Inhibition of Sox2-Dependent Activation of Shh in the Ventral
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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
POU Domain Family Values: Flexibility, Partnerships, and Developmental Codes
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW POU domain family values: flexibility, partnerships, and developmental codes Aimee K. Ryan and Michael G. Rosenfeld 1 Howard Hughes Medical Institute, Department and School of Medicine, University of California at San Diego, La Jolla, Califiornia 92093-0648 USA Transcription factors serve critical roles in the progres- primary focus of this review. Crystallization of the Oct-1 sive development of general body plan, organ commit- and Pit-1 POU domains on DNA and in vitro studies ment, and finally, specific cell types. It has been the hope examining the specificity of POU domain cofactor inter- of most developmental biologists that comparison of the actions suggest that the flexibility with which the POU biological roles of a series of individual members within domain recognizes DNA-binding sites is a critical com- a family will permit at least some predictive generaliza- ponent of its ability to regulate gene expression. The tions regarding the developmental events that are likely implications of these data with respect to the mecha- to be regulated by a particular class of transcription fac- nisms utilized by the POU domain family of transcrip- tors. Here, we present an overview of the developmental tion factors to control developmental events will also be functions of the family of transcription factors charac- discussed. terized by the POU DNA-binding motif afforded by re- cent in vivo studies. Conformation of the POU domain on DNA The POU domain family of transcription factors was defined following the observation that the products of High-affinity site-specific DNA binding by POU domain three mammalian genes, Pit-l, Oct-l, and Oct-2 and the transcription factors requires both the POU-specific do- protein encoded by the Caenorhabditis elegans gene main and the POU homeodomain (Sturm and Herr 1988; unc-86 shared a region of homology, known as the POU Ingraham et al. -
Abnormal Mesenchymal Differentiation in the Superior Semicircular Canal of Brn4/Pou3f4 Knockout Mice
ORIGINAL ARTICLE 2 Abnormal Mesenchymal Differentiation in the Superior Semicircular Canal of Brn4/Pou3f4 Knockout Mice Steven E. Sobol, MD, MSc; Xiuyin Teng, MSc; E. Bryan Crenshaw III, PhD Objective: To examine the developmental time course of the SSCC in Brn4 knockout mice was initially detect- of the mutant phenotype and cellular mechanisms that able at P14. Interestingly, the mutant SSCC is indistin- result in malformations of the superior semicircular ca- guishable from control mice at earlier neonatal time points. nal (SSCC) in Brn4 knockout mice. Mutations in the Brn4/ In mutant neonates, there is persistence of immature wo- Pou3f4 gene result in characteristic inner ear abnormali- ven bone with high cellularity surrounding the perilym- ties in mutant mouse pedigrees, and the findings in these phatic space of the SSCC. These findings are not pres- mice are similar to those in human X-linked deafness type ent in control animal specimens, which demonstrate III. appropriate lamellar bony architecture. Design: Mutant and control mice were killed at vari- Conclusions: In Brn4 knockout mice, constriction of the ous neonatal time points to assess the development of SSCC with narrowing of the bony labyrinth develops in the SSCC. Measurements of SSCC diameter were made the postnatal period at approximately P14. The persis- on paint-perfused specimens at postnatal day (P) 0, P7, tence of immature bone in affected mice indicates that P10, and P14. Histologic evaluation of the SSCC was signaling abnormalities disrupt normal mesenchymal dif- made on hematoxylin-eosin–stained sections at P10. ferentiation in the SSCC. Results: A dysmorphic constriction of the superior arc Arch Otolaryngol Head Neck Surg. -
Tpit (TBX19) (NM 005149) Human Recombinant Protein Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP310787 Tpit (TBX19) (NM_005149) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human T-box 19 (TBX19) Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 48.1 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Bioactivity: ELISpot (PMID: 30008158) Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_005140 Locus ID: 9095 UniProt ID: O60806, B3KRD9 RefSeq Size: 2882 Cytogenetics: 1q24.2 RefSeq ORF: 1344 Synonyms: dJ747L4.1; TBS19; TPIT This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 Tpit (TBX19) (NM_005149) Human Recombinant Protein – TP310787 Summary: This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Mutations in this gene were found in patients with isolated deficiency of pituitary POMC-derived ACTH, suggesting an essential role for this gene in differentiation of the pituitary POMC lineage. -
Genome-Wide DNA Methylation Profiling Reveals Methylation Markers
Author Manuscript Published OnlineFirst on January 24, 2017; DOI: 10.1158/1078-0432.CCR-16-2641 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 1 Genome-wide DNA methylation profiling reveals methylation markers 2 associated with 3q gain for detection of cervical pre-cancer and cancer 3 4 Wina Verlaat1, Peter J.F. Snijders1, Putri W. Novianti1,2, Saskia M. Wilting1, Lise M.A. De Strooper1, 5 Geert Trooskens3,Johan Vandersmissen3, Wim Van Criekinge3, G. Bea A. Wisman4, Chris J.L.M. 6 Meijer1, Daniëlle A.M. Heideman1, Renske D.M. Steenbergen1 * 7 8 1Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands 9 2Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The 10 Netherlands 11 3Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, 12 Belgium. 13 4Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, 14 University Medical Center Groningen, Groningen, The Netherlands 15 16 Running title: 17 Methylation markers at 3q for cervical pre(cancer) detection 18 19 Key words: 20 Methyl Binding Domain/MBD-Seq, epigenetics, copy number aberrations, cervical carcinogenesis, 21 biomarkers 22 23 Additional information: 24 * Corresponding author: 25 Renske D.M. Steenbergen, PhD, Department of Pathology, VU University Medical Center, PO Box 26 7057, 1007 MB Amsterdam; The Netherlands, E-mail: [email protected] 27 28 Financial support: 29 This study was sponsored by Eurostars E!6679 Cervix-care and the European Research Council (ERC 30 advanced 2012- AdG, proposal 322986; Mass-Care). The sources of funding did not have any 31 influence on the design of the study, collection, analysis and interpretation of the data and in writing 32 the manuscript. -
Chemical Agent and Antibodies B-Raf Inhibitor RAF265
Supplemental Materials and Methods: Chemical agent and antibodies B-Raf inhibitor RAF265 [5-(2-(5-(trifluromethyl)-1H-imidazol-2-yl)pyridin-4-yloxy)-N-(4-trifluoromethyl)phenyl-1-methyl-1H-benzp{D, }imidazol-2- amine] was kindly provided by Novartis Pharma AG and dissolved in solvent ethanol:propylene glycol:2.5% tween-80 (percentage 6:23:71) for oral delivery to mice by gavage. Antibodies to phospho-ERK1/2 Thr202/Tyr204(4370), phosphoMEK1/2(2338 and 9121)), phospho-cyclin D1(3300), cyclin D1 (2978), PLK1 (4513) BIM (2933), BAX (2772), BCL2 (2876) were from Cell Signaling Technology. Additional antibodies for phospho-ERK1,2 detection for western blot were from Promega (V803A), and Santa Cruz (E-Y, SC7383). Total ERK antibody for western blot analysis was K-23 from Santa Cruz (SC-94). Ki67 antibody (ab833) was from ABCAM, Mcl1 antibody (559027) was from BD Biosciences, Factor VIII antibody was from Dako (A082), CD31 antibody was from Dianova, (DIA310), and Cot antibody was from Santa Cruz Biotechnology (sc-373677). For the cyclin D1 second antibody staining was with an Alexa Fluor 568 donkey anti-rabbit IgG (Invitrogen, A10042) (1:200 dilution). The pMEK1 fluorescence was developed using the Alexa Fluor 488 chicken anti-rabbit IgG second antibody (1:200 dilution).TUNEL staining kits were from Promega (G2350). Mouse Implant Studies: Biopsy tissues were delivered to research laboratory in ice-cold Dulbecco's Modified Eagle Medium (DMEM) buffer solution. As the tissue mass available from each biopsy was limited, we first passaged the biopsy tissue in Balb/c nu/Foxn1 athymic nude mice (6-8 weeks of age and weighing 22-25g, purchased from Harlan Sprague Dawley, USA) to increase the volume of tumor for further implantation. -
Evolving Principles Underlying Neural Lineage Conversion
F1000Research 2019, 8(F1000 Faculty Rev):1548 Last updated: 16 SEP 2019 REVIEW Evolving principles underlying neural lineage conversion and their relevance for biomedical translation [version 1; peer review: 4 approved] Lea Jessica Flitsch, Oliver Brüstle Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany First published: 30 Aug 2019, 8(F1000 Faculty Rev):1548 ( Open Peer Review v1 https://doi.org/10.12688/f1000research.18926.1) Latest published: 30 Aug 2019, 8(F1000 Faculty Rev):1548 ( https://doi.org/10.12688/f1000research.18926.1) Reviewer Status Abstract Invited Reviewers Scientific and technological advances of the past decade have shed light 1 2 3 4 on the mechanisms underlying cell fate acquisition, including its transcriptional and epigenetic regulation during embryonic development. version 1 This knowledge has enabled us to purposefully engineer cell fates in vitro published by manipulating expression levels of lineage-instructing transcription 30 Aug 2019 factors. Here, we review the state of the art in the cell programming field with a focus on the derivation of neural cells. We reflect on what we know about the mechanisms underlying fate changes in general and on the F1000 Faculty Reviews are written by members of degree of epigenetic remodeling conveyed by the distinct reprogramming the prestigious F1000 Faculty. They are and direct conversion strategies available. Moreover, we discuss the commissioned and are peer reviewed before implications of residual epigenetic memory for biomedical applications such publication to ensure that the final, published version as disease modeling and neuroregeneration. Finally, we cover recent developments approaching cell fate conversion in the living brain and is comprehensive and accessible. -
The Global Gene Expression Profile of the Secondary Transition During Pancreatic Development
ÔØ ÅÒÙ×Ö ÔØ The global gene expression profile of the secondary transition during pancre- atic development Stefanie J. Willmann, Nikola S. Mueller, Silvia Engert, Michael Sterr, Ingo Burtscher, Aurelia Raducanu, Martin Irmler, Johannes Beckers, Steffen Sass, Fabian J. Theis, Heiko Lickert PII: S0925-4773(15)30037-X DOI: doi: 10.1016/j.mod.2015.11.004 Reference: MOD 3386 To appear in: Received date: 19 June 2015 Revised date: 26 November 2015 Accepted date: 27 November 2015 Please cite this article as: Willmann, Stefanie J., Mueller, Nikola S., Engert, Sil- via, Sterr, Michael, Burtscher, Ingo, Raducanu, Aurelia, Irmler, Martin, Beckers, Johannes, Sass, Steffen, Theis, Fabian J., Lickert, Heiko, The global gene expres- sion profile of the secondary transition during pancreatic development, (2015), doi: 10.1016/j.mod.2015.11.004 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT The global gene expression profile of the secondary transition during pancreatic development Stefanie J. Willmann*1,5, Nikola S. Mueller*2, Silvia Engert1, Michael Sterr1, Ingo Burtscher1, Aurelia Raducanu1, Martin Irmler3, Johannes Beckers3,4,5, -
A Novel TBX19 Gene Mutation in a Case of Congenital Isolated Adrenocorticotropic Hormone Deficiency Presenting with Recurrent Respiratory Tract Infections
CASE REPORT published: 18 April 2017 doi: 10.3389/fendo.2017.00064 A Novel TBX19 Gene Mutation in a Case of Congenital Isolated Adrenocorticotropic Hormone Deficiency Presenting with Recurrent Respiratory Tract Infections Nese Akcan1, Nedime Serakıncı2, Burcu Turkgenc3, Ruveyde Bundak4, Nerin Bahceciler5 and Sehime G. Temel6,7* 1 Faculty of Medicine, Department of Pediatric Endocrinology, University of Near East, Nicosia, Cyprus, 2 Faculty of Medicine, Department of Medical Genetics, University of Near East, Nicosia, Cyprus, 3 Genetic Diagnostic Center, University of Acıbadem, Istanbul, Turkey, 4 Faculty of Medicine, Department of Pediatric Endocrinology, University of Kyrenia, Kyrenia, Cyprus, 5 Faculty of Medicine, Department of Pediatric Allergy and Immunology, University of Near East, Nicosia, Cyprus, 6 Faculty of Medicine, Department of Histology and Embryology, University of Near East, Nicosia, Cyprus, 7 Faculty of Medicine, Department of Histology and Embryology, University of Uludag, Bursa, Turkey Introduction: Congenital isolated adrenocorticotropic hormone deficiency (CIAD) is a rare disease characterized by low adrenocorticotropic hormone (ACTH) and cortisol levels. To date, recurrent pulmonary infections in infancy have not been reported as an Edited by: Mohamad Maghnie, accompanying symptom of CIAD. University of Genoa, Italy Case presentation: A 7-year-old boy was hospitalized nine times for recurrent lower Reviewed by: Laurie E. Cohen, respiratory tract infections. The results of all tests for the possible causes of wheezing Boston Children’s Hospital, USA were within the normal limits. His ACTH and cortisol levels were persistently low. All Marco Cappa, Bambino Gesù Ospedale other pituitary hormone levels, and adrenal ultrasound and pituitary magnetic resonance Pediatrico (IRCCS), Italy imaging results, were normal. -
Embryonic Origins of Virus-Induced Hearing Loss: Overview of Molecular Etiology
viruses Review Embryonic Origins of Virus-Induced Hearing Loss: Overview of Molecular Etiology Maryam Karimi-Boroujeni 1,†, Ali Zahedi-Amiri 2,3,† and Kevin M. Coombs 2,3,4,* 1 School of Rehabilitation Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada; [email protected] 2 Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; [email protected] 3 Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada 4 Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada * Correspondence: [email protected] † These authors have contributed equally to this work. Abstract: Hearing loss, one of the most prevalent chronic health conditions, affects around half a billion people worldwide, including 34 million children. The World Health Organization estimates that the prevalence of disabling hearing loss will increase to over 900 million people by 2050. Many cases of congenital hearing loss are triggered by viral infections during different stages of pregnancy. However, the molecular mechanisms by which viruses induce hearing loss are not sufficiently explored, especially cases that are of embryonic origins. The present review first describes the cellular and molecular characteristics of the auditory system development at early stages of embryogenesis. These developmental hallmarks, which initiate upon axial specification of the otic placode as the primary root of the inner ear morphogenesis, involve the stage-specific regulation of several molecules and pathways, such as retinoic acid signaling, Sonic hedgehog, and Wnt. Different RNA and DNA viruses contributing to congenital and acquired hearing loss are then discussed in terms of their potential effects on the expression of molecules that control the formation of the auditory and Citation: Karimi-Boroujeni, M.; vestibular compartments following otic vesicle differentiation. -
Separation of the PROX1 Gene from Upstream Conserved Elements in a Complex Inversion/ Translocation Patient with Hypoplastic Left Heart
European Journal of Human Genetics (2009) 17, 1423 – 1431 & 2009 Macmillan Publishers Limited All rights reserved 1018-4813/09 $32.00 www.nature.com/ejhg ARTICLE Separation of the PROX1 gene from upstream conserved elements in a complex inversion/ translocation patient with hypoplastic left heart Harinder K Gill1,2, Sian R Parsons3, Cosma Spalluto3, Angela F Davies4, Victoria J Knorz3, Clare EG Burlinson1, Bee Ling Ng5, Nigel P Carter5, Caroline Mackie Ogilvie1,4, David I Wilson3 and Roland G Roberts*,1 1Division of Genetics and Molecular Medicine, Department of Medical and Molecular Genetics, King’s College London, London, UK; 2Department of Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK; 3Centre for Human Development, Stem Cells and Regeneration, Human Genetics Division, University of Southampton, Southampton General Hospital, Southampton, UK; 4Department of Cytogenetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK; 5Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Hypoplastic left heart (HLH) occurs in at least 1 in 10 000 live births but may be more common in utero. Its causes are poorly understood but a number of affected cases are associated with chromosomal abnormalities. We set out to localize the breakpoints in a patient with sporadic HLH and a de novo translocation. Initial studies showed that the apparently simple 1q41;3q27.1 translocation was actually combined with a 4-Mb inversion, also de novo, of material within 1q41. We therefore localized all four breakpoints and found that no known transcription units were disrupted. However we present a case, based on functional considerations, synteny and position of highly conserved non-coding sequence elements, and the heterozygous Prox1 þ /À mouse phenotype (ventricular hypoplasia), for the involvement of dysregulation of the PROX1 gene in the aetiology of HLH in this case.