Why Is Lamin B Receptor Downregulated in Senescence?
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The Role of Nuclear Lamin B1 in Cell Proliferation and Senescence
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press The role of nuclear lamin B1 in cell proliferation and senescence Takeshi Shimi,1 Veronika Butin-Israeli,1 Stephen A. Adam,1 Robert B. Hamanaka,2 Anne E. Goldman,1 Catherine A. Lucas,1 Dale K. Shumaker,1 Steven T. Kosak,1 Navdeep S. Chandel,2 and Robert D. Goldman1,3 1Department of Cell and Molecular Biology, 2Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA Nuclear lamin B1 (LB1) is a major structural component of the nucleus that appears to be involved in the regulation of many nuclear functions. The results of this study demonstrate that LB1 expression in WI-38 cells decreases during cellular senescence. Premature senescence induced by oncogenic Ras also decreases LB1 expression through a retinoblastoma protein (pRb)-dependent mechanism. Silencing the expression of LB1 slows cell proliferation and induces premature senescence in WI-38 cells. The effects of LB1 silencing on proliferation require the activation of p53, but not pRb. However, the induction of premature senescence requires both p53 and pRb. The proliferation defects induced by silencing LB1 are accompanied by a p53-dependent reduction in mitochondrial reactive oxygen species (ROS), which can be rescued by growth under hypoxic conditions. In contrast to the effects of LB1 silencing, overexpression of LB1 increases the proliferation rate and delays the onset of senescence of WI-38 cells. This overexpression eventually leads to cell cycle arrest at the G1/S boundary. -
Revealing the Mechanism of Xist-Mediated Silencing
Revealing the Mechanism of Xist-mediated Silencing Thesis by Chun-Kan Chen In Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy CALIFORNIA INSTITUTE OF TECHNOLOGY Pasadena, California 2018 Defended November 1, 2017 ii 2017 Chun-Kan Chen ORCID: 0000-0002-1194-9137 iii ACKNOWLEDGEMENTS First of all, I’d like to thank my great mentor, Dr. Mitch Guttman (California Institute of Technology, Pasadena, CA), who led me to become an independent researcher and gave me valuable advice that guided me to accomplish this thesis. He has always been supportive of my future plans and career goals. I really enjoyed every discussion we have had. We often generated some interesting ideas for projects during our discussions. I would also like to send my thanks to my lab mates, Amy Chow, Mario Blanco, and Erik Aznauryan, who helped me with many experiments to move the project forward. I’d like to acknowledge Dr. Kathrin Plath (University of California, Los Angeles, Los Angeles, CA) for the collaboration and his critical comments on this project. Also, I want to thank Jesse Engreitz and Patrick McDonel, who provided helpful comments and suggestions to the project. I want to thank my parents, brother, and parents-in-law who provided both instrumental and emotional support to assist me in completing my Ph.D. degree. I also want to thank my friends, Lily Chen, Pei-Ying Lin, Tzu-Yao Wang, and Wei Li, for giving me valuable social support during my years in graduate school. Last but not least, I would like to send my special thanks to my wife, Christine Juang, who has always been supportive. -
Supplementary Materials
1 Supplementary Materials: Supplemental Figure 1. Gene expression profiles of kidneys in the Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice. (A) A heat map of microarray data show the genes that significantly changed up to 2 fold compared between Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice (N=4 mice per group; p<0.05). Data show in log2 (sample/wild-type). 2 Supplemental Figure 2. Sting signaling is essential for immuno-phenotypes of the Fcgr2b-/-lupus mice. (A-C) Flow cytometry analysis of splenocytes isolated from wild-type, Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice at the age of 6-7 months (N= 13-14 per group). Data shown in the percentage of (A) CD4+ ICOS+ cells, (B) B220+ I-Ab+ cells and (C) CD138+ cells. Data show as mean ± SEM (*p < 0.05, **p<0.01 and ***p<0.001). 3 Supplemental Figure 3. Phenotypes of Sting activated dendritic cells. (A) Representative of western blot analysis from immunoprecipitation with Sting of Fcgr2b-/- mice (N= 4). The band was shown in STING protein of activated BMDC with DMXAA at 0, 3 and 6 hr. and phosphorylation of STING at Ser357. (B) Mass spectra of phosphorylation of STING at Ser357 of activated BMDC from Fcgr2b-/- mice after stimulated with DMXAA for 3 hour and followed by immunoprecipitation with STING. (C) Sting-activated BMDC were co-cultured with LYN inhibitor PP2 and analyzed by flow cytometry, which showed the mean fluorescence intensity (MFI) of IAb expressing DC (N = 3 mice per group). 4 Supplemental Table 1. Lists of up and down of regulated proteins Accession No. -
Vitellogenic Oocytes
CELL STRUCTURE AND FUNCTION 26: 693–703 (2001) © 2001 by Japan Society for Cell Biology Somatic Lamins in Germinal Vesicles of Goldfish (Carassius auratus) Vitellogenic Oocytes Akihiko Yamaguchi1 and Yoshitaka Nagahama Laboratory of Reproductive Biology, Department of Developmental Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan 1Present address: Laboratory of Marine Biology, Department of Animal and Marine Bioresouruce Science, Faculty of Agriculture, Kyushu Univsity, Fukuoka, Japan ABSTRACT. In fish and amphibians, B-type lamins are divided into somatic (B1, B2) and oocyte-type (B3) lamins. In this study, we purified nuclear lamins from rainbow trout erythrocytes, raised an anti-lamin mono- clonal antibody (L-200) that recognizes goldfish somatic-lamins, and isolated cDNAs encoding goldfish B-type lamins (B1 and B2) from a goldfish cell culture cDNA library. Goldfish B-type lamins are structurally similar to lamins found in other vertebrates with minor amino acid substitutions in the conserved region. Western blot anal- ysis showed that goldfish oocytes contained mainly GV-lamin B3 as well as some somatic lamins. Laser-confocal microscope observations revealed that lamin B3 was present only in GV nuclear lamina, whereas somatic lamins were present in dense fibrillar structures throughout nuclear gels of isolated GVs. Similar nuclear filamentous structures were also observed in GVs of paraffin embedded oocytes. Epitope mapping indicated that L-200 recognized a conserved region containing a short stretch of the -helix coiled-coil rod domain (Y(E/Q)(Q/E)LL). A similar motif is also present in other cytoplasmic intermediate filaments (i.e., vimentin, desmin, peripherin and GFAP). Taken together, these findings suggest that lamins or lamin-related intermediate filaments are an impor- tant component of the interior architecture of goldfish vitellogenic oocyte nuclei (GVs). -
Non-Coding RNA: X-Chromosome Inactivation Unravelled
RESEARCH HIGHLIGHTS Nature Reviews Molecular Cell Biology | AOP, published online 8 May 2015; doi:10.1038/nrm3998 NON-CODING RNA X-chromosome inactivation unravelled The long non-coding RNA (lncRNA) specific and reproducible set of ten suggesting that SAFA acts to localize Xist (X inactive-specific transcript) is proteins that directly interact with Xist to genomic DNA. Depleting required for the transcriptional silenc- Xist. Of these proteins, knocking Xist binds to SHARP led to the retention of Pol II ing of one X chromosome in each cell, down the genes encoding scaffold SHARP to at Xist-coated X chromosomes, in a process known as X-chromosome attachment factor A (SAFA; also recruit SMRT indicating that SHARP might be inactivation (XCI) that occurs during known as HNRNPU), SMRT- and required for initiating transcriptional mammalian female development. HDAC1-associated repressor protein and activate silencing following Xist localization, Owing to technical limitations, little (SHARP; also known as SPEN or HDAC3 … possibly by recruiting the transcrip- is known about the mechanism of MSX2-interacting protein) and resulting in tional co-repressors SMRT and transcriptional silencing during XCI. lamin-B receptor (LBR) largely abol- HDAC3. Indeed, depleting SMRT McHugh et al. now describe using ished the silencing of XCI‑affected gene silencing or HDAC3 (but not other HDACs) RNA antisense purification followed genes in the male ES cells as well as in abrogated Xist-dependent gene by quantitative mass spectrometry differentiating female ES cells. These silencing. Another feature of XCI (RAP–MS) — a novel approach for three proteins are therefore required is the recruitment of the Polycomb identifying proteins that directly for Xist-mediated gene silencing. -
Nuclear Envelope Laminopathies: Evidence for Developmentally Inappropriate Nuclear Envelope-Chromatin Associations
Nuclear Envelope Laminopathies: Evidence for Developmentally Inappropriate Nuclear Envelope-Chromatin Associations by Jelena Perovanovic M.S. in Molecular Biology and Physiology, September 2009, University of Belgrade M.Phil. in Molecular Medicine, August 2013, The George Washington University A Dissertation submitted to The Faculty of The Columbian College of Arts and Sciences of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 31, 2015 Dissertation directed by Eric P. Hoffman Professor of Integrative Systems Biology The Columbian College of Arts and Sciences of The George Washington University certifies that Jelena Perovanovic has passed the Final Examination for the degree of Doctor of Philosophy as of May 5, 2015. This is the final and approved form of the dissertation. Nuclear Envelope Laminopathies: Evidence for Developmentally Inappropriate Nuclear Envelope-Chromatin Associations Jelena Perovanovic Dissertation Research Committee: Eric P. Hoffman, Professor of Integrative Systems Biology, Dissertation Director Anamaris Colberg-Poley, Professor of Integrative Systems Biology, Committee Member Robert J. Freishtat, Associate Professor of Pediatrics, Committee Member Vittorio Sartorelli, Senior Investigator, National Institutes of Health, Committee Member ii © Copyright 2015 by Jelena Perovanovic All rights reserved iii Acknowledgments I am deeply indebted to countless individuals for their support and encouragement during the past five years of graduate studies. First and foremost, I would like to express my gratitude to my mentor, Dr. Eric P. Hoffman, for his unwavering support and guidance, and keen attention to my professional development. This Dissertation would not have been possible without the critical input he provided and the engaging environment he created. -
The Microtubule Poison Vinorelbine Kills Cells Independently of Mitotic Arrest and Targets Cells Lacking the APC Tumour Suppressor More Effectively
Research Article 887 The microtubule poison vinorelbine kills cells independently of mitotic arrest and targets cells lacking the APC tumour suppressor more effectively Daniel M. Klotz1, Scott A. Nelson1, Karin Kroboth2, Ian P. Newton1, Sorina Radulescu3, Rachel A. Ridgway3, Owen J. Sansom3, Paul L. Appleton1 and Inke S. Na¨thke1,* 1Division of Cell and Developmental Biology, 2Division of Molecular Medicine, University of Dundee, Dow Street, Dundee, DD1 5EH, UK 3The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK *Author for correspondence ([email protected]) Accepted 28 September 2011 Journal of Cell Science 125, 887–895 ß 2012. Published by The Company of Biologists Ltd doi: 10.1242/jcs.091843 Summary Colorectal cancers commonly carry truncation mutations in the adenomatous polyposis coli (APC) gene. The APC protein contributes to the stabilization of microtubules. Consistently, microtubules in cells lacking APC depolymerize more readily in response to microtubule-destabilizing drugs. This raises the possibility that such agents are suitable for treatment of APC-deficient cancers. However, APC-deficient cells have a compromised spindle assembly checkpoint, which renders them less sensitive to killing by microtubule poisons whose toxicity relies on the induction of prolonged mitotic arrest. Here, we describe the novel discovery that the clinically used microtubule-depolymerizing drug vinorelbine (Navelbine) kills APC-deficient cells in culture and in intestinal tissue more effectively than it kills wild-type cells. This is due to the ability of vinorelbine to kill cells in interphase independently of mitotic arrest. Consistent with a role for p53 in cell death in interphase, depletion of p53 renders cells less sensitive to vinorelbine, but only in the presence of wild-type APC. -
Deficiencies in Lamin B1 and Lamin B2 Cause Neurodevelopmental Defects and Distinct Nuclear Shape Abnormalities in Neurons
M BoC | ARTICLE Deficiencies in lamin B1 and lamin B2 cause neurodevelopmental defects and distinct nuclear shape abnormalities in neurons Catherine Coffiniera, Hea-Jin Jungb, Chika Nobumoria, Sandy Changa, Yiping Tua, Richard H. Barnes IIa, Yuko Yoshinagac, Pieter J. de Jongc, Laurent Vergnesd, Karen Reued, Loren G. Fonga, and Stephen G. Younga,d aDepartment of Medicine and bMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095; cChildren’s Hospital Oakland Research Institute, Oakland, CA 94609; dDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 ABSTRACT Neuronal migration is essential for the development of the mammalian brain. Monitoring Editor Here, we document severe defects in neuronal migration and reduced numbers of neurons in Thomas Michael Magin lamin B1–deficient mice. Lamin B1 deficiency resulted in striking abnormalities in the nuclear University of Leipzig shape of cortical neurons; many neurons contained a solitary nuclear bleb and exhibited an Received: Jun 13, 2011 asymmetric distribution of lamin B2. In contrast, lamin B2 deficiency led to increased numbers Revised: Sep 9, 2011 of neurons with elongated nuclei. We used conditional alleles for Lmnb1 and Lmnb2 to create Accepted: Sep 23, 2011 forebrain-specific knockout mice. The forebrain-specificLmnb1- and Lmnb2-knockout models had a small forebrain with disorganized layering of neurons and nuclear shape abnormalities, similar to abnormalities identified in the conventional knockout mice. A more severe pheno- type, complete atrophy of the cortex, was observed in forebrain-specific Lmnb1/Lmnb2 double-knockout mice. This study demonstrates that both lamin B1 and lamin B2 are essential for brain development, with lamin B1 being required for the integrity of the nuclear lamina, and lamin B2 being important for resistance to nuclear elongation in neurons. -
Supplementary Table S4
Supplementary Table 4. Proteins with differentially regulated phosphopeptides corresponding to the cytoskeleton group according to DAVID GO analysis. Phosphopeptides corresponding to 91 different proteins were found differentially regulated and enriched in the cluster group cytoskeleton by GO analysis. Swissprot Accession numbers and Protein Names are listed. Swissprot Accession Protein Name 796257 A kinase (PRKA) anchor protein 12 805574 CAP, adenylate cyclase-associated protein 1 (yeast) 791903 CTTNBP2 N-terminal like 822287 DEAH (Asp-Glu-Ala-His) box polypeptide 9 811814 FERM domain containing 4A 776468 FK506 binding protein 15, 133kDa 789474 G protein-coupled receptor kinase interacting ArfGAP 1 779713 LIM domain and actin binding 1 825345 MAP7 domain containing 1 811248 MYC binding protein 2 817876 N-myc downstream regulated 1 795829 PDZ and LIM domain 7 (enigma) 774165 PTK2 protein tyrosine kinase 2 816535 Rho GTPase activating protein 21 818916 Rho/Rac guanine nucleotide exchange factor (GEF) 2 797168 SH3 and PX domains 2A 823031 SH3-domain kinase binding protein 1 800683 TPX2, microtubule-associated, homolog (Xenopus laevis) 782161 abl-interactor 1 794307 adducin 1 (alpha) 778958 adducin 3 (gamma) 805050 anillin, actin binding protein 788291 ankyrin 3, node of Ranvier (ankyrin G) 817614 annexin A1 815142 cell division cycle 2, G1 to S and G2 to M 824974 cell division cycle associated 8 824809 centrosomal protein 170kDa 803713 chromobox homolog 1 (HP1 beta homolog Drosophila ) 809850 chromosome 13 open reading frame 3 823922 cortactin -
Irreversible Modifications of Chromatin and the Nuclear Lamina: a Review Inside the Nuclear Origin of Alzheimer's Disease
Revista Mexicana de Neurociencia REVIEW ARTICLE Irreversible modifications of chromatin and the nuclear lamina: A review inside the nuclear origin of Alzheimer’s disease Laura Gil1¶, Gabriela Capdeville2*¶, Ildefonso Rodríguez-Leyva3, Sandra A. Niño4, and María E. Jiménez-Capdeville4 1Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, Madrid, España; 2Escuela de Medicina, Universidad Panamericana, Mexico City; 3Servicio de Neurología, Hospital Central “Ignacio Morones Prieto”, San Luis Potosí; 4Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico ¶These authors contributed equally in this study. Abstract Dementia is a public health problem with an extraordinary increase in recent years. Alzheimer’s disease (AD) is the most common cause of dementia. This disease has been considered a consequence of cytoplasmic and extracellular accumula- tions of Tau protein and β- amyloid, respectively. Nevertheless, a nuclear origin of AD has recently emerged. Both Tau protein and the nuclear lamin protect the nuclear and chromatin organization for proper gene expression throughout neuronal life. Accumulation of DNA damage, mainly as a result of aging, drives post-mitotic neurons to initiate DNA repair by entering the cell cycle. The complexity of the nucleus-cytoskeleton prevents neurons from dividing and condemns them to a state of hyperdiploidy ending in neuronal death, after transiently prolonging their life. In AD, hippocampal neurons survive their fatal fate by triggering an aberrant structural and functional transformation of the nucleus. Lamin A expression and Tau protein transfer to the cytoplasm results in loss of the protector role of nuclear Tau and the subsequent global chromatin disorgani- zation. -
A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 2021. 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 4.0 International license. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases Julia Y. Wang1*, Michael W. Roehrl1, Victor B. Roehrl1, and Michael H. Roehrl2* 1 Curandis, New York, USA 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA * Correspondence: [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 2021. 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 4.0 International license. Abstract Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. -
Lamin B1 Is Required for Mature Neuron-Specific Gene Expression
ARTICLE Received 4 Jul 2016 | Accepted 28 Feb 2017 | Published 20 Apr 2017 DOI: 10.1038/ncomms15098 OPEN Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation Crystal M. Gigante1,2, Michele Dibattista3,4, Frederick N. Dong1, Xiaobin Zheng2, Sibiao Yue2, Stephen G. Young5, Johannes Reisert3, Yixian Zheng2 & Haiqing Zhao1 B-type lamins are major constituents of the nuclear lamina in all metazoan cells, yet have specific roles in the development of certain cell types. Although they are speculated to regulate gene expression in developmental contexts, a direct link between B-type lamins and developmental gene expression in an in vivo system is currently lacking. Here, we identify lamin B1 as a key regulator of gene expression required for the formation of functional olfactory sensory neurons. By using targeted knockout in olfactory epithelial stem cells in adult mice, we show that lamin B1 deficient neurons exhibit attenuated response to odour stimulation. This deficit can be explained by decreased expression of genes involved in mature neuron function, along with increased expression of genes atypical of the olfactory lineage. These results support that the broadly expressed lamin B1 regulates expression of a subset of genes involved in the differentiation of a specific cell type. 1 Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA. 2 Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA. 3 Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104, USA. 4 Department of Basic Medical Sciences, Neuroscience and Sensory Organs, University of Bari ‘A. Moro’, Bari 70121, Italy. 5 Department of Medicine, Molecular Biology Institute and Department of Human Genetics, University of California, Los Angeles, California 90095, USA.