervous system. Here, we investigate the presence of the primary cilium in neural crest cells and their derivatives in the trunk of developing chicken embryos in vivo. We found that neural crest cells, sensory neurons, and boundary cap cells all bear a primary cilium during key stages of early peripheral nervous system formation. Moreover, we describe differences in the ciliation of neuronal cultures of different populations from the peripheral and central nervous systems. Our results offer a framework for further in vivo and in vitro investigations on specific roles that the primary cilium might play during peripheral nervous system formation.
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Affiliation(s)
| | | | - Esther T. Stoeckli
- Department of Molecular Life Sciences and Neuroscience Center Zurich, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (E.Y.); (A.D.)
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29
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Mata M, Zurriaga J, Milian L, Reula A, Armengot M, Ruiz-Sauri A, Carda C. IFT46 Expression in the Nasal Mucosa of Primary Ciliary Dyskinesia Patients: Preliminary Study. ALLERGY & RHINOLOGY 2021; 12:2152656721989288. [PMID: 33628615 PMCID: PMC7883161 DOI: 10.1177/2152656721989288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Primary ciliary dyskinesia (PCD) is characterised by an imbalance in mucociliary clearance leading to chronic respiratory infections. Cilia length is considered to be a contributing factor in cilia movement. Recently, IFT46 protein has been related to cilia length. Therefore, this work aims to study IFT46 expression in a PCD patients cohort and analyse its relationship with cilia length and function, as it was not previously described. Materials and methods The expression of one intraflagellar transport (IFT46) and two regulating ciliary architecture (FOXJ1 and DNAI2) genes, as well as cilia length of 27 PCD patients, were measured. PCD patients were diagnosed based on clinical data, and cilia function and ultrastructure. Gene expression was estimated by real-time RT-PCR and cilia length by electron microscopy in nasal epithelium biopsies. Results and conclusions: While IFT46 expression was only diminished in patients with short cilia, FOXJ1, and DNAI2 expression were reduced in all PCD patient groups compared to controls levels. Among the PCD patients, cilia were short in 44% (5.9 ± 0.70 µm); nine of these (33% from the total) patients’ cilia also had an abnormal ultrastructure. Cilia length was normal in 33% of patients (6.4 ± 0.39 µm), and only three patients’ biopsies indicated decreased expression of dynein.
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Affiliation(s)
- Manuel Mata
- Pathology Department, Faculty of Medicine, University of Valencia, Valencia, Spain.,Research Institute of the University Clinical Hospital of Valencia (INCLIVA), Valencia, Spain.,Networking Research Center on Respiratory Diseases (CIBERER), Mallorca, Illes Balears, Spain
| | - Javier Zurriaga
- Research Institute of the University Clinical Hospital of Valencia (INCLIVA), Valencia, Spain
| | - Lara Milian
- Pathology Department, Faculty of Medicine, University of Valencia, Valencia, Spain.,Research Institute of the University Clinical Hospital of Valencia (INCLIVA), Valencia, Spain
| | - Ana Reula
- Pathology Department, Faculty of Medicine, University of Valencia, Valencia, Spain.,Grupo de Biomedicina Molecular, Celular y Genómica IIS La Fe, Valencia, Spain.,Biomedical Sciences Department, Faculty of Health Sciences, CEU-Cardenal Herrera University, Valencia, Spain
| | - Miguel Armengot
- Networking Research Center on Respiratory Diseases (CIBERER), Mallorca, Illes Balears, Spain.,Grupo de Biomedicina Molecular, Celular y Genómica IIS La Fe, Valencia, Spain.,Surgery Department, Faculty of Medicine, University of Valencia, Valencia, Spain.,ENT Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Amparo Ruiz-Sauri
- Pathology Department, Faculty of Medicine, University of Valencia, Valencia, Spain.,Research Institute of the University Clinical Hospital of Valencia (INCLIVA), Valencia, Spain
| | - Carmen Carda
- Pathology Department, Faculty of Medicine, University of Valencia, Valencia, Spain.,Research Institute of the University Clinical Hospital of Valencia (INCLIVA), Valencia, Spain
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30
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Hasenpusch-Theil K, Theil T. The Multifaceted Roles of Primary Cilia in the Development of the Cerebral Cortex. Front Cell Dev Biol 2021; 9:630161. [PMID: 33604340 PMCID: PMC7884624 DOI: 10.3389/fcell.2021.630161] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
The primary cilium, a microtubule based organelle protruding from the cell surface and acting as an antenna in multiple signaling pathways, takes center stage in the formation of the cerebral cortex, the part of the brain that performs highly complex neural tasks and confers humans with their unique cognitive capabilities. These activities require dozens of different types of neurons that are interconnected in complex ways. Due to this complexity, corticogenesis has been regarded as one of the most complex developmental processes and cortical malformations underlie a number of neurodevelopmental disorders such as intellectual disability, autism spectrum disorders, and epilepsy. Cortical development involves several steps controlled by cell–cell signaling. In fact, recent findings have implicated cilia in diverse processes such as neurogenesis, neuronal migration, axon pathfinding, and circuit formation in the developing cortex. Here, we will review recent advances on the multiple roles of cilia during cortex formation and will discuss the implications for a better understanding of the disease mechanisms underlying neurodevelopmental disorders.
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Affiliation(s)
- Kerstin Hasenpusch-Theil
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas Theil
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
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31
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Andreu-Cervera A, Catala M, Schneider-Maunoury S. Cilia, ciliopathies and hedgehog-related forebrain developmental disorders. Neurobiol Dis 2020; 150:105236. [PMID: 33383187 DOI: 10.1016/j.nbd.2020.105236] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/18/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023] Open
Abstract
Development of the forebrain critically depends on the Sonic Hedgehog (Shh) signaling pathway, as illustrated in humans by the frequent perturbation of this pathway in holoprosencephaly, a condition defined as a defect in the formation of midline structures of the forebrain and face. The Shh pathway requires functional primary cilia, microtubule-based organelles present on virtually every cell and acting as cellular antennae to receive and transduce diverse chemical, mechanical or light signals. The dysfunction of cilia in humans leads to inherited diseases called ciliopathies, which often affect many organs and show diverse manifestations including forebrain malformations for the most severe forms. The purpose of this review is to provide the reader with a framework to understand the developmental origin of the forebrain defects observed in severe ciliopathies with respect to perturbations of the Shh pathway. We propose that many of these defects can be interpreted as an imbalance in the ratio of activator to repressor forms of the Gli transcription factors, which are effectors of the Shh pathway. We also discuss the complexity of ciliopathies and their relationships with forebrain disorders such as holoprosencephaly or malformations of cortical development, and emphasize the need for a closer examination of forebrain defects in ciliopathies, not only through the lens of animal models but also taking advantage of the increasing potential of the research on human tissues and organoids.
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Affiliation(s)
- Abraham Andreu-Cervera
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS) UMR7622, Institut national pour la Santé et la Recherche Médicale (Inserm) U1156, Institut de Biologie Paris Seine - Laboratoire de Biologie du Développement (IBPS-LBD), 9 Quai Saint-Bernard, 75005 Paris, France; Instituto de Neurociencias, Universidad Miguel Hernández - CSIC, Campus de San Juan; Avda. Ramón y Cajal s/n, 03550 Alicante, Spain
| | - Martin Catala
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS) UMR7622, Institut national pour la Santé et la Recherche Médicale (Inserm) U1156, Institut de Biologie Paris Seine - Laboratoire de Biologie du Développement (IBPS-LBD), 9 Quai Saint-Bernard, 75005 Paris, France.
| | - Sylvie Schneider-Maunoury
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS) UMR7622, Institut national pour la Santé et la Recherche Médicale (Inserm) U1156, Institut de Biologie Paris Seine - Laboratoire de Biologie du Développement (IBPS-LBD), 9 Quai Saint-Bernard, 75005 Paris, France.
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32
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Legendre M, Zaragosi LE, Mitchison HM. Motile cilia and airway disease. Semin Cell Dev Biol 2020; 110:19-33. [PMID: 33279404 DOI: 10.1016/j.semcdb.2020.11.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/10/2020] [Accepted: 11/14/2020] [Indexed: 01/10/2023]
Abstract
A finely regulated system of airway epithelial development governs the differentiation of motile ciliated cells of the human respiratory tract, conferring the body's mucociliary clearance defence system. Human cilia dysfunction can arise through genetic mutations and this is a cause of debilitating disease morbidities that confer a greatly reduced quality of life. The inherited human motile ciliopathy disorder, primary ciliary dyskinesia (PCD), can arise from mutations in genes affecting various aspects of motile cilia structure and function through deficient production, transport and assembly of cilia motility components or through defective multiciliogenesis. Our understanding about the development of the respiratory epithelium, motile cilia biology and the implications for human pathology has expanded greatly over the past 20 years since isolation of the first PCD gene, rising to now nearly 50 genes. Systems level insights about cilia motility in health and disease have been made possible through intensive molecular and omics (genomics, transcriptomics, proteomics) research, applied in ciliate organisms and in animal and human disease modelling. Here, we review ciliated airway development and the genetic stratification that underlies PCD, for which the underlying genotype can increasingly be connected to biological mechanism and disease prognostics. Progress in this field can facilitate clinical translation of research advances, with potential for great medical impact, e.g. through improvements in ciliopathy disease diagnosis, management, family counselling and by enhancing the potential for future genetically tailored approaches to disease therapeutics.
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Affiliation(s)
- Marie Legendre
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Childhood Genetic Disorders, Département de Génétique Médicale, Hôpital Armand-Trousseau, Assistance Publique-Hôpitaux de Paris, Paris 75012, France
| | | | - Hannah M Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK; NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK.
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33
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Lemeille S, Paschaki M, Baas D, Morlé L, Duteyrat JL, Ait-Lounis A, Barras E, Soulavie F, Jerber J, Thomas J, Zhang Y, Holtzman MJ, Kistler WS, Reith W, Durand B. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis. Nucleic Acids Res 2020; 48:9019-9036. [PMID: 32725242 PMCID: PMC7498320 DOI: 10.1093/nar/gkaa625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 in mouse ependymal cells. We show that these three TFs have both redundant and specific functions in ependymal cells. Whereas RFX1, RFX2 and RFX3 occupy many shared genomic loci, only RFX2 and RFX3 play a prominent and redundant function in the control of motile ciliogenesis in mice. Our results provide a valuable list of candidate ciliary genes. They also reveal stunning differences between compensatory processes operating in vivo and ex vivo.
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Affiliation(s)
- Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Dominique Baas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Laurette Morlé
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Jean-Luc Duteyrat
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Fabien Soulavie
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Julie Jerber
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Joëlle Thomas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Yong Zhang
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Holtzman
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - W Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Bénédicte Durand
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
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Greaney AM, Adams TS, Brickman Raredon MS, Gubbins E, Schupp JC, Engler AJ, Ghaedi M, Yuan Y, Kaminski N, Niklason LE. Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing. Cell Rep 2020; 30:4250-4265.e6. [PMID: 32209482 PMCID: PMC7175071 DOI: 10.1016/j.celrep.2020.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/24/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, here, we isolate and culture a population of pharmacologically expanded basal cells (peBCs) from rat tracheas. At peak basal marker expression, we simultaneously split peBCs into four in vitro platforms: organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples are evaluated using single-cell RNA sequencing (scRNA-seq) and computational pipelines are developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium is also evaluated by scRNA-seq as a control for engineered epithelium. Overall, this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.
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Affiliation(s)
- Allison M Greaney
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA.
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Medical Scientist Training Program, Yale University, New Haven, CT 06511, USA
| | - Elise Gubbins
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Alexander J Engler
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA
| | - Mahboobe Ghaedi
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Yifan Yuan
- Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT 06511, USA; Department of Anesthesiology, Yale University, New Haven, CT 06510, USA
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35
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Rapiteanu R, Karagyozova T, Zimmermann N, Singh K, Wayne G, Martufi M, Belyaev NN, Hessel EM, Michalovich D, Macarron R, Rowan WC, Cairns WJ, Roger J, Betts J, Beinke S, Maratou K. Highly efficient genome editing in primary human bronchial epithelial cells differentiated at air–liquid interface. Eur Respir J 2020; 55:13993003.00950-2019. [DOI: 10.1183/13993003.00950-2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 01/31/2020] [Indexed: 12/25/2022]
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36
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Sagittal Craniosynostosis with Uncommon Anatomical Pathologies in a 56-Year-Old Male Cadaver. Case Rep Pathol 2019; 2019:8034021. [PMID: 31885995 PMCID: PMC6925784 DOI: 10.1155/2019/8034021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/09/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022] Open
Abstract
Sagittal craniosynostosis (CS) is a pathologic condition that results in premature fusion of the sagittal suture, restricting the transverse growth of the skull leading in some cases to elevated intracranial pressure and neurodevelopmental delay. There is still much to be learned about the etiology of CS. Here, we report a case of 56-year-old male cadaver that we describe as sagittal CS with torus palatinus being an additional anomaly. The craniotomy was unsuccessful (cephalic index, CI = 56) and resulted in abnormal vertical outgrowth of the craniotomized bone strip. The histological analysis of the latter revealed atypical, noncompensatory massive bone overproduction. Exome sequencing of DNA extracted from the cadaveric tissue specimen performed on the Next Generation Sequencing (NGS) platform yielded 81 genetic variants identified as pathologic. Nine of those variants could be directly linked to CS with five of them targeting RhoA GTPase signaling, with a potential to make it sustained in nature. The latter could trigger upregulated calvarial osteogenesis leading to premature suture fusion, skull bone thickening, and craniotomized bone strip outgrowth observed in the present case.
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37
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Kurrle Y, Kunesch K, Bogusch S, Schweickert A. Serotonin and MucXS release by small secretory cells depend on
Xpod
, a SSC specific marker gene. Genesis 2019; 58:e23344. [DOI: 10.1002/dvg.23344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Yvonne Kurrle
- Institute of ZoologyUniversity of Hohenheim Stuttgart Germany
| | | | - Susanne Bogusch
- Institute of ZoologyUniversity of Hohenheim Stuttgart Germany
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38
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Pereira R, Oliveira ME, Santos R, Oliveira E, Barbosa T, Santos T, Gonçalves P, Ferraz L, Pinto S, Barros A, Oliveira J, Sousa M. Characterization of CCDC103 expression profiles: further insights in primary ciliary dyskinesia and in human reproduction. J Assist Reprod Genet 2019; 36:1683-1700. [PMID: 31273583 PMCID: PMC6708006 DOI: 10.1007/s10815-019-01509-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/13/2019] [Indexed: 01/14/2023] Open
Abstract
PROPOSE To study CCDC103 expression profiles and understand how pathogenic variants in CCDC103 affect its expression profile at mRNA and protein level. METHODS To increase the knowledge about the CCDC103, we attempted genotype-phenotype correlations in two patients carrying novel homozygous (missense and frameshift) CCDC103 variants. Whole-exome sequencing, quantitative PCR, Western blot, electron microscopy, immunohistochemistry, immunocytochemistry, and immunogold labelling were performed to characterize CCDC103 expression profiles in reproductive and somatic cells. RESULTS Our data demonstrate that pathogenic variants in CCDC103 gene negatively affect gene and protein expression in both patients who presented absence of DA on their axonemes. Further, we firstly report that CCDC103 is expressed at different levels in reproductive tissues and somatic cells and described that CCDC103 protein forms oligomers with tissue-specific sizes, which suggests that CCDC103 possibly undergoes post-translational modifications. Moreover, we reported that CCDC103 was restricted to the midpiece of sperm and is present at the cytoplasm of the other cells. CONCLUSIONS Overall, our data support the CCDC103 involvement in PCD and suggest that CCDC103 may have different assemblies and roles in cilia and sperm flagella biology that are still unexplored.
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Affiliation(s)
- R. Pereira
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, Porto, Portugal
| | - M. E. Oliveira
- Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, Porto, Portugal
- Molecular Genetics Unit, Center of Medical Genetics Dr. Jacinto Magalhães (CGMJM), University Hospital Centre of Porto (CHUP), Praça Pedro Nunes, 88, 4099-028 Porto, Portugal
| | - R. Santos
- Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, Porto, Portugal
- Molecular Genetics Unit, Center of Medical Genetics Dr. Jacinto Magalhães (CGMJM), University Hospital Centre of Porto (CHUP), Praça Pedro Nunes, 88, 4099-028 Porto, Portugal
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Biochemistry, Faculty of Pharmacy, University of Porto (FFUP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - E. Oliveira
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, Porto, Portugal
| | - T. Barbosa
- Department of Pediatrics, Maternal Child Centre of the North (CMIN), University Hospital Centre of Porto (CHUP), Largo da Maternidade, 4050-371 Porto, Portugal
| | - T. Santos
- Department of Otorhinolaryngology, S. Sebastião Hospital, Hospital Centre of entre Douro e Vouga, Rua Dr. Cândido Pinho 5, 4520-211 Santa Maria da Feira, Portugal
| | - P. Gonçalves
- Department of Otorhinolaryngology, S. Sebastião Hospital, Hospital Centre of entre Douro e Vouga, Rua Dr. Cândido Pinho 5, 4520-211 Santa Maria da Feira, Portugal
| | - L. Ferraz
- Department of Urology, Hospital Centre of Vila Nova de Gaia/Espinho, Unit 1, Rua Conceição Fernandes 1079, 4434-502 Vila Nova de Gaia, Portugal
| | - S. Pinto
- Centre for Reproductive Genetics Prof. Alberto Barros (CGR), Av. do Bessa, 240, 1° Dto. Frente, 4100-012 Porto, Portugal
| | - A. Barros
- Centre for Reproductive Genetics Prof. Alberto Barros (CGR), Av. do Bessa, 240, 1° Dto. Frente, 4100-012 Porto, Portugal
- Department of Genetics, Faculty of Medicine, University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - J. Oliveira
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, Porto, Portugal
- Molecular Genetics Unit, Center of Medical Genetics Dr. Jacinto Magalhães (CGMJM), University Hospital Centre of Porto (CHUP), Praça Pedro Nunes, 88, 4099-028 Porto, Portugal
| | - M. Sousa
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Multidisciplinary Unit for Biomedical Research (UMIB), ICBAS-UP, Porto, Portugal
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Reilly ML, Benmerah A. Ciliary kinesins beyond IFT: Cilium length, disassembly, cargo transport and signalling. Biol Cell 2019; 111:79-94. [PMID: 30720881 DOI: 10.1111/boc.201800074] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 02/06/2023]
Abstract
Cilia and flagella are microtubule-based antenna which are highly conserved among eukaryotes. In vertebrates, primary and motile cilia have evolved to exert several key functions during development and tissue homoeostasis. Ciliary dysfunction in humans causes a highly heterogeneous group of diseases called ciliopathies, a class of genetic multisystemic disorders primarily affecting kidney, skeleton, retina, lung and the central nervous system. Among key ciliary proteins, kinesin family members (KIF) are microtubule-interacting proteins involved in many diverse cellular functions, including transport of cargo (organelles, proteins and lipids) along microtubules and regulating the dynamics of cytoplasmic and spindle microtubules through their depolymerising activity. Many KIFs are also involved in diverse ciliary functions including assembly/disassembly, motility and signalling. We here review these ciliary kinesins in vertebrates and focus on their involvement in ciliopathy-related disorders.
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Affiliation(s)
- Madeline Louise Reilly
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Paris Descartes University, Imagine Institute, Paris, 75015, France.,Paris Diderot University, Paris, 75013, France
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163, Paris Descartes University, Imagine Institute, Paris, 75015, France
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40
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Yepiskoposyan H, Talikka M, Vavassori S, Martin F, Sewer A, Gubian S, Luettich K, Peitsch MC, Hoeng J. Construction of a Suite of Computable Biological Network Models Focused on Mucociliary Clearance in the Respiratory Tract. Front Genet 2019; 10:87. [PMID: 30828347 PMCID: PMC6384416 DOI: 10.3389/fgene.2019.00087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
Mucociliary clearance (MCC), considered as a collaboration of mucus secreted from goblet cells, the airway surface liquid layer, and the beating of cilia of ciliated cells, is the airways’ defense system against airborne contaminants. Because the process is well described at the molecular level, we gathered the available information into a suite of comprehensive causal biological network (CBN) models. The suite consists of three independent models that represent (1) cilium assembly, (2) ciliary beating, and (3) goblet cell hyperplasia/metaplasia and that were built in the Biological Expression Language, which is both human-readable and computable. The network analysis of highly connected nodes and pathways demonstrated that the relevant biology was captured in the MCC models. We also show the scoring of transcriptomic data onto these network models and demonstrate that the models capture the perturbation in each dataset accurately. This work is a continuation of our approach to use computational biological network models and mathematical algorithms that allow for the interpretation of high-throughput molecular datasets in the context of known biology. The MCC network model suite can be a valuable tool in personalized medicine to further understand heterogeneity and individual drug responses in complex respiratory diseases.
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Affiliation(s)
| | - Marja Talikka
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Florian Martin
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Sylvain Gubian
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Karsta Luettich
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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41
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Peng Y, Guan WJ, Tan KS, Zhu Z, Chen Z, Hong H, Wang Z, Tian T, Zi X, Ong YK, Thong M, Shi L, Yang Q, Qiu Q, Wang DY. Aberrant localization of FOXJ1 correlates with the disease severity and comorbidities in patients with nasal polyps. Allergy Asthma Clin Immunol 2018; 14:71. [PMID: 30459817 PMCID: PMC6234688 DOI: 10.1186/s13223-018-0296-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/28/2018] [Indexed: 12/13/2022] Open
Abstract
Background Upper airway inflammatory diseases are associated with abnormal expression of nasal epithelial forkhead-box J1 (FOXJ1) which regulates motile cilia formation. We sought to investigate whether aberrant FOXJ1 localizations correlate with the disease severity and the co-existence of allergic rhinitis (AR) or asthma in patients with nasal polyps (NPs). Methods We elucidated localization patterns of FOXJ1 by performing immunofluorescence assays in nasal specimens and cytospin samples from controls and patients with NPs. We also assayed mRNA expression levels of FOXJ1 by using quantitative real-time polymerase chain reaction. Four localization patterns [normal (N), intermediate (I), mislocalization (M), and absence (A)] were defined. A semi-quantitative scoring system was applied for demonstrating FOXJ1 localization in five areas per paraffin section, with individual sections being scored between 0 and 2. Results FOXJ1 localization score was significantly higher in samples from NPs than in controls (P < 0.001). Elevated FOXJ1 localization scores and down-regulation of FOXJ1 mRNA levels were observed in NPs with co-existing AR or asthma (all P < 0.05). Moreover, FOXJ1 localization scores positively correlated with Lund–Mackay score (r = 0.362, P = 0.007). Of primary cytospin samples, the mean percentage of patients with FOXJ1 localization patterns N, I, M and A was 15.0%, 3.3%, 53.3% and 28.3% in NPs, and 82.5%, 5.0%, 5.0% and 7.5% in controls, respectively (P < 0.001). Conclusions Aberrant localization of FOXJ1 correlates with the severity and co-existence of AR or asthma in patients with NPs, and might be a novel target for assessment and intervention in NPs. Electronic supplementary material The online version of this article (10.1186/s13223-018-0296-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Peng
- 1Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong China.,2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore.,3State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wei-Jie Guan
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore.,3State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Kai Sen Tan
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Zhenchao Zhu
- 1Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong China.,4Department of Otolaryngology Head & Neck Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong China
| | - Zhuo Chen
- 5Department of Otolaryngology Head & Neck Surgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan China
| | - Haiyu Hong
- 6Department of Otolaryngology-Head and Neck Surgery, The 5th Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong China
| | - Zhaoni Wang
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore.,7Department of Pediatrics, The 3rd Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tengfei Tian
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore.,8Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi China
| | - Xiaoxue Zi
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore.,9Department of Otolaryngology, The Second Hospital, Shandong University, Jinan, China
| | - Yew Kwang Ong
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Mark Thong
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Li Shi
- 9Department of Otolaryngology, The Second Hospital, Shandong University, Jinan, China
| | - Qintai Yang
- 10Department of Otorhinolaryngology-Head and Neck Surgery, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Qianhui Qiu
- 1Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong China.,4Department of Otolaryngology Head & Neck Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong China.,12Department of Otolaryngology Head and Neck Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 Guangdong China
| | - De-Yun Wang
- 2Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore.,3State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,11Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore, 119228 Singapore
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Hearn T. ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits. J Mol Med (Berl) 2018; 97:1-17. [PMID: 30421101 PMCID: PMC6327082 DOI: 10.1007/s00109-018-1714-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Alström syndrome (AS) is characterised by metabolic deficits, retinal dystrophy, sensorineural hearing loss, dilated cardiomyopathy and multi-organ fibrosis. Elucidating the function of the mutated gene, ALMS1, is critical for the development of specific treatments and may uncover pathways relevant to a range of other disorders including common forms of obesity and type 2 diabetes. Interest in ALMS1 is heightened by the recent discovery of its involvement in neonatal cardiomyocyte cell cycle arrest, a process with potential relevance to regenerative medicine. ALMS1 encodes a ~ 0.5 megadalton protein that localises to the base of centrioles. Some studies have suggested a role for this protein in maintaining centriole-nucleated sensory organelles termed primary cilia, and AS is now considered to belong to the growing class of human genetic disorders linked to ciliary dysfunction (ciliopathies). However, mechanistic details are lacking, and recent studies have implicated ALMS1 in several processes including endosomal trafficking, actin organisation, maintenance of centrosome cohesion and transcription. In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. This review outlines the evidence for both ciliary and extra-ciliary functions of ALMS1.
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Affiliation(s)
- Tom Hearn
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK.
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43
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Chen B, Niu J, Kreuzer J, Zheng B, Jarugumilli GK, Haas W, Wu X. Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis. Proc Natl Acad Sci U S A 2018; 115:E8403-E8412. [PMID: 30127002 PMCID: PMC6130365 DOI: 10.1073/pnas.1800949115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Defects in cilia have been associated with an expanding human disease spectrum known as ciliopathies. Regulatory Factor X 3 (RFX3) is one of the major transcription factors required for ciliogenesis and cilia functions. In addition, RFX3 regulates pancreatic islet cell differentiation and mature β-cell functions. However, how RFX3 protein is regulated at the posttranslational level remains poorly understood. Using chemical reporters of protein fatty acylation and mass spectrometry analysis, here we show that RFX3 transcriptional activity is regulated by S-fatty acylation at a highly conserved cysteine residue in the dimerization domain. Surprisingly, RFX3 undergoes enzyme-independent, "self-catalyzed" auto-fatty acylation and displays preferences for 18-carbon stearic acid and oleic acid. The fatty acylation-deficient mutant of RFX3 shows decreased homodimerization; fails to promote ciliary gene expression, ciliogenesis, and elongation; and impairs Hedgehog signaling. Our findings reveal a regulation of RFX3 transcription factor and link fatty acid metabolism and protein lipidation to the regulation of ciliogenesis.
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Affiliation(s)
- Baoen Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Jixiao Niu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Baohui Zheng
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Gopala K Jarugumilli
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129;
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Gabbasov R, Xiao F, Howe CG, Bickel LE, O'Brien SW, Benrubi D, Do TV, Zhou Y, Nicolas E, Cai KQ, Litwin S, Seo S, Golemis EA, Connolly DC. NEDD9 promotes oncogenic signaling, a stem/mesenchymal gene signature, and aggressive ovarian cancer growth in mice. Oncogene 2018; 37:4854-4870. [PMID: 29773902 PMCID: PMC6119087 DOI: 10.1038/s41388-018-0296-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 03/23/2018] [Accepted: 04/13/2018] [Indexed: 12/20/2022]
Abstract
Neural precursor cell expressed, developmentally downregulated 9 (NEDD9) supports oncogenic signaling in a number of solid and hematologic tumors. Little is known about the role of NEDD9 in ovarian carcinoma (OC), but available data suggest elevated mRNA and protein expression in advanced stage high-grade cancers. We used a transgenic MISIIR-TAg mouse OC model combined with genetic ablation of Nedd9 to investigate its action in the development and progression of OC. A Nedd9-/- genotype delayed tumor growth rate, reduced incidence of ascites, and reduced expression and activation of signaling proteins including SRC, STAT3, E-cadherin, and AURKA. Cell lines established from MISIIR-TAg;Nedd9-/- and MISIIR-TAg;Nedd9+/+ mice exhibited altered migration and invasion. Growth of these cells in a syngeneic allograft model indicated that systemic Nedd9 loss in the microenvironment had little impact on tumor allograft growth, but in a Nedd9 wild-type background Nedd9-/- allografts exhibited significantly reduced growth, dissemination, and oncogenic signaling compared to Nedd9+/+ allografts. Gene expression analysis revealed that Nedd9+/+ tumors exhibited more mesenchymal "stem-like" transcriptional program, including increased expression of Aldh1a1 and Aldh1a2. Conversely, loss of Nedd9 resulted in increased expression of differentiation genes, including fallopian tube markers Foxj1, Ovgp1, and Pax8. Collectively, these data suggest that tumor cell-intrinsic Nedd9 expression promotes OC development and progression by broad induction of oncogenic protein signaling and stem/mesenchymal gene expression.
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Affiliation(s)
- Rashid Gabbasov
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan, Russia
| | - Fang Xiao
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Caitlin G Howe
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Laura E Bickel
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Shane W O'Brien
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Daniel Benrubi
- Division of Gynecologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Thuy-Vy Do
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Kathy Q Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Samuel Litwin
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sachiko Seo
- Department of Hematology & Oncology, National Cancer Research Center East, Kashiwa, Japan
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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45
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Peng Y, Chen Z, Guan WJ, Zhu Z, Tan KS, Hong H, Zi X, Zeng J, Li Y, Ong YK, Thong M, Shi L, Yang Q, Qiu Q, Wang DY. Downregulation and Aberrant Localization of Forkhead Box J1 in Allergic Nasal Mucosa. Int Arch Allergy Immunol 2018; 176:115-123. [PMID: 29635245 DOI: 10.1159/000488014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/12/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Forkhead box J1 (FOXJ1) plays pivotal roles in motile cilia formation. However, it remains unclear whether abnormal expression or localization of FOXJ1 in nasal mucosa tissues is associated with allergic rhinitis (AR), in which impaired mucociliary clearance is implicated. OBJECTIVE We sought to investigate the expression and localization of FOXJ1 in inferior turbinate from patients with AR and controls. METHODS We assayed mRNA levels of FOXJ1, DNAI1, DNALI1, and DNAH9 by using whole-genome expression array and quantitative real-time polymerase chain reaction. We elucidated the localization of FOXJ1 by using immunofluorescence assays in paraffin sections and primary single cells. Four patterns of FOXJ1 localization (normal, N; intermediate, I; mislocalization, M; absence, A) were defined. We developed a semiquantitative scoring system to elucidate their localization in 5 areas per paraffin section, with individual sections being assigned a score between 0 and 2. RESULTS The mRNA levels of FOXJ1, DNAI1, DNALI1, and DNAH9 were significantly reduced in patients with AR compared with controls (all p < 0.05). The median (1st and 3rd quartile) of the FOXJ1 score was 0.4 (0.0 and 0.85) in patients with AR, and 0.2 (0.0 and 0.4) in controls (p < 0.05). For primary cytospin samples, the mean percentages of FOXJ1 localization patterns N, I, M, and A were 46.7, 10.0, 30.0, and 26.7% in patients with AR, and 82.5, 5.0, 5.0, and 7.5% in controls, respectively (p < 0.05). CONCLUSION Downregulation and aberrant localization of FOXJ1 may be crucial characteristics of the allergic nasal mucosa.
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Affiliation(s)
- Yang Peng
- Department of Otolaryngology, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Otolaryngology Head and Neck Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Zhuo Chen
- Department of Otolaryngology - Head and Neck Surgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenchao Zhu
- Department of Otolaryngology Head and Neck Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kai Sen Tan
- Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Haiyu Hong
- Department of Otolaryngology - Head and Neck Surgery, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Xiaoxue Zi
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Jie Zeng
- Department of Otolaryngology, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yixuan Li
- Department of Otolaryngology, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yew Kwang Ong
- Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Mark Thong
- Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
| | - Li Shi
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Qintai Yang
- Department of Otorhinolaryngology - Head and Neck Surgery, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qianhui Qiu
- Department of Otolaryngology Head and Neck Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - De-Yun Wang
- Department of Otolaryngology, National University of Singapore, National University Health System, Singapore, Singapore
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46
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Zhou D, Alver BM, Li S, Hlady RA, Thompson JJ, Schroeder MA, Lee JH, Qiu J, Schwartz PH, Sarkaria JN, Robertson KD. Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues. Genome Biol 2018; 19:43. [PMID: 29587824 PMCID: PMC5872397 DOI: 10.1186/s13059-018-1420-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/12/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Glioma stem cells (GSCs) are a subpopulation of stem-like cells that contribute to glioblastoma (GBM) aggressiveness, recurrence, and resistance to radiation and chemotherapy. Therapeutically targeting the GSC population may improve patient survival, but unique vulnerabilities need to be identified. RESULTS We isolate GSCs from well-characterized GBM patient-derived xenografts (PDX), characterize their stemness properties using immunofluorescence staining, profile their epigenome including 5mC, 5hmC, 5fC/5caC, and two enhancer marks, and define their transcriptome. Fetal brain-derived neural stem/progenitor cells are used as a comparison to define potential unique and common molecular features between these different brain-derived cells with stem properties. Our integrative study reveals that abnormal expression of ten-eleven-translocation (TET) family members correlates with global levels of 5mC and 5fC/5caC and may be responsible for the distinct levels of these marks between glioma and neural stem cells. Heterogenous transcriptome and epigenome signatures among GSCs converge on several genes and pathways, including DNA damage response and cell proliferation, which are highly correlated with TET expression. Distinct enhancer landscapes are also strongly associated with differential gene regulation between glioma and neural stem cells; they exhibit unique co-localization patterns with DNA epigenetic mark switching events. Upon differentiation, glioma and neural stem cells exhibit distinct responses with regard to TET expression and DNA mark changes in the genome and GSCs fail to properly remodel their epigenome. CONCLUSIONS Our integrative epigenomic and transcriptomic characterization reveals fundamentally distinct yet potentially targetable biologic features of GSCs that result from their distinct epigenomic landscapes.
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Affiliation(s)
- Dan Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Bonnie M Alver
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Shuang Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Joyce J Thompson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Mark A Schroeder
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.,Epigenomics Translational Program, Mayo Clinic, Rochester, MN, USA
| | - Jingxin Qiu
- Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Philip H Schwartz
- National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, CA, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. .,Epigenomics Translational Program, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN, USA.
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47
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Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
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Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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Conditional ablation of the RFX4 isoform 1 transcription factor: Allele dosage effects on brain phenotype. PLoS One 2018; 13:e0190561. [PMID: 29298325 PMCID: PMC5752003 DOI: 10.1371/journal.pone.0190561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/21/2017] [Indexed: 11/25/2022] Open
Abstract
Regulatory factor X4 (RFX4) isoform 1 is a recently discovered isoform of the winged helix transcription factor RFX4, which can bind to X-box consensus sequences that are enriched in the promoters of cilia-related genes. Early insertional mutagenesis studies in mice first identified this isoform, and demonstrated that it was crucial for mouse brain development. RFX4 isoform 1 is the only RFX4 isoform significantly expressed in the mouse fetal and adult brain. In this study, we evaluated conditional knock-out (KO) mice in which one or two floxed alleles of Rfx4 were deleted early in development through the use of a Sox2-Cre transgene. Heterozygous deletion of Rfx4 resulted in severe, non-communicating congenital hydrocephalus associated with hypoplasia of the subcommissural organ. Homozygous deletion of Rfx4 resulted in formation of a single ventricle in the forebrain, and severe dorsoventral patterning defects in the telencephalon and midbrain at embryonic day 12.5, a collection of phenotypes that resembled human holoprosencephaly. No anatomical abnormalities were noted outside the brain in either case. At the molecular level, transcripts encoded by the cilia-related gene Foxj1 were significantly decreased, and Foxj1 was identified as a direct gene target of RFX4 isoform 1. The phenotypes were similar to those observed in the previous Rfx4 insertional mutagenesis studies. Thus, we provide a novel conditional KO animal model in which to investigate the downstream genes directly and/or indirectly regulated by RFX4 isoform 1. This model could provide new insights into the pathogenesis of obstructive hydrocephalus and holoprosencephaly in humans, both relatively common and disabling birth defects.
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49
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Lin CY, Tsai MY, Liu YH, Lu YF, Chen YC, Lai YR, Liao HC, Lien HW, Yang CH, Huang CJ, Hwang SPL. Klf8 regulates left-right asymmetric patterning through modulation of Kupffer's vesicle morphogenesis and spaw expression. J Biomed Sci 2017; 24:45. [PMID: 28716076 PMCID: PMC5513281 DOI: 10.1186/s12929-017-0351-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although vertebrates are bilaterally symmetric organisms, their internal organs are distributed asymmetrically along a left-right axis. Disruption of left-right axis asymmetric patterning often occurs in human genetic disorders. In zebrafish embryos, Kupffer's vesicle, like the mouse node, breaks symmetry by inducing asymmetric expression of the Nodal-related gene, spaw, in the left lateral plate mesoderm (LPM). Spaw then stimulates transcription of itself and downstream genes, including lft1, lft2, and pitx2, specifically in the left side of the diencephalon, heart and LPM. This developmental step is essential to establish subsequent asymmetric organ positioning. In this study, we evaluated the role of krüppel-like factor 8 (klf8) in regulating left-right asymmetric patterning in zebrafish embryos. METHODS Zebrafish klf8 expression was disrupted by both morpholino antisense oligomer-mediated knockdown and a CRISPR-Cas9 system. Whole-mount in situ hybridization was conducted to evaluate gene expression patterns of Nodal signalling components and the positions of heart and visceral organs. Dorsal forerunner cell number was evaluated in Tg(sox17:gfp) embryos and the length and number of cilia in Kupffer's vesicle were analyzed by immunocytochemistry using an acetylated tubulin antibody. RESULTS Heart jogging, looping and visceral organ positioning were all defective in zebrafish klf8 morphants. At the 18-22 s stages, klf8 morphants showed reduced expression of genes encoding Nodal signalling components (spaw, lft1, lft2, and pitx2) in the left LPM, diencephalon, and heart. Co-injection of klf8 mRNA with klf8 morpholino partially rescued spaw expression. Furthermore, klf8 but not klf8△zf overexpressing embryos showed dysregulated bilateral expression of Nodal signalling components at late somite stages. At the 10s stage, klf8 morphants exhibited reductions in length and number of cilia in Kupffer's vesicle, while at 75% epiboly, fewer dorsal forerunner cells were observed. Interestingly, klf8 mutant embryos, generated by a CRISPR-Cas9 system, showed bilateral spaw expression in the LPM at late somite stages. This observation may be partly attributed to compensatory upregulation of klf12b, because klf12b knockdown reduced the percentage of klf8 mutants exhibiting bilateral spaw expression. CONCLUSIONS Our results demonstrate that zebrafish Klf8 regulates left-right asymmetric patterning by modulating both Kupffer's vesicle morphogenesis and spaw expression in the left LPM.
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Affiliation(s)
- Che-Yi Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Present address: Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Yuan Tsai
- Graduate Institute of Life Sciences, National Defence Medical Center, National Defence University, Neihu, Taipei, Taiwan.,Present address: Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsiu Liu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Fen Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yi-Chung Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yun-Ren Lai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Hsin-Chi Liao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Huang-Wei Lien
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Chang-Jen Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping L Hwang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan. .,Department of Life Science, National Taiwan University, Taipei, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
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Ulk4 Is Essential for Ciliogenesis and CSF Flow. J Neurosci 2017; 36:7589-600. [PMID: 27445138 DOI: 10.1523/jneurosci.0621-16.2016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/19/2016] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Ciliopathies are an emerging class of devastating disorders with pleiotropic symptoms affecting both the central and peripheral systems and commonly associated with hydrocephalus. Even though ciliary components and three master transcriptional regulators have been identified, little is known about the signaling molecules involved. We previously identified a novel gene, Unc51-like-kinase 4 (ULK4), as a risk factor of neurodevelopmental disorders. Here we took multidisciplinary approaches and uncovered essential roles of Ulk4 in ciliogenesis. We show that Ulk4 is predominantly expressed in the ventricular system, and Ulk4(tm1a/tm1a) ependymal cells display reduced/disorganized cilia with abnormal axonemes. Ulk4(tm1a/tm1a) mice exhibit dysfunctional subcommissural organs, obstructive aqueducts, and impaired CSF flow. Mechanistically, we performed whole-genome RNA sequencing and discovered that Ulk4 regulates the Foxj1 pathway specifically and an array of other ciliogenesis molecules. This is the first evidence demonstrating that ULK4 plays a vital role in ciliogenesis and that deficiency of ULK4 can cause hydrocephalus and ciliopathy-related disorders. SIGNIFICANCE STATEMENT Ciliopathies are an emerging class of devastating disorders with pleiotropic symptoms affecting both the central and peripheral systems. Ciliopathies are commonly associated with hydrocephalus, and Unc51-like-kinase 4 (Ulk4) has been identified as one of 12 genes causing hydrocephalus in mutants. Here we uncover an essential role of Ulk4 in ciliogenesis. Ulk4 is predominantly expressed in the ventricles, and mutant ependymal cells display reduced/disorganized/nonfunctional motile cilia with abnormal axonemes and impaired CSF flow. Ulk4 modulates expression of the master regulator of ciliogenesis, Foxj1, and other ciliogenesis molecules. This is the first report demonstrating a vital role of Ulk4 in ciliogenesis. ULK4 deficiency may be implicated in human hydrocephalus and other ciliopathy-related disorders.
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