Sui Et Al Supplementary Figures
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Supplemental Figure 1. Vimentin
Double mutant specific genes Transcript gene_assignment Gene Symbol RefSeq FDR Fold- FDR Fold- FDR Fold- ID (single vs. Change (double Change (double Change wt) (single vs. wt) (double vs. single) (double vs. wt) vs. wt) vs. single) 10485013 BC085239 // 1110051M20Rik // RIKEN cDNA 1110051M20 gene // 2 E1 // 228356 /// NM 1110051M20Ri BC085239 0.164013 -1.38517 0.0345128 -2.24228 0.154535 -1.61877 k 10358717 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 /// BC 1700025G04Rik NM_197990 0.142593 -1.37878 0.0212926 -3.13385 0.093068 -2.27291 10358713 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 1700025G04Rik NM_197990 0.0655213 -1.71563 0.0222468 -2.32498 0.166843 -1.35517 10481312 NM_027283 // 1700026L06Rik // RIKEN cDNA 1700026L06 gene // 2 A3 // 69987 /// EN 1700026L06Rik NM_027283 0.0503754 -1.46385 0.0140999 -2.19537 0.0825609 -1.49972 10351465 BC150846 // 1700084C01Rik // RIKEN cDNA 1700084C01 gene // 1 H3 // 78465 /// NM_ 1700084C01Rik BC150846 0.107391 -1.5916 0.0385418 -2.05801 0.295457 -1.29305 10569654 AK007416 // 1810010D01Rik // RIKEN cDNA 1810010D01 gene // 7 F5 // 381935 /// XR 1810010D01Rik AK007416 0.145576 1.69432 0.0476957 2.51662 0.288571 1.48533 10508883 NM_001083916 // 1810019J16Rik // RIKEN cDNA 1810019J16 gene // 4 D2.3 // 69073 / 1810019J16Rik NM_001083916 0.0533206 1.57139 0.0145433 2.56417 0.0836674 1.63179 10585282 ENSMUST00000050829 // 2010007H06Rik // RIKEN cDNA 2010007H06 gene // --- // 6984 2010007H06Rik ENSMUST00000050829 0.129914 -1.71998 0.0434862 -2.51672 -
Impairments in Contractility and Cytoskeletal Organisation Cause Nuclear Defects in Nemaline Myopathy
bioRxiv preprint doi: https://doi.org/10.1101/518522; this version posted January 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Impairments in contractility and cytoskeletal organisation cause nuclear defects in nemaline myopathy Jacob A Ross1, Yotam Levy1, Michela Ripolone2, Justin S Kolb3, Mark Turmaine4, Mark Holt5, Maurizio Moggio2, Chiara Fiorillo6, Johan Lindqvist3, Nicolas Figeac5, Peter S Zammit5, Heinz Jungbluth5,7,8, John Vissing9, Nanna Witting9, Henk Granzier3, Edmar Zanoteli10, Edna C Hardeman11, Carina Wallgren- Pettersson12, Julien Ochala1,5. 1. Centre for Human & Applied Physiological Sciences, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, Guy’s Campus, King’s College London, SE1 1UL, UK 2. Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan 20122, Italy 3. Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, 85721, USA 4. Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK 5. Randall Centre for Cell and Molecular Biophysics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, Guy’s Campus, King’s College London, SE1 1UL, UK 6. Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa and Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genoa, Italy 7. Department of Paediatric Neurology, Neuromuscular Service, Evelina's Children Hospital, Guy's and St Thomas' Hospital National Health Service Foundation Trust, London, SE1 9RT, UK 8. Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College, London, SE1 1UL, UK 9. -
Assembly and Maintenance of Sarcomere Thin Filaments and Associated Diseases
International Journal of Molecular Sciences Review Assembly and Maintenance of Sarcomere Thin Filaments and Associated Diseases Kendal Prill and John F. Dawson * Centre for Cardiovascular Investigations, Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] * Correspondence: [email protected] Received: 17 December 2019; Accepted: 12 January 2020; Published: 15 January 2020 Abstract: Sarcomere assembly and maintenance are essential physiological processes required for cardiac and skeletal muscle function and organism mobility. Over decades of research, components of the sarcomere and factors involved in the formation and maintenance of this contractile unit have been identified. Although we have a general understanding of sarcomere assembly and maintenance, much less is known about the development of the thin filaments and associated factors within the sarcomere. In the last decade, advancements in medical intervention and genome sequencing have uncovered patients with novel mutations in sarcomere thin filaments. Pairing this sequencing with reverse genetics and the ability to generate patient avatars in model organisms has begun to deepen our understanding of sarcomere thin filament development. In this review, we provide a summary of recent findings regarding sarcomere assembly, maintenance, and disease with respect to thin filaments, building on the previous knowledge in the field. We highlight debated and unknown areas within these processes to clearly define open research questions. Keywords: sarcomere assembly; sarcomere maintenance; sarcomere thin filaments; thin filament assembly; thin filament maintenance; thin filament turnover; actin turnover; chaperone; sarcomere; myopathy 1. Introduction Striated muscle requires the coordination of hundreds of proteins not only for cellular function but also for assembly of the contractile sarcomere units within the myofibril. -
A Cell Line P53 Mutation Type UM
A Cell line p53 mutation Type UM-SCC 1 wt UM-SCC5 Exon 5, 157 GTC --> TTC Missense mutation by transversion (Valine --> Phenylalanine UM-SCC6 wt UM-SCC9 wt UM-SCC11A wt UM-SCC11B Exon 7, 242 TGC --> TCC Missense mutation by transversion (Cysteine --> Serine) UM-SCC22A Exon 6, 220 TAT --> TGT Missense mutation by transition (Tyrosine --> Cysteine) UM-SCC22B Exon 6, 220 TAT --> TGT Missense mutation by transition (Tyrosine --> Cysteine) UM-SCC38 Exon 5, 132 AAG --> AAT Missense mutation by transversion (Lysine --> Asparagine) UM-SCC46 Exon 8, 278 CCT --> CGT Missense mutation by transversion (Proline --> Alanine) B 1 Supplementary Methods Cell Lines and Cell Culture A panel of ten established HNSCC cell lines from the University of Michigan series (UM-SCC) was obtained from Dr. T. E. Carey at the University of Michigan, Ann Arbor, MI. The UM-SCC cell lines were derived from eight patients with SCC of the upper aerodigestive tract (supplemental Table 1). Patient age at tumor diagnosis ranged from 37 to 72 years. The cell lines selected were obtained from patients with stage I-IV tumors, distributed among oral, pharyngeal and laryngeal sites. All the patients had aggressive disease, with early recurrence and death within two years of therapy. Cell lines established from single isolates of a patient specimen are designated by a numeric designation, and where isolates from two time points or anatomical sites were obtained, the designation includes an alphabetical suffix (i.e., "A" or "B"). The cell lines were maintained in Eagle's minimal essential media supplemented with 10% fetal bovine serum and penicillin/streptomycin. -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
Β-Catenin Knockdown Affects Mitochondrial Biogenesis and Lipid Metabolism in Breast Cancer Cells
ORIGINAL RESEARCH published: 27 July 2017 doi: 10.3389/fphys.2017.00544 β-Catenin Knockdown Affects Mitochondrial Biogenesis and Lipid Metabolism in Breast Cancer Cells Daniele Vergara 1, 2 †, Eleonora Stanca 1, 2 †, Flora Guerra 1, Paola Priore 3, Antonio Gaballo 3, Julien Franck 4, Pasquale Simeone 5, Marco Trerotola 6, Stefania De Domenico 7, Isabelle Fournier 4, Cecilia Bucci 1, Michel Salzet 4, Anna M. Giudetti 1* and Michele Maffia 1, 2* 1 Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy, 2 Laboratory of Clinical Proteomic, “Giovanni Paolo II” Hospital, Lecce, Italy, 3 CNR NANOTEC - Institute of Nanotechnology, Lecce, Italy, 4 University of Lille, Institut national de la santé et de la recherche médicale, U-1192 - Laboratoire Protéomique, Réponse Edited by: Inflammatoire et Spectrométrie de Masse-PRISM, Lille, France, 5 Unit of Cytomorphology, CeSI-MeT and Department of Andrei Surguchov, Medicine and Aging Sciences, School of Medicine and Health Sciences, University “G. d’Annunzio,” Chieti, Italy, 6 Unit of Kansas University of Medical Center Cancer Pathology, CeSI-MeT and Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio,” Research Institute, United States Chieti, Italy, 7 C.N.R. Unit of Lecce, Institute of Food Production Sciences, Lecce, Italy Reviewed by: Kamal Datta, β-catenin plays an important role as regulatory hub in several cellular processes including Georgetown University, United States Silvana Gaetani, cell adhesion, metabolism, and epithelial mesenchymal transition. This is mainly achieved Sapienza Università di Roma, Italy by its dual role as structural component of cadherin-based adherens junctions, and as Clizia Chinello, University of Milano-Bicocca, Italy a key nuclear effector of the Wnt pathway. -
Study for Pathogenesis of Congenital Cholesteatoma with Comparison of Proteins Expressed in Congenital Cholesteatoma, Acquired C
Study for pathogenesis of congenital cholesteatoma with comparison of proteins expressed in congenital cholesteatoma, acquired cholesteatoma and skin of the external auditory canal through proteomics Seung Ho Shin Department of Medicine The Graduate School, Yonsei University Study for pathogenesis of congenital cholesteatoma with comparison of proteins expressed in congenital cholesteatoma, acquired cholesteatoma and skin of the external auditory canal through proteomics Directed by Professor Jae Young Choi The Doctoral Dissertation submitted to the Department of Medicine, the Graduate School of Yonsei University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Seung Ho Shin June 2014 ACKNOWLEDGEMENTS In the initial period of my fellowship, I wrote a book, Temporal Bone Dissection Manual as a coauthor with Professor Won Sang Lee, Ho-Ki Lee and Jae Young Choi. Through this book, I learned about much knowledge from them. Professor Jae Young Choi advised me to go for a Ph.D. I admitted graduate school for a Ph.D. in 2007. In my doctoral course, he has instructed me in detail on the basic research. He has demonstrated precise and delicate laboratory techniques and showed outstanding ability to create new ideas. Also, he has often said to me that a researcher must be honest to his colleagues and even to himself. After the summer of 2013, he gave me an idea for this paper, which was for congenital cholesteatoma analysis with proteomics. He always displayed endless energy and enthusiasm for scientific experiments even after many demanding surgeries. His passion motivated me to follow suit and seven months of our work at last bore fruit. -
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. -
1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN. -
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). -
Identification of the Key Micrornas and Mirna- Mrna Interaction Networks During the Ovarian Development of Hens
Article Identification of the Key microRNAs and miRNA- mRNA Interaction Networks During the Ovarian Development of Hens Jing Li †, Chong Li †, Qi Li, Wen-Ting Li, Hong Li, Guo-Xi Li, Xiang-Tao Kang, Xiao-Jun Liu and Ya-Dong Tian * College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; [email protected] (J.L.); [email protected] (C.L.); [email protected] (Q.L.); [email protected] (W.-T.L.); [email protected] (H.L.); [email protected] (G.-X.L.); [email protected] (X.-T.K.); [email protected] (X.-J.L.) * Correspondence: [email protected] † These two authors contributed equally to this work. Received: 27 July 2020; Accepted: 15 September 2020; Published: date Supplementary Material Animals 2020, 10, x; doi: www.mdpi.com/journal/animals Animals 2020, 10, x 2 of 24 Table 1. The list of the interaction network, the expression levels and Pearson’s correlation coefficient of DE miRNAs and DE mRNAs. Expression Level ( TPM) Expression Level ( FPKM) sRNA Transcript Id Gene Id Gene Name Correlatio 15W 20W 30W 68W 15W 20W 30W 68W gga-miR-1560-3p 3.253 6.030 4.295 2.565 ENSGALT00000087050 ENSGALG00000005902 RAB7A 17.832 0.031 6.674 0.077 -0.324 gga-miR-143-3p 25118.987 49390.256 87681.664 32277.275 ENSGALT00000069072 ENSGALG00000041760 CLTCL1 2.189 0.000 1.321 1.252 -0.268 gga-miR-7472-5p 0.054 0.264 0.466 0.000 ENSGALT00000066785 ENSGALG00000014582 CADM1 6.810 2.342 0.000 0.000 -0.394 gga-miR-7472-5p 0.054 0.264 0.466 0.000 ENSGALT00000033172 ENSGALG00000008121 CYP17A1 722.987 -
Regulation of Canonical Wnt Signalling by the Ciliopathy Protein MKS1 and the E2
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.08.897959; this version posted March 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Regulation of canonical Wnt signalling by the ciliopathy protein MKS1 and the E2 ubiquitin-conjugating enzyme UBE2E1. Katarzyna Szymanska1, Karsten Boldt2, Clare V. Logan1, Matthew Adams1, Philip A. Robinson1+, Marius Ueffing2, Elton Zeqiraj3, Gabrielle Wheway1,4#, Colin A. Johnson1#* *corresponding author: [email protected] ORCID: 0000-0002-2979-8234 # joint last authors + deceased 1 Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK 2 Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany 3 Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK 4 Faculty of Medicine, University of Southampton, Human Development and Health, UK; University Hospital Southampton NHS Foundation Trust, UK 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.08.897959; this version posted March 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract A functional primary cilium is essential for normal and regulated signalling. Primary ciliary defects cause a group of developmental conditions known as ciliopathies, but the precise mechanisms of signal regulation by the cilium remain unclear.