Club Cell-Specific Role of Programmed Cell Death 5 in Pulmonary Fibrosis
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Lung Organoids and Their Use to Study Cell-Cell Interaction
Curr Pathobiol Rep (2017) 5:223–231 DOI 10.1007/s40139-017-0137-7 ORGANOID CULTURES (M HUCH, SECTION EDITOR) Lung Organoids and Their Use To Study Cell-Cell Interaction Marko Z. Nikolić1 & Emma L. Rawlins1 Published online: 24 April 2017 # The Author(s) 2017. This article is an open access publication Abstract types which self-organise through cell sorting and spatially Purpose of Review The lung research field has pioneered the restricted lineage commitment in a manner reminiscent of use of organoids for the study of cell-cell interactions. the native organ with some degree of organ functionality [1, Recent Findings The use of organoids for airway basal cells is 2]. Organoids have also been referred to as “mini-organs” and routine. However, the development of organoids for the other enable in vitro modelling of organ development, disease regions of the lung is still in its infancy. Such cultures usually modelling and drug screening. The 3D culture preserves na- rely on cell-cell interactions between the stem cells and a tive DNA integrity and prevents the cells from being trans- putative niche cell for their growth and differentiation. formed [13]. Organoids were first successfully derived from Summary The use of co-culture organoid systems has facili- mouse small intestine using single Lgr5+ stem cells [3]. These tated the in vitro cultivation of previously inaccessible stem organoids were entirely epithelial illustrating that organoids cell populations, providing a novel method for dissecting the can be built without a non-epithelial cellular niche. The molecular requirements of these cell-cell interactions. Future organoid was structured as crypt-villus units, with a similar technology development will allow the growth of epithelial- stem cell hierarchy to in vivo, showing epithelial cell interac- only organoids in more defined media and also the introduc- tions are sufficient for the creation of crypt-villus units. -
Systematic Review of Drug Effects in Humans and Models with Surfactant-Processing Disease
REVIEW DRUG EFFECTS Systematic review of drug effects in humans and models with surfactant-processing disease Dymph Klay1, Thijs W. Hoffman1, Ankie M. Harmsze2, Jan C. Grutters1,3 and Coline H.M. van Moorsel1,3 Affiliations: 1Interstitial Lung Disease Center of Excellence, Dept of Pulmonology, St Antonius Hospital, Nieuwegein, The Netherlands. 2Dept of Clinical Pharmacy, St Antonius Hospital, Nieuwegein, The Netherlands. 3Division of Heart and Lung, University Medical Center Utrecht, Utrecht, The Netherlands. Correspondence: Coline H.M. van Moorsel, Interstitial Lung Disease Center of Excellence, St Antonius Hospital, Koekoekslaan 1, Nieuwegein, 3435CM, The Netherlands. E-mail: [email protected] @ERSpublications Drug effects in disease models of surfactant-processing disease are highly dependent on mutation http://ow.ly/ZYZH30k3RkK Cite this article as: Klay D, Hoffman TW, Harmsze AM, et al. Systematic review of drug effects in humans and models with surfactant-processing disease. Eur Respir Rev 2018; 27: 170135 [https://doi.org/10.1183/ 16000617.0135-2017]. ABSTRACT Fibrotic interstitial pneumonias are a group of rare diseases characterised by distortion of lung interstitium. Patients with mutations in surfactant-processing genes, such as surfactant protein C (SFTPC), surfactant protein A1 and A2 (SFTPA1 and A2), ATP binding cassette A3 (ABCA3) and Hermansky–Pudlak syndrome (HPS1, 2 and 4), develop progressive pulmonary fibrosis, often culminating in fatal respiratory insufficiency. Although many mutations have been described, little is known about the optimal treatment strategy for fibrotic interstitial pneumonia patients with surfactant-processing mutations. We performed a systematic literature review of studies that described a drug effect in patients, cell or mouse models with a surfactant-processing mutation. -
University of Groningen Developmental and Pathological Roles of BMP/Follistatin-Like 1 in the Lung Tania, Navessa
University of Groningen Developmental and pathological roles of BMP/follistatin-like 1 in the lung Tania, Navessa IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2017 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Tania, N. (2017). Developmental and pathological roles of BMP/follistatin-like 1 in the lung. University of Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 01-10-2021 CHAPTER 7 1 Variant club cell differentiation is driven by bone morphogenetic protein 4 in adult human airway epithelium: Implications for goblet cell metaplasia and basal cell hyperplasia in COPD Navessa P. -
Nuclear Translocation of PDCD5 (TFAR19): Provided by Elsevier - Publisher Connector an Early Signal for Apoptosis?
FEBS 25453 FEBS Letters 509 (2001) 191^196 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Nuclear translocation of PDCD5 (TFAR19): provided by Elsevier - Publisher Connector an early signal for apoptosis? Yingyu Chen, Ronghua Sun, Wenling Han, Yingmei Zhang, Quansheng Song, Chunhui Di, Dalong Ma* Laboratory of Medical Immunology, School of Basic Medical Science, Peking University, 38 Xueyuan Road, Beijing 100083, PR China Received 20 July 2001; revised 14 September 2001; accepted 16 October 2001 First published online 7 November 2001 Edited by Vladimir Skulachev could accelerate apoptosis of some tumor cells (HeLa, TF-1, Abstract The programmed cell death 5 (PDCD5) protein is a novel protein related to regulation of cell apoptosis. In this HL60, MCG-803, MCF-7) [5,7]. In order to further study the report, we demonstrate that the level of PDCD5 protein biological activities of PDCD5, we successfully produced spe- expressed in cells undergoing apoptosis is significantly increased ci¢c monoclonal antibodies against PDCD5. Then, we used compared with normal cells, then the protein translocates rapidly these monoclonal antibodies as probes to observe the expres- from the cytoplasm to the nucleus of cells. The appearance of sion and localization of PDCD5 in cell apoptosis process. We PDCD5 in the nuclei of apoptotic cells precedes the externaliza- demonstrate that PDCD5 protein can translocate to the nu- tion of phosphatidylserine and fragmentation of chromosome cleus rapidly in cells undergoing apoptosis and the accumu- DNA. This phenomenon is parallel to the loss of mitochondrial lation of PDCD5 in the nucleus precedes the chromosome membrane potential, independent of the feature of apoptosis- DNA fragmentation and phosphatidylserine (PS) externaliza- inducing stimuli and also independent of the cell types and the tion. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Structure–Function Correlation of Human Programmed Cell Death 5 Protein
Archives of Biochemistry and Biophysics 486 (2009) 141–149 Contents lists available at ScienceDirect Archives of Biochemistry and Biophysics journal homepage: www.elsevier.com/locate/yabbi Structure–function correlation of human programmed cell death 5 protein Hongwei Yao a,1, Lanjun Xu b,1, Yingang Feng a, Dongsheng Liu a, Yingyu Chen b,*, Jinfeng Wang a,* a National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China b Laboratory of Medical Immunology, School of Basic Medical Science, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100083, China article info abstract Article history: Human programmed cell death 5 (PDCD5) is a translocatory protein playing an important role in the Received 4 March 2009 apoptotic process of cells. Although there are accumulated data about PDCD5 function, the correlation and in revised form 25 March 2009 of the structure with the function of PDCD5 has not been investigated. Here, we report the studies of Available online 7 April 2009 structure–function relationship of PDCD5 by multidimensional NMR methods and by FACScan flow cytometer and fluorescence microscope. The 3D structure of intact PDCD5 and the internal motions of Keywords: PDCD5 have been determined. PDCD5 has a compact core structure of low flexibility with two mobile PDCD5 a-helices at N-terminal region and a flexible unstructured C-terminal region. The flow cytometry and NMR internalization measurements of different PDCD5 fragments indicate that the charged residues are crucial Structure–function relationship Cell translocation for the ability of apoptosis-promoting and cell translocation of the protein. Combined analyses reveal a Fragments of PDCD5 fact that the regions that seem to be most involved in the function also are more flexible in PDCD5. -
The 5V-Upstream Region of Human Programmed Cell Death 5 Gene Contains a Highly Active TATA-Less Promoter That Is Up-Regulated by Etoposide
http://www.paper.edu.cn Gene 329 (2004) 39–49 www.elsevier.com/locate/gene The 5V-upstream region of human programmed cell death 5 gene contains a highly active TATA-less promoter that is up-regulated by etoposide Mingxu Xu*, Ning Cheng, Liming Gui, Mouyi Lai, Ying Wang, Donglan Xia, Min Rui, Yingmei Zhang, Dalong Ma Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Center for Human Disease Genomics, 38 Xueyuan Road, Beijing 100083, China Received 9 June 2003; received in revised form 3 December 2003; accepted 23 December 2003 Received by R. Di Lauro Abstract The PDCD5 (programmed cell death 5), a novel apoptosis related gene, is functionally associated with cell apoptosis, exhibits a ubiquitous expression pattern and is up-regulated in some types of tumor cells undergoing apoptosis. To study the transcriptional regulation of the PDCD5 gene, we have cloned 1.1 kb of its 5V-upstream region. The DNA sequencing analysis revealed a major transcriptional start site at 72 base pairs in front of the ATG translational start codon. The upstream of the transcriptional start site lacks a canonical TATA box and CAAT box. Transient transfection and luciferase assay demonstrate that this region presents extremely strong promoter activity. The 5V- deleted sequences fused to a luciferase reporter gene demonstrated that the À 555/ À 383 region from the transcription start site is crucial for transcriptional regulation, and the luciferase reporter gene’s expression significantly increased in the early stage of cell apoptosis induced by etoposide. These results imply that the PDCD5 gene may be a target gene under the control of some important apoptosis-related transcriptional factors during the cell apoptosis. -
Bioinformatics Analysis for the Identification of Differentially Expressed Genes and Related Signaling Pathways in H
Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells Dingyu Chen*, Chao Li, Yan Zhao, Jianjiang Zhou, Qinrong Wang and Yuan Xie* Key Laboratory of Endemic and Ethnic Diseases , Ministry of Education, Guizhou Medical University, Guiyang, China * These authors contributed equally to this work. ABSTRACT Aim. Helicobacter pylori cytotoxin-associated protein A (CagA) is an important vir- ulence factor known to induce gastric cancer development. However, the cause and the underlying molecular events of CagA induction remain unclear. Here, we applied integrated bioinformatics to identify the key genes involved in the process of CagA- induced gastric epithelial cell inflammation and can ceration to comprehend the potential molecular mechanisms involved. Materials and Methods. AGS cells were transected with pcDNA3.1 and pcDNA3.1::CagA for 24 h. The transfected cells were subjected to transcriptome sequencing to obtain the expressed genes. Differentially expressed genes (DEG) with adjusted P value < 0.05, | logFC |> 2 were screened, and the R package was applied for gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The differential gene protein–protein interaction (PPI) network was constructed using the STRING Cytoscape application, which conducted visual analysis to create the key function networks and identify the key genes. Next, the Submitted 20 August 2020 Kaplan–Meier plotter survival analysis tool was employed to analyze the survival of the Accepted 11 March 2021 key genes derived from the PPI network. Further analysis of the key gene expressions Published 15 April 2021 in gastric cancer and normal tissues were performed based on The Cancer Genome Corresponding author Atlas (TCGA) database and RT-qPCR verification. -
Miz1 Is Required to Maintain Autophagic Flux
ARTICLE Received 3 Apr 2013 | Accepted 3 Sep 2013 | Published 3 Oct 2013 DOI: 10.1038/ncomms3535 Miz1 is required to maintain autophagic flux Elmar Wolf1,*, Anneli Gebhardt1,*, Daisuke Kawauchi2, Susanne Walz1, Bjo¨rn von Eyss1, Nicole Wagner3, Christoph Renninger3, Georg Krohne1, Esther Asan3, Martine F. Roussel2 & Martin Eilers1,4 Miz1 is a zinc finger protein that regulates the expression of cell cycle inhibitors as part of a complex with Myc. Cell cycle-independent functions of Miz1 are poorly understood. Here we use a Nestin-Cre transgene to delete an essential domain of Miz1 in the central nervous system (Miz1DPOZNes). Miz1DPOZNes mice display cerebellar neurodegeneration characterized by the progressive loss of Purkinje cells. Chromatin immunoprecipitation sequencing and biochemical analyses show that Miz1 activates transcription upon binding to a non-palin- dromic sequence present in core promoters. Target genes of Miz1 encode regulators of autophagy and proteins involved in vesicular transport that are required for autophagy. Miz1DPOZ neuronal progenitors and fibroblasts show reduced autophagic flux. Consistently, polyubiquitinated proteins and p62/Sqtm1 accumulate in the cerebella of Miz1DPOZNes mice, characteristic features of defective autophagy. Our data suggest that Miz1 may link cell growth and ribosome biogenesis to the transcriptional regulation of vesicular transport and autophagy. 1 Theodor Boveri Institute, Biocenter, University of Wu¨rzburg, Am Hubland, 97074 Wu¨rzburg, Germany. 2 Department of Tumor Cell Biology, MS#350, Danny Thomas Research Center, 5006C, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA. 3 Institute for Anatomy and Cell Biology, University of Wu¨rzburg, Koellikerstrasse 6, 97070 Wu¨rzburg, Germany. 4 Comprehensive Cancer Center Mainfranken, Josef-Schneider-Strasse 6, 97080 Wu¨rzburg, Germany. -
University of Groningen Lung Epithelial Cell Differentiation in Human and Mouse Song, Juan
University of Groningen Lung epithelial cell differentiation in human and mouse Song, Juan IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2016 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Song, J. (2016). Lung epithelial cell differentiation in human and mouse: Environment, epigenetics and epigenetic editing. University of Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 01-10-2021 Chapter 2 Smoking during pregnancy inhibits ciliated cell differentiation and up regulates secretory cell related genes in neonatal offspring Junjun Cao 1,2,3 , Juan Song 1,2 , Marjan Reinders-Luinge 1,2 , Wierd Kooistra 1,2 , Kim van der Sloot 1,2 , Xia Huo 3, Wim Timens 1,2 , Susanne Krauss-Etschmann 4 and Machteld N. -
Differentiation of Club Cells to Alveolar Epithelial Cells in Vitro
Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Zheng, Dahai; Soh, Boon-Seng; Yin, Lu; Hu, Guangan; Chen, Qingfeng; Choi, Hyungwon; Han, Jongyoon; Chow, Vincent T. K. and Chen, Jianzhu. “Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro.” Scientific Reports 7 (January 2017): 41661 © 2017 The Author(s) As Published http://dx.doi.org/10.1038/srep41661 Publisher Nature Publishing Group Version Final published version Citable link http://hdl.handle.net/1721.1/110075 Terms of Use Creative Commons Attribution 4.0 International License Detailed Terms http://creativecommons.org/licenses/by/4.0/ www.nature.com/scientificreports OPEN Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro Dahai Zheng1,2, Boon-Seng Soh2,3, Lu Yin4, Guangan Hu5, Qingfeng Chen2, Hyungwon Choi6, Jongyoon Han4,7, Vincent T. K. Chow8 & Jianzhu Chen1,5 Received: 18 November 2016 Club cells are known to function as regional progenitor cells to repair the bronchiolar epithelium in Accepted: 21 December 2016 response to lung damage. By lineage tracing in mice, we have shown recently that club cells also give Published: 27 January 2017 rise to alveolar type 2 cells (AT2s) and alveolar type 1 cells (AT1s) during the repair of the damaged alveolar epithelium. Here, we show that when highly purified, anatomically and phenotypically confirmed club cells are seeded in 3-dimensional culture either in bulk or individually, they proliferate and differentiate into both AT2- and AT1-like cells and form alveolar-like structures. -
Chromatin Conformation Links Distal Target Genes to CKD Loci
BASIC RESEARCH www.jasn.org Chromatin Conformation Links Distal Target Genes to CKD Loci Maarten M. Brandt,1 Claartje A. Meddens,2,3 Laura Louzao-Martinez,4 Noortje A.M. van den Dungen,5,6 Nico R. Lansu,2,3,6 Edward E.S. Nieuwenhuis,2 Dirk J. Duncker,1 Marianne C. Verhaar,4 Jaap A. Joles,4 Michal Mokry,2,3,6 and Caroline Cheng1,4 1Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and 2Department of Pediatrics, Wilhelmina Children’s Hospital, 3Regenerative Medicine Center Utrecht, Department of Pediatrics, 4Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, 5Department of Cardiology, Division Heart and Lungs, and 6Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands ABSTRACT Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chro- mosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis.