Brain Specific Human Genes, NELL1 and NELL2, Are Predominantly Expressed in Neuroblastoma and Other Embryonal Neuroepithelial Tumors
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Experimental Validation of the Regulated Expression of Large Numbers of Non-Coding Rnas from the Mouse Genome
Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Article Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome Timothy Ravasi,1,4,5 Harukazu Suzuki,2,4 Ken C. Pang,1,3,4 Shintaro Katayama,2,4 Masaaki Furuno,2,4,6 Rie Okunishi,2 Shiro Fukuda,2 Kelin Ru,1 Martin C. Frith,1,2 M. Milena Gongora,1 Sean M. Grimmond,1 David A. Hume,1 Yoshihide Hayashizaki,2 and John S. Mattick1,7 1ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia; 2Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; 3T Cell Laboratory, Ludwig Institute for Cancer Research, Austin & Repatriation Medical Centre, Heidelberg VIC 3084, Australia Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific “transcriptional noise.” Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated. -
Neural Epidermal Growth Factor-Like 1 Protein Variant Increases Survival
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.08.430254; this version posted February 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neural epidermal growth factor-like 1 protein variant increases survival and modulates the inflammatory and immune responses in human ACE-2 transgenic mice infected with SARS-CoV-2 Roopa Biswas1*#, Shannon Eaker2, Dharmendra Kumar Soni1, Swagata Kar3, Denae LoBato4, and Cymbeline Culiat2*# 1 Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 2 NellOne Therapeutics Inc., 11020 Solway School Road, Suite 101, Knoxville, TN 37931 3 Bioqual Inc., 9600 Medical Center Drive, Suite 101, Rockville, MD 20850 4 Biomedical and Diagnostic Services, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, TN 37996 Short title: NELL1-NV1 therapy for COVID-19 # Contributed equally to this manuscript * Corresponding Authors Roopa Biswas, Department of Anatomy, Physiology and Genetics, Room B4024, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814. Email address: [email protected]; Cymbeline Culiat, NellOne Therapeutics Inc., 11020 Solway School Road, Suite 101, Knoxville, TN 37931. Email address: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.08.430254; this version posted February 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Coronavirus disease 2019 (COVID-19) is a viral illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is a worsening global pandemic. -
Molecular Effects of Isoflavone Supplementation Human Intervention Studies and Quantitative Models for Risk Assessment
Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis committee Promotors Prof. Dr Pieter van ‘t Veer Professor of Nutritional Epidemiology Wageningen University Prof. Dr Evert G. Schouten Emeritus Professor of Epidemiology and Prevention Wageningen University Co-promotors Dr Anouk Geelen Assistant professor, Division of Human Nutrition Wageningen University Dr Lydia A. Afman Assistant professor, Division of Human Nutrition Wageningen University Other members Prof. Dr Jaap Keijer, Wageningen University Dr Hubert P.J.M. Noteborn, Netherlands Food en Consumer Product Safety Authority Prof. Dr Yvonne T. van der Schouw, UMC Utrecht Dr Wendy L. Hall, King’s College London This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 20 June 2014 at 13.30 p.m. in the Aula. Vera van der Velpen Molecular effects of isoflavone supplementation: Human intervention studies and quantitative models for risk assessment 154 pages PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN: 978-94-6173-952-0 ABSTRact Background: Risk assessment can potentially be improved by closely linked experiments in the disciplines of epidemiology and toxicology. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Analysis of Dynamic Molecular Networks for Pancreatic Ductal
Pan et al. Cancer Cell Int (2018) 18:214 https://doi.org/10.1186/s12935-018-0718-5 Cancer Cell International PRIMARY RESEARCH Open Access Analysis of dynamic molecular networks for pancreatic ductal adenocarcinoma progression Zongfu Pan1†, Lu Li2†, Qilu Fang1, Yiwen Zhang1, Xiaoping Hu1, Yangyang Qian3 and Ping Huang1* Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest solid tumors. The rapid progression of PDAC results in an advanced stage of patients when diagnosed. However, the dynamic molecular mechanism underlying PDAC progression remains far from clear. Methods: The microarray GSE62165 containing PDAC staging samples was obtained from Gene Expression Omnibus and the diferentially expressed genes (DEGs) between normal tissue and PDAC of diferent stages were profled using R software, respectively. The software program Short Time-series Expression Miner was applied to cluster, compare, and visualize gene expression diferences between PDAC stages. Then, function annotation and pathway enrichment of DEGs were conducted by Database for Annotation Visualization and Integrated Discovery. Further, the Cytoscape plugin DyNetViewer was applied to construct the dynamic protein–protein interaction networks and to analyze dif- ferent topological variation of nodes and clusters over time. The phosphosite markers of stage-specifc protein kinases were predicted by PhosphoSitePlus database. Moreover, survival analysis of candidate genes and pathways was per- formed by Kaplan–Meier plotter. Finally, candidate genes were validated by immunohistochemistry in PDAC tissues. Results: Compared with normal tissues, the total DEGs number for each PDAC stage were 994 (stage I), 967 (stage IIa), 965 (stage IIb), 1027 (stage III), 925 (stage IV), respectively. The stage-course gene expression analysis showed that 30 distinct expressional models were clustered. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
NELL1 (N-15): Sc-240728
SAN TA C RUZ BI OTEC HNOL OG Y, INC . NELL1 (N-15): sc-240728 BACKGROUND PRODUCT NELL1 (NEL-like 1), also known as NRP1 or IDH3GL (NAD +-dependent isoci trate Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide dehydrogenase 3 γ-like), is an 810 amino acid secreted protein that con tains and 0.1% gelatin. one TSP N-terminal domain, 5 VWFC domains and 6 EGF-like domains. Ex- Blocking peptide available for competition studies, sc-240728 P, (100 µg pressed in craniofacial anomalies, NELL1 exists as a homotrimer that inter acts peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). with PKC β and is involved in the regulation of cell growth and differentiation. Human NELL1 shares 50% amino acid identity with its chicken counterpart, APPLICATIONS suggesting that NELL1 may have a conserved role between species. The gene encoding NELL1 maps to human chromosome 11, which houses over NELL1 (N-15) is recommended for detection of NELL1 of mouse, rat and 1,400 genes and comprises nearly 4% of the human genome. Jervell and human origin by Western Blotting (starting dilution 1:200, dilution range Lange-Nielsen syndrome, Jacobsen syndrome, Niemann-Pick disease, heredi - 1:100-1:1000), immunofluorescence (starting dilution 1:50, dilution range tary angioedema and Smith-Lemli-Opitz syndrome are associated with defects 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution range in genes that maps to chromosome 11. 1:30-1:3000); non cross-reactive with NELL2. -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
Role of Genomic Variants in the Response to Biologics Targeting Common Autoimmune Disorders
Role of genomic variants in the response to biologics targeting common autoimmune disorders by Gordana Lenert, PhD The thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Master of Science Ottawa-Carleton Joint Program in Bioinformatics Carleton University Ottawa, Canada © 2016 Gordana Lenert Abstract Autoimmune diseases (AID) are common chronic inflammatory conditions initiated by the loss of the immunological tolerance to self-antigens. Chronic immune response and uncontrolled inflammation provoke diverse clinical manifestations, causing impairment of various tissues, organs or organ systems. To avoid disability and death, AID must be managed in clinical practice over long periods with complex and closely controlled medication regimens. The anti-tumor necrosis factor biologics (aTNFs) are targeted therapeutic drugs used for AID management. However, in spite of being very successful therapeutics, aTNFs are not able to induce remission in one third of AID phenotypes. In our research, we investigated genomic variability of AID phenotypes in order to explain unpredictable lack of response to aTNFs. Our hypothesis is that key genetic factors, responsible for the aTNFs unresponsiveness, are positioned at the crossroads between aTNF therapeutic processes that generate remission and pathogenic or disease processes that lead to AID phenotypes expression. In order to find these key genetic factors at the intersection of the curative and the disease pathways, we combined genomic variation data collected from publicly available curated AID genome wide association studies (AID GWAS) for each disease. Using collected data, we performed prioritization of genes and other genomic structures, defined the key disease pathways and networks, and related the results with the known data by the bioinformatics approaches. -
A Search for Modifying Genetic Factors in CHEK2:C.1100Delc Breast Cancer Patients Camilla Wendt1*, Taru A
www.nature.com/scientificreports OPEN A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients Camilla Wendt1*, Taru A. Muranen2, Lotta Mielikäinen2, Jessada Thutkawkorapin3, Carl Blomqvist4, Xiang Jiao3, Hans Ehrencrona5, Emma Tham3, Brita Arver6, Beatrice Melin7, Ekaterina Kuchinskaya8, Marie Stenmark Askmalm8, Ylva Paulsson‑Karlsson9, Zakaria Einbeigi10, Anna von Wachenfeldt Väppling1, Eija Kalso11, Tiina Tasmuth11, Anne Kallioniemi12, Kristiina Aittomäki13, Heli Nevanlinna2, Åke Borg14 & Annika Lindblom3 The risk of breast cancer associated with CHEK2:c.1100delC is 2–threefold but higher in carriers with a family history of breast cancer than without, suggesting that other genetic loci in combination with CHEK2:c.1100delC confer an increased risk in a polygenic model. Part of the excess familial risk has been associated with common low‑penetrance variants. This study aimed to identify genetic loci that modify CHEK2:c.1100delC‑associated breast cancer risk by searching for candidate risk alleles that are overrepresented in CHEK2:c.1100delC carriers with breast cancer compared with controls. We performed whole‑exome sequencing in 28 breast cancer cases with germline CHEK2:c.1100delC, 28 familial breast cancer cases and 70 controls. Candidate alleles were selected for validation in larger cohorts. One recessive synonymous variant, rs16897117, was suggested, but no overrepresentation of homozygous CHEK2:c.1100delC carriers was found in the following validation. Furthermore, 11 non‑synonymous candidate alleles were suggested for further testing, but no signifcant diference in allele frequency could be detected in the validation in CHEK2:c.1100delC cases compared with familial breast cancer, sporadic breast cancer and controls. With this method, we found no support for a CHEK2:c.1100delC‑specifc genetic modifer. -
Signaling Crosstalk in Mesenchymal Stem Cells and Applications in Regenerative Medicine
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Genes Dis Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 December 20. Published in final edited form as: Genes Dis. 2017 September ; 4(3): 127–137. doi:10.1016/j.gendis.2017.07.006. Neural EGF-like protein 1 (NELL-1): Signaling crosstalk in mesenchymal stem cells and applications in regenerative medicine Mikhail Pakvasaa,b, Alex Alverdyb,c, Sami Mostafaa,b, Eric Wangd, Lucy Fud, Alexander Lid, Leonardo Oliveirad, Aravind Athivirahamd, Michael J. Leed, Jennifer Moriatis Wolfd, Tong- Chuan Hed, Guillermo A. Ameere,f,g, and Russell R. Reida,b,* aThe University of Chicago, Pritzker School of Medicine, Chicago, IL 60637, USA bLaboratory of Craniofacial Biology and Development, Section of Plastic and Reconstructive Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA cRosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA dMolecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA eDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA fCenter for Advanced Regenerative Engineering, Northwestern University, Evanston, IL 60208, USA gDepartment of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA Abstract Bone tissue regeneration holds the potential to solve both osteoporosis and large skeletal defects, two problems associated with significant morbidity. The differentiation of mesenchymal stem cells into the osteogenic lineage requires a specific microenvironment and certain osteogenic growth factors. Neural EGF Like-Like molecule 1 (NELL-1) is a secreted glycoprotein that has proven, both in vitro and in vivo, to be a potent osteo-inductive factor. -
A Systematic Genome-Wide Association Analysis for Inflammatory Bowel Diseases (IBD)
A systematic genome-wide association analysis for inflammatory bowel diseases (IBD) Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von Dipl.-Biol. ANDRE FRANKE Kiel, im September 2006 Referent: Prof. Dr. Dr. h.c. Thomas C.G. Bosch Koreferent: Prof. Dr. Stefan Schreiber Tag der mündlichen Prüfung: Zum Druck genehmigt: der Dekan “After great pain a formal feeling comes.” (Emily Dickinson) To my wife and family ii Table of contents Abbreviations, units, symbols, and acronyms . vi List of figures . xiii List of tables . .xv 1 Introduction . .1 1.1 Inflammatory bowel diseases, a complex disorder . 1 1.1.1 Pathogenesis and pathophysiology. .2 1.2 Genetics basis of inflammatory bowel diseases . 6 1.2.1 Genetic evidence from family and twin studies . .6 1.2.2 Single nucleotide polymorphisms (SNPs) . .7 1.2.3 Linkage studies . .8 1.2.4 Association studies . 10 1.2.5 Known susceptibility genes . 12 1.2.5.1 CARD15. .12 1.2.5.2 CARD4. .15 1.2.5.3 TNF-α . .15 1.2.5.4 5q31 haplotype . .16 1.2.5.5 DLG5 . .17 1.2.5.6 TNFSF15 . .18 1.2.5.7 HLA/MHC on chromosome 6 . .19 1.2.5.8 Other proposed IBD susceptibility genes . .20 1.2.6 Animal models. 21 1.3 Aims of this study . 23 2 Methods . .24 2.1 Laboratory information management system (LIMS) . 24 2.2 Recruitment. 25 2.3 Sample preparation. 27 2.3.1 DNA extraction from blood. 27 2.3.2 Plate design .