Zebrafish Mutants Calamity and Catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism Erik C
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Stelios Pavlidis3, Matthew Loza3, Fred Baribaud3, Anthony
Supplementary Data Th2 and non-Th2 molecular phenotypes of asthma using sputum transcriptomics in UBIOPRED Chih-Hsi Scott Kuo1.2, Stelios Pavlidis3, Matthew Loza3, Fred Baribaud3, Anthony Rowe3, Iaonnis Pandis2, Ana Sousa4, Julie Corfield5, Ratko Djukanovic6, Rene 7 7 8 2 1† Lutter , Peter J. Sterk , Charles Auffray , Yike Guo , Ian M. Adcock & Kian Fan 1†* # Chung on behalf of the U-BIOPRED consortium project team 1Airways Disease, National Heart & Lung Institute, Imperial College London, & Biomedical Research Unit, Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom; 2Department of Computing & Data Science Institute, Imperial College London, United Kingdom; 3Janssen Research and Development, High Wycombe, Buckinghamshire, United Kingdom; 4Respiratory Therapeutic Unit, GSK, Stockley Park, United Kingdom; 5AstraZeneca R&D Molndal, Sweden and Areteva R&D, Nottingham, United Kingdom; 6Faculty of Medicine, Southampton University, Southampton, United Kingdom; 7Faculty of Medicine, University of Amsterdam, Amsterdam, Netherlands; 8European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, Université de Lyon, France. †Contributed equally #Consortium project team members are listed under Supplementary 1 Materials *To whom correspondence should be addressed: [email protected] 2 List of the U-BIOPRED Consortium project team members Uruj Hoda & Christos Rossios, Airways Disease, National Heart & Lung Institute, Imperial College London, UK & Biomedical Research Unit, Biomedical Research Unit, Royal -
PROTEOMIC ANALYSIS of HUMAN URINARY EXOSOMES. Patricia
ABSTRACT Title of Document: PROTEOMIC ANALYSIS OF HUMAN URINARY EXOSOMES. Patricia Amalia Gonzales Mancilla, Ph.D., 2009 Directed By: Associate Professor Nam Sun Wang, Department of Chemical and Biomolecular Engineering Exosomes originate as the internal vesicles of multivesicular bodies (MVBs) in cells. These small vesicles (40-100 nm) have been shown to be secreted by most cell types throughout the body. In the kidney, urinary exosomes are released to the urine by fusion of the outer membrane of the MVBs with the apical plasma membrane of renal tubular epithelia. Exosomes contain apical membrane and cytosolic proteins and can be isolated using differential centrifugation. The analysis of urinary exosomes provides a non- invasive means of acquiring information about the physiological or pathophysiological state of renal cells. The overall objective of this research was to develop methods and knowledge infrastructure for urinary proteomics. We proposed to conduct a proteomic analysis of human urinary exosomes. The first objective was to profile the proteome of human urinary exosomes using liquid chromatography-tandem spectrometry (LC- MS/MS) and specialized software for identification of peptide sequences from fragmentation spectra. We unambiguously identified 1132 proteins. In addition, the phosphoproteome of human urinary exosomes was profiled using the neutral loss scanning acquisition mode of LC-MS/MS. The phosphoproteomic profiling identified 19 phosphorylation sites corresponding to 14 phosphoproteins. The second objective was to analyze urinary exosomes samples isolated from patients with genetic mutations. Polyclonal antibodies were generated to recognize epitopes on the gene products of these genetic mutations, NKCC2 and MRP4. The potential usefulness of urinary exosome analysis was demonstrated using the well-defined renal tubulopathy, Bartter syndrome type I and using the single nucleotide polymorphism in the ABCC4 gene. -
Theranostics Deficiency of ATP6V1H Causes Bone Loss by Inhibiting
Theranostics 2016, Vol. 6, Issue 12 2183 Ivyspring International Publisher Theranostics 2016; 6(12): 2183-2195. doi: 10.7150/thno.17140 Research Paper Deficiency of ATP6V1H Causes Bone Loss by Inhibiting Bone Resorption and Bone Formation through the TGF-β1 Pathway Xiaohong Duan1*, Jin Liu1*, Xueni Zheng1*, Zhe Wang1, Yanli Zhang1, Ying Hao1, Tielin Yang2, Hongwen Deng3 1. State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Oral Diseases, Department of Oral Biology, Clinic of Oral Rare and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, Xi’an, 710032, People’s Republic of China. 2. Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, People’s Republic of China. 3. School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA. *Contributed equally to this work. Corresponding author: Xiaohong Duan, State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Oral Diseases, Department of Oral Biology, Clinic of Oral Rare and Genetic Diseases, School of Stomatology, the Fourth Military Medical University, 145 West Changle Road, Xi’an 710032, P. R. China. Tel: 86-29-84776169; Fax: 86-29-84776169; E-mail: [email protected]. © Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions. Received: 2016.08.08; Accepted: 2016.08.15; Published: 2016.09.13 Abstract Vacuolar-type H +-ATPase (V-ATPase) is a highly conserved, ancient enzyme that couples the energy of ATP hydrolysis to proton transport across vesicular and plasma membranes of eukaryotic cells. -
Molecular Mechanism of Embryo Transport and Embryo
MOLECULAR MECHANISM OF EMBRYO TRANSPORT AND EMBRYO IMPLANTATION IN MICE By SHUO XIAO (Under the Direction of Xiaoqin Ye) ABSTRACT Embryo transport and embryo implantation are essential events in mammalian reproduction during pregnancy. This dissertation was conducted to investigate the effect of bisphenol A (BPA) on early pregnancy and the molecular mechanism (s) of embryo transport and embryo implantation. Timed pregnant female mice were treated subcutaneously with 0, 0.025, 0.5, 10, 40, and 100 mg/kg/day BPA from gestation day 0.5 (D0.5, mating night as D0) to D3.5. High dose of preimplantation BPA exposure resulted in delayed embryo transport and preimplantation embryo development, and delayed/failed embryo implantation, indicating the adverse effect of BPA on early pregnancy. Preimplantation 17β-estradiol (E2) exposure at 1 and 10 µg/kg/day from D0.5 to D2.5 delayed embryo transport in the ampulla-isthmus junction of oviduct in mice, which is associated with the oviductal epithelium hyperplasia. Microarray analysis revealed 53 differentially expressed genes in the oviduct upon 10 µg/kg/day E2 treatment, which may have potential function in embryo transport regulation. Embryo implantation is a process that the receptive uterus accepts an embryo to implant into the uterine wall. Microarray analysis of the preimplantation D3.5 and postimplantation D4.5 uterine luminal epithelium (LE) identified 627 differentially expressed genes and 21 significantly changed signaling pathways upon embryo implantation. 12 of these genes were newly characterized and showed spatiotemporal expression patterns in the mouse periimplantation uterine LE. The most upregulated gene in the D4.5 LE Atp6v0d2 (34.7x) is a subunit of vacuolar-type H+-ATPase (V-ATPase) that regulates the cell acidification through ATP hydrolysis and proton translocation. -
ELMO1 Signaling Is a Promoter of Osteoclast Function and Bone Loss ✉ Sanja Arandjelovic 1 , Justin S
ARTICLE https://doi.org/10.1038/s41467-021-25239-6 OPEN ELMO1 signaling is a promoter of osteoclast function and bone loss ✉ Sanja Arandjelovic 1 , Justin S. A. Perry 1, Ming Zhou 2, Adam Ceroi3, Igor Smirnov4, Scott F. Walk1, Laura S. Shankman1, Isabelle Cambré3, Suna Onengut-Gumuscu 5, Dirk Elewaut 3, Thomas P. Conrads 2 & ✉ Kodi S. Ravichandran 1,3 Osteoporosis affects millions worldwide and is often caused by osteoclast induced bone loss. 1234567890():,; Here, we identify the cytoplasmic protein ELMO1 as an important ‘signaling node’ in osteoclasts. We note that ELMO1 SNPs associate with bone abnormalities in humans, and that ELMO1 deletion in mice reduces bone loss in four in vivo models: osteoprotegerin deficiency, ovariectomy, and two types of inflammatory arthritis. Our transcriptomic analyses coupled with CRISPR/Cas9 genetic deletion identify Elmo1 associated regulators of osteoclast function, including cathepsin G and myeloperoxidase. Further, we define the ‘ELMO1 inter- actome’ in osteoclasts via proteomics and reveal proteins required for bone degradation. ELMO1 also contributes to osteoclast sealing zone on bone-like surfaces and distribution of osteoclast-specific proteases. Finally, a 3D structure-based ELMO1 inhibitory peptide reduces bone resorption in wild type osteoclasts. Collectively, we identify ELMO1 as a signaling hub that regulates osteoclast function and bone loss, with relevance to osteoporosis and arthritis. 1 Center for Cell Clearance, Department of Microbiology, Immunology, and Cancer Biology and Carter Immunology Center, University of Virginia, Charlottesville, VA, USA. 2 Inova Schar Cancer Institute, Inova Center for Personalized Health, Fairfax, VA, USA. 3 Inflammation Research Centre, VIB, and the Department of Biomedical Molecular Biology, Ghent Univeristy, Ghent, Belgium. -
Mechanisms of Copper Deficiency in the Zebrafish Embryo Erik Madsen Washington University in St
Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) January 2010 Mechanisms of Copper Deficiency in the Zebrafish Embryo Erik Madsen Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Madsen, Erik, "Mechanisms of Copper Deficiency in the Zebrafish Embryo" (2010). All Theses and Dissertations (ETDs). 220. https://openscholarship.wustl.edu/etd/220 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY Division of Biology and Biomedical Sciences Molecular Cell Biology Dissertation Examination Committee Jonathan Gitlin, Chair John Atkinson Guojun Bu Aaron DiAntonio Steven Johnson Jeanne Nerbonne David Wilson MECHANISMS OF COPPER DEFICIENCY IN THE ZEBRAFISH EMBRYO by Erik Christian Madsen A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2010 Saint Louis, Missouri ABSTRACT OF THE DISSERTATION Mechanisms of Copper Deficiency in the Zebrafish Embryo By Erik Christian Madsen Doctor of Philosophy in Biology and Biomedical Sciences (Molecular Cell Biology) Washington University in St. Louis, 2010 Professor Jonathan D. Gitlin, Chairperson Proper maternal nutrition is critical for early embryonic development. Despite overwhelming epidemiologic data indicating the benefits nutrient supplementation for the developing organism we do not fully understand the genetics of predisposition to abnormal developmental phenotypes when faced with suboptimal nutrient levels. -
Expression Profiling of Substantia Nigra in Parkinson Disease, Progressive Supranuclear Palsy, and Frontotemporal Dementia with Parkinsonism
ORIGINAL CONTRIBUTION Expression Profiling of Substantia Nigra in Parkinson Disease, Progressive Supranuclear Palsy, and Frontotemporal Dementia With Parkinsonism Michael A. Hauser, PhD; Yi-Ju Li, PhD; Hong Xu, MA; Maher A. Noureddine, PhD; Yujun S. Shao, PhD; Steven R. Gullans, PhD; Clemens R. Scherzer, MD; Roderick V. Jensen, PhD; Adam C. McLaurin, BA; Jason R. Gibson, BA; Burton L. Scott, MD; Rita M. Jewett, RN; Judith E. Stenger, PhD; Donald E. Schmechel, MD; Christine M. Hulette, MD, PhD; Jeffery M. Vance, MD, PhD Background: Parkinson disease (PD) is characterized Results: There were 142 genes that were significantly by loss of dopaminergic neurons in the substantia nigra. differentially expressed between PD cases and controls Genes contributing to rare mendelian forms of PD have and 96 genes that were significantly differentially ex- been identified, but the genes involved in the more com- pressed between the combined progressive supra- mon idiopathic PD are not well understood. nuclear palsy and frontotemporal dementia with parkin- sonism cases and controls. The 12 genes common to all Objectives: To identify genes important to PD patho- 3 disorders may be related to secondary effects. Hierar- genesis using microarrays and to investigate their poten- chical cluster analysis after exclusion of these 12 genes tial to aid in diagnosing parkinsonism. differentiated 4 of the 6 PD cases from progressive su- pranuclear palsy and frontotemporal dementia with par- Design: Microarray expression analysis of postmortem kinsonism. substantia nigra tissue. Conclusions: Four main molecular pathways are al- Patients: Substantia nigra samples from 14 unrelated tered in PD substantia nigra: chaperones, ubiquitina- individuals were analyzed, including 6 with PD, 2 with tion, vesicle trafficking, and nuclear-encoded mitochon- progressive supranuclear palsy, 1 with frontotemporal de- drial genes. -
Kidney V-Atpase-Rich Cell Proteome Database
A comprehensive list of the proteins that are expressed in V-ATPase-rich cells harvested from the kidneys based on the isolation by enzymatic digestion and fluorescence-activated cell sorting (FACS) from transgenic B1-EGFP mice, which express EGFP under the control of the promoter of the V-ATPase-B1 subunit. In these mice, type A and B intercalated cells and connecting segment principal cells of the kidney express EGFP. The protein identification was performed by LC-MS/MS using an LTQ tandem mass spectrometer (Thermo Fisher Scientific). For questions or comments please contact Sylvie Breton ([email protected]) or Mark A. Knepper ([email protected]). -
Molecular Architecture Underlying Fluid Absorption by the Developing Inner
RESEARCH ARTICLE Molecular architecture underlying fluid absorption by the developing inner ear Keiji Honda1†, Sung Huhn Kim2‡, Michael C Kelly3, Joseph C Burns3§, Laura Constance2, Xiangming Li2#, Fei Zhou2, Michael Hoa4, Matthew W Kelley3, Philine Wangemann2*, Robert J Morell5, Andrew J Griffith1* 1Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 2Anatomy and Physiology Department, Kansas State University, Manhattan, United States; 3Developmental Neuroscience Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 4Auditory Development and Restoration Program, National Institute on *For correspondence: Deafness and Other Communication Disorders, National Institutes of Health, [email protected] (PW); Bethesda, United States; 5Genomics and Computational Biology Core, National [email protected] (AJG) Institute on Deafness and Other Communication Disorders, National Institutes of Present address: Health, Bethesda, United States †Otolaryngology Department, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan; ‡Department of Abstract Mutations of SLC26A4 are a common cause of hearing loss associated with Otorhinolaryngology, Head and enlargement of the endolymphatic sac (EES). Slc26a4 expression in the developing mouse Neck Surgery, Yonsei University College of Medicine, Seoul, endolymphatic sac is required for acquisition of normal inner ear structure and function. Here, we Korea; §Decibel Therapeutics, show that the mouse endolymphatic sac absorbs fluid in an SLC26A4-dependent fashion. Fluid Cambridge, United States; absorption was sensitive to ouabain and gadolinium but insensitive to benzamil, bafilomycin and #Technique R and D-Drug S3226. Single-cell RNA-seq analysis of pre- and postnatal endolymphatic sacs demonstrates two Substance, GlaxoSmithKline types of differentiated cells. -
Robles JTO Supplemental Digital Content 1
Supplementary Materials An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma based on mRNA, microRNA and DNA Methylation Biomarkers Ana I. Robles1, Eri Arai2, Ewy A. Mathé1, Hirokazu Okayama1, Aaron Schetter1, Derek Brown1, David Petersen3, Elise D. Bowman1, Rintaro Noro1, Judith A. Welsh1, Daniel C. Edelman3, Holly S. Stevenson3, Yonghong Wang3, Naoto Tsuchiya4, Takashi Kohno4, Vidar Skaug5, Steen Mollerup5, Aage Haugen5, Paul S. Meltzer3, Jun Yokota6, Yae Kanai2 and Curtis C. Harris1 Affiliations: 1Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 2Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 3Genetics Branch, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 4Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 5Department of Chemical and Biological Working Environment, National Institute of Occupational Health, NO-0033 Oslo, Norway. 6Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona (Barcelona), Spain. List of Supplementary Materials Supplementary Materials and Methods Fig. S1. Hierarchical clustering of based on CpG sites differentially-methylated in Stage I ADC compared to non-tumor adjacent tissues. Fig. S2. Confirmatory pyrosequencing analysis of DNA methylation at the HOXA9 locus in Stage I ADC from a subset of the NCI microarray cohort. 1 Fig. S3. Methylation Beta-values for HOXA9 probe cg26521404 in Stage I ADC samples from Japan. Fig. S4. Kaplan-Meier analysis of HOXA9 promoter methylation in a published cohort of Stage I lung ADC (J Clin Oncol 2013;31(32):4140-7). Fig. S5. Kaplan-Meier analysis of a combined prognostic biomarker in Stage I lung ADC. -
Large-Scale Proteomics and Phosphoproteomics of Urinary Exosomes
JASN Express. Published on December 3, 2008 as doi: 10.1681/ASN.2008040406 BASIC RESEARCH www.jasn.org Large-Scale Proteomics and Phosphoproteomics of Urinary Exosomes Patricia A. Gonzales,*† Trairak Pisitkun,* Jason D. Hoffert,* Dmitry Tchapyjnikov,* ʈ Robert A. Star,‡ Robert Kleta,§ ¶ Nam Sun Wang,† and Mark A. Knepper* *Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, ‡Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases, §Section of Human ʈ Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, and Office of Rare Diseases, Office of the Director, National Institutes of Health, Bethesda, and †Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland; and ¶London Epithelial Group, Centre for Nephrology, University College London, London, United Kingdom ABSTRACT Normal human urine contains large numbers of exosomes, which are 40- to 100-nm vesicles that originate as the internal vesicles in multivesicular bodies from every renal epithelial cell type facing the urinary space. Here, we used LC-MS/MS to profile the proteome of human urinary exosomes. Overall, the analysis identified 1132 proteins unambiguously, including 177 that are represented on the Online Mendelian Inheritance in Man database of disease-related genes, suggesting that exosome analysis is a potential approach to discover urinary biomarkers. We extended the proteomic analysis to phospho- proteomic profiling using neutral loss scanning, and this yielded multiple novel phosphorylation sites, including serine-811 in the thiazide-sensitive Na-Cl co-transporter, NCC. To demonstrate the potential use of exosome analysis to identify a genetic renal disease, we carried out immunoblotting of exosomes from urine samples of patients with a clinical diagnosis of Bartter syndrome type I, showing an absence of the sodium-potassium-chloride co-transporter 2, NKCC2. -
Proteomic Analysis of Aged Microglia
Flowers et al. Journal of Neuroinflammation (2017) 14:96 DOI 10.1186/s12974-017-0840-7 RESEARCH Open Access Proteomic analysis of aged microglia: shifts in transcription, bioenergetics, and nutrient response Antwoine Flowers1,2, Harris Bell-Temin3, Ahmad Jalloh1,2, Stanley M. Stevens Jr.3 and Paula C. Bickford1,2,4* Abstract Background: Age is the primary risk factor for many diseases. As such, age is a critical co-factor for examination in order to understand the progression and potential intervention in disease progression. Studies examining both the phenotype and transcriptome of aged microglia demonstrated a propensity for the development of a pro-inflammatory phenotype. Less well studied is the concomitant blunting of anti-inflammatory aspects of microglial function with age which also impact plasticity and repair in the CNS. Methods: This study utilizes mass spectrometry-based proteomics to compare primary microglia from young andagedanimals. Results: This study revealed alterations in three clusters of inter-related proteins. The three pathways were inflammatory signaling, mitochondrial function, and cellular metabolism. Analysis of these clusters identified the protein rapamycin-insensitive companion of mTOR (RICTOR), a component of the mTORC2 complex, as a novel upstream regulator of several biological functions that are altered with age and potentially linked to phenotype development. A decrease in mTORC2-dependent AKT S473 phosphorylation, as assessed by insulin growth factor (IGF) treatment, was observed in aged microglia. This novel finding was confirmed by genetic manipulation of the microglial cell line. BV2 cells with diminished RICTOR displayed a phenotype that was strikingly similar to that of aged microglia. This finding is particularly relevant as the mTOR pathway already has a number of pharmacological modulators used clinically.