DOCSLIB.ORG

Epigenetics Meets Metabolism Through PHB-Mediated Histone H3.3 Deposition by HIRA

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Epigenetics Meets Metabolism Through PHB-Mediated Histone H3.3 Deposition by HIRA Editorial Page 1 of 5 Epigenetics meets metabolism through PHB-mediated histone H3.3 deposition by HIRA Ronen Marmorstein1, Peter D. Adams2 1Department of Biochemistry and Biophysics, the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; 2Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA Correspondence to: Ronen Marmorstein. Department of Biochemistry and Biophysics, the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Email: [email protected]. Provenance: This is an invited Editorial commissioned by Editor-in-Chief Zhizhuang Joe Zhao (Pathology Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, USA). Comment on: Zhu Z, Li C, Zeng Y, et al. PHB Associates with the HIRA Complex to Control an Epigenetic-Metabolic Circuit in Human ESCs. Cell Stem Cell 2017;20:274-89.e7. Received: 16 April 2017; Accepted: 25 April 2017; Published: 26 May 2017. doi: 10.21037/sci.2017.05.08 View this article at: http://dx.doi.org/10.21037/sci.2017.05.08 The regulation of chromatin, the histone-mediated pluripotency/self-renewal factors in human embryonic packaged form of DNA in the eukaryotic nucleus, underlies stem cells (hESCs), leading to the identification of the epigenetic control of gene expression (1). Epigenetic prohibitin (PHB) as one such factor (Figure 1). PHB is an regulators include DNA and histone modifying enzymes, evolutionarily conserved and ubiquitous expressed protein proteins that specifically target native or modified DNA that has previously been implicated in mitochondrial and histones, non-coding RNA molecules and histone function and morphology, cell signaling and transcriptional chaperone and ATP-dependent remodeling complexes regulation (6). To validate the importance of PHB as a that deposit, move or evict canonical or variant histones. pluripotency factor in hESCs, Zhu et al. observed that While the mode of chromatin targeting of many epigenetic PHB expression was high in undifferentiated hESCs and factors has been delineated (2), the mechanism of histone showed that PHB knock down (KD) induced extensive chaperone complex recruitment for specific histone differentiation in hESCs. A global gene expression analysis deposition is not understood. One such histone chaperone of a PHB KD in hESCs revealed that upregulated genes complex contains the proteins HIRA, Ubinuclein-1 (UBN1), are associated with cell differentiation and organismal CABIN1 and transiently associated ASF1 to deposit the development, while down-regulated genes are associated histone H3.3 variant at the promoters of active and poised with gene ontology terms chromatin modification, glucose genes, bodies of active genes, developmental genes, active metabolism and RNA processing, together suggesting that enhancers and sites of DNA and chromatin damage and PHB might mediate self-renewal through maintaining repair (3) (Figure 1). A recent study demonstrates that the hESC chromatin landscape and metabolic state. The the single stranded DNA-binding protein replication connection of PHB to chromatin regulation was reinforced protein A (RPA) cooperates with the HIRA complex to by the finding that, compared to control cells, PHB KD deposit newly synthesized H3.3 during the G1 phase of hESCs had higher levels of mono-, di-, and tri-methylated the cell cycle at gene transcription regulatory elements (4) histone 3 lysine 4 (H3K4), histone 3 lysine 27 (H3K27) as (Figure 1). However, how HIRA mediates H3.3 deposition well as tri-methylated histone 3 lysine 9 (H3K9) and histone independent of the cell cycle remained unknown. A recent 3 lysine 36 (H3K36). report by Zhu et al. sheds some light on this area (5). To understand more about the molecular function of Zhu et al. carried out a genome-wide siRNA screen for PHB, Zhu et al. searched for associated proteins through © Stem Cell Investigation. All rights reserved. sci.amegroups.com Stem Cell Investig 2017;4:46 Page 2 of 5 Stem Cell Investigation, 2017 H3.3 dep. at pluripotency and key metabolic genes including IDH PHB RPA PRC2 H3.3 H3.3 dep. at H3.3 dep. HIRA Complex developmentally regulated poised during G1 H4 genes ??? H3.3 dep. at promoters, enhancers, gene bodies and sites of repair Figure 1 HIRA-mediated histone H3.3 deposition pathways. An illustration of the different modes of HIRA complex-mediated histone H3.3/H4 deposition (dep.). The four pathways are not necessarily mutually exclusive. PHB, prohibitin; RPA, replication protein A. immunoprecipitation and mass spectrometry, leading to fate (7). One example of this is the metabolite α-ketoglutarate the identification of HIRA as an associated factor. This (α-KG), a TCA cycle intermediate generated by isocitrate interaction was validated through co-immunoprecipitation dehydrogenases (IDHs) (8). α-KG is also an essential (co-IP) experiments and subsequently mapped, through cofactor of dioxygenases, such as jumonji (JMJ) family deletion analysis to primarily an N-terminal WD40 histone demethylases (9) and ten-eleven translocation (TET) repeat of HIRA and a central conserved PHB domain of family methylated DNA hydroxylases (10). While the TET PHB. Interaction of these two proteins was subsequently enzymes can mediate one or more steps in a multi-step DNA demonstrated with recombinant proteins, thus implicating a demethylation process, at least some of the JMJ enzymes are direct interaction. bona fide histone demethylases. Given that HIRA forms a complex with UBN1 and Given that the elevated histone methylation phenotype CABIN1, the authors asked if PHB could interact with induced by PHB or HIRA KD in hESCs resembled the these other subunits of the HIRA complex. As expected, histone methylation alterations observed with IDH1 the authors found that PHB could co-IP each of the HIRA mutations and reduced α-KG production, Zhu et al. asked complex subunits from HEK293T cells. Moreover, gel whether disruption of the PHB and HIRA complexes could filtration analysis indicated that PHB and each of the HIRA affect the IDH/α-KG metabolic pathway. They found that complex subunits and H3.3 coexist in the same gel filtration PHB or HIRA KD in hESCs decreased IDH and α-KG fraction. PHB was also found in HIRA free fractions, levels, and that the levels of α-KG correlated inversely with suggesting that a proportion of PHB exists unbound to the same methylated histones after KD of PHB and HIRA HIRA. To validate the functional importance of the PHB/ levels in hESCs. Taken together, this data links PHB and HIRA complex interaction in expression of pluripotency the HIRA histone chaperone complex to the expression genes in hESC, Zhu et al. demonstrated that, like PHB KD, of IDH genes and hence production of α-KG and histone HIRA−/− hESCs displayed a differentiated cell morphology demethylation (Figure 1). and had reduced expression levels of core pluripotency To understand how PHB and HIRA are functionally factors, with concomitant upregulation of various lineage connected to IDH gene expression and thus α-KG levels, marker genes, and exhibited the same perturbed histone Zhu et al. carried out genome wide H3.3 ChIP-seq in modification patterns as thePHB KD. hESCs stably expressing H3.3B-HA treated with NT Metabolic states of the cell have been shown to impact (control), PHB, or HIRA siRNA. As anticipated, they found the role of epigenetic mechanisms in determining stem cell that H3.3 is selectively enriched at transcriptionally active © Stem Cell Investigation. All rights reserved. sci.amegroups.com Stem Cell Investig 2017;4:46 Stem Cell Investigation, 2017 Page 3 of 5 genes over less active genes. In addition, KD of PHB or chromatin dynamics in non-proliferating senescent cells (12). HIRA reduced H3.3 levels at active genes. Bioinformatics The important role of HIRA in contributing to the analysis of the H3.3 regions with >1.5 reduction of ChIP- maintenance of both senescence and hESCs through histone seq reads in both PHB and HIRA KD cells indicated that H3.3 deposition implicates a broader role of the HIRA these regions were enriched at genes involved in cellular histone chaperone complex and the histone H3.3 histone metabolic processes, the cell cycle, chromatin binding, and variant in maintaining cell identity. Consistent with this, Allis transcription regulation. Subsequent ChIP-seq of PHB and and coworkers previously revealed a role for HIRA in lineage HIRA demonstrated that these proteins were simultaneously determination in ESCs (13). recruited to IDH genes, as well as other pluripotency and The mechanism for how PHB contributes to HIRA- development-associated genes in hESCs, such as OCT4 and mediated histone H3.3 deposition is not clear. The studies NANOG (11). Moreover, KD of PHB and HIRA decreased by Zhu et al. demonstrate that HIRA and PHB directly H3.3 deposition at all these genes, and decreased the active interact. Given that PHB has been shown to interact transcription markers H3K4me3, RNA polymerase II S5P with DNA-binding transcription factors such as nuclear and elongation RNA polymerase II S2P. This data links receptors (14,15), it is possible that it might mediate the PHB to HIRA-mediated H3.3 deposition to activation of recruitment of the HIRA histone chaperone complex to transcription of IDH genes to produce α-KG, a cofactor for specific chromatin regions for histone H3.3 deposition. histone demethylation. Gel filtration analysis of proteins from hESC cells reveals To further investigate the temporal relationship between a fraction that contains PHB and each of the components PHB function, the epigenetic-metabolic circuitry and of the HIRA complex and histone H3.3. However, the hESC identify, Zhu et al. characterized PHB-depleted elution pattern of each of the proteins does not precisely hESC cells from 0 to 4 days. These studies suggested that a co-migrate, suggesting that both HIRA and PHB are also reduction of HIRA complex components could be the first part of other complexes.
Load more

Recommended publications
  • REPORT Germline Mutation of INI1/SMARCB1 in Familial Schwannomatosis
    REPORT Germline Mutation of INI1/SMARCB1 in Familial Schwannomatosis Theo J. M. Hulsebos, Astrid S. Plomp, Ruud A. Wolterman, Els C. Robanus-Maandag, Frank Baas, and Pieter Wesseling Patients with schwannomatosis develop multiple schwannomas but no vestibular schwannomas diagnostic of neurofi- bromatosis type 2. We report an inactivating germline mutation in exon 1 of the tumor-suppressor gene INI1 in a father and daughter who both had schwannomatosis. Inactivation of the wild-type INI1 allele, by a second mutation in exon 5 or by clear loss, was found in two of four investigated schwannomas from these patients. All four schwannomas displayed complete loss of nuclear INI1 protein expression in part of the cells. Although the exact oncogenetic mechanism in these schwannomas remains to be elucidated, our findings suggest that INI1 is the predisposing gene in familial schwannomatosis. Schwannomatosis (MIM 162091) is characterized by the 10 Only two families with an INI1 germline mutation, an development of multiple spinal, peripheral, and cranial- exon 4 frameshift mutation,11 and an exon 7 donor splice nerve schwannomas in the absence of vestibular schwan- site mutation12 have been described in which multiple nomas.1 The presence of vestibular schwannomas is di- generations were affected by malignant (rhabdoid) tumors agnostic of neurofibromatosis type 2 (NF2 [MIM 101000]). in infancy. In both of these families, clear cases of no- Molecular analyses identified somatically acquired mu- nexpressing obligate carriers of the INI1 mutation were
    [Show full text]
  • 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.
    [Show full text]
  • The H3.3 Chaperone Hira Complex Orchestrates Oocyte Developmental Competence
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.25.114124; this version posted May 26, 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. The H3.3 chaperone Hira complex orchestrates oocyte developmental competence Rowena Smith1, *, Zongliang Jiang2, *, Andrej Susor3, Hao Ming2, Janet Tait1, Marco Conti4, and Chih-Jen Lin1,5 1MRC Centre For Reproductive Health, University oF Edinburgh Queen’s Medical Research Institute 47 Little France Crescent, Edinburgh, United Kingdom, EH16 4TJ 2 School oF Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA, 70803, USA 3 Laboratory oF Biochemistry and Molecular Biology oF Germ Cells, Institute oF Animal Physiology and Genetics, CAS, Rumburska 89, 277 21 Libechov, Czech Republic 4Center For Reproductive Sciences, University oF CaliFornia, San Francisco, CA 94143, USA 5To whom correspondence should be addressed. Tel: +44 131 242 6237; Email: [email protected] *equal contribution bioRxiv preprint doi: https://doi.org/10.1101/2020.05.25.114124; this version posted May 26, 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 Reproductive success relies on a healthy oocyte competent For Fertilisation and capable of sustaining early embryo development. By the end oF oogenesis, the oocyte is characterised by a transcriptionally silenced state, but the signiFicance oF this state and how it is achieved remains poorly understood.
    [Show full text]
  • Control Association Analysis of CABIN1 with Schizophrenia in a Japanese Population
    Journal of Human Genetics (2010) 55, 179–181 & 2010 The Japan Society of Human Genetics All rights reserved 1434-5161/10 $32.00 www.nature.com/jhg SHORT COMMUNICATION A case–control association analysis of CABIN1 with schizophrenia in a Japanese population Yuichiro Watanabe1,2, Ayako Nunokawa1, Naoshi Kaneko1 and Toshiyuki Someya1 Calcineurin (CN) is a calcium/calmodulin-dependent serine/threonine protein phosphatase and regulates neuronal structure, neurotransmission and activity-dependent gene expression. Several studies have indicated that CN signaling is likely to be involved in the pathogenesis of schizophrenia. The gene encoding CN-binding protein 1 (CABIN1) is located on 22q11.23, one of the common susceptibility loci for schizophrenia. Therefore, CABIN1 is a promising functional and positional candidate gene for schizophrenia. To assess whether CABIN1 is implicated in vulnerability to schizophrenia, we conducted a case–control association study between CABIN1 and schizophrenia. The results showed no evidence of an association between CABIN1 and schizophrenia using 11 tagging single nucleotide polymorphisms in 1193 Japanese subjects. Our results suggest that CABIN1 may not confer increased susceptibility for schizophrenia in the Japanese population. Journal of Human Genetics (2010) 55, 179–181; doi:10.1038/jhg.2009.136; published online 15 January 2010 Keywords: CABIN1; case–control study; schizophrenia; tagging SNP Schizophrenia is a complex genetic disorder that affects approximately one study. Fallin et al.10 examined seven polymorphisms in CABIN1 1% of the global population. The pathogenesis of schizophrenia is with an average density of one marker per 20.9 kb and failed to find currently unclear, but there is cumulative evidence that calcineurin any association with schizophrenia.
    [Show full text]
  • Molecular-Genetic Mechanisms of Memory Formation in Mouse Models of Neurodevelopmental and Neuropsychiatric Disorders
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2014 Molecular-Genetic Mechanisms of Memory Formation in Mouse Models of Neurodevelopmental and Neuropsychiatric Disorders Hannah Schoch University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Neuroscience and Neurobiology Commons Recommended Citation Schoch, Hannah, "Molecular-Genetic Mechanisms of Memory Formation in Mouse Models of Neurodevelopmental and Neuropsychiatric Disorders" (2014). Publicly Accessible Penn Dissertations. 1435. https://repository.upenn.edu/edissertations/1435 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1435 For more information, please contact [email protected]. Molecular-Genetic Mechanisms of Memory Formation in Mouse Models of Neurodevelopmental and Neuropsychiatric Disorders Abstract Neurodevelopmental and neuropsychiatric disorders are a significant and expanding global health crisis. Many individuals affected by these disorders have social and cognitive symptoms represent significant sources of ongoing disability that are refractory to available treatment options. The search for cures and therapies for disorders fundamentally requires an understanding of the core neuropathology and insight into the underlying molecular mechanisms at work. In this dissertation, I describe experiments that we performed to explore molecular and genetic mechanisms underlying memory impairment and enhancement
    [Show full text]
  • Whole-Exome Sequencing of 81 Individuals from 27 Multiply Affected Bipolar Disorder Families Andreas J
    Forstner et al. Translational Psychiatry (2020) 10:57 https://doi.org/10.1038/s41398-020-0732-y Translational Psychiatry ARTICLE Open Access Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families Andreas J. Forstner1,2,3,4, Sascha B. Fischer 3,5,LorenaM.Schenk2,JanaStrohmaier 6,7, Anna Maaser-Hecker2, Céline S. Reinbold3,5,8, Sugirthan Sivalingam 2, Julian Hecker9,FabianStreit 6, Franziska Degenhardt2, Stephanie H. Witt 6, Johannes Schumacher1,2, Holger Thiele10, Peter Nürnberg10, José Guzman-Parra11, Guillermo Orozco Diaz12, Georg Auburger13,MargotAlbus14, Margitta Borrmann-Hassenbach14,MariaJoséGonzaleź 11, Susana Gil Flores15, Francisco J. Cabaleiro Fabeiro16, Francisco del Río Noriega17, Fermin Perez Perez18, Jesus Haro González19,FabioRivas20, Fermin Mayoral20,MichaelBauer 21, Andrea Pfennig21, Andreas Reif 22, Stefan Herms 2,3,5, Per Hoffmann2,3,5,23, Mehdi Pirooznia24, Fernando S. Goes 24, Marcella Rietschel 6, Markus M. Nöthen2 and Sven Cichon2,3,5,23 Abstract Bipolar disorder (BD) is a highly heritable neuropsychiatric disease characterized by recurrent episodes of depression and mania. Research suggests that the cumulative impact of common alleles explains 25–38% of phenotypic variance, and that rare variants may contribute to BD susceptibility. To identify rare, high-penetrance susceptibility variants for BD, whole-exome sequencing (WES) was performed in three affected individuals from each of 27 multiply affected families from Spain and Germany. WES identified 378 rare, non-synonymous, and potentially functional variants. These spanned 368 genes, and were carried by all three affected members in at least one family. Eight of the 368 genes harbored rare variants that were implicated in at least two independent families.
    [Show full text]
  • Ubinuclein-1 Confers Histone H3.3-Specific-Binding by the HIRA
    ARTICLE Received 22 Apr 2015 | Accepted 1 Jun 2015 | Published 10 Jul 2015 DOI: 10.1038/ncomms8711 OPEN Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex M. Daniel Ricketts1,2, Brian Frederick3, Henry Hoff3, Yong Tang3, David C. Schultz3, Taranjit Singh Rai4,5, Maria Grazia Vizioli4, Peter D. Adams4 & Ronen Marmorstein1,2,6 Histone chaperones bind specific histones to mediate their storage, eviction or deposition from/or into chromatin. The HIRA histone chaperone complex, composed of HIRA, ubinuclein-1 (UBN1) and CABIN1, cooperates with the histone chaperone ASF1a to mediate H3.3-specific binding and chromatin deposition. Here we demonstrate that the conserved UBN1 Hpc2-related domain (HRD) is a novel H3.3-specific-binding domain. Biochemical and biophysical studies show the UBN1-HRD preferentially binds H3.3/H4 over H3.1/H4. X-ray crystallographic and mutational studies reveal that conserved residues within the UBN1-HRD and H3.3 G90 as key determinants of UBN1–H3.3-binding specificity. Comparison of the structure with the unrelated H3.3-specific chaperone DAXX reveals nearly identical points of contact between the chaperone and histone in the proximity of H3.3 G90, although the mechanism for H3.3 G90 recognition appears to be distinct. This study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA complex. 1 Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. 2 Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
    [Show full text]
  • Discovery and Systematic Characterization of Risk Variants and Genes For
    medRxiv preprint doi: https://doi.org/10.1101/2021.05.24.21257377; this version posted June 2, 2021. 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. It is made available under a CC-BY 4.0 International license . 1 Discovery and systematic characterization of risk variants and genes for 2 coronary artery disease in over a million participants 3 4 Krishna G Aragam1,2,3,4*, Tao Jiang5*, Anuj Goel6,7*, Stavroula Kanoni8*, Brooke N Wolford9*, 5 Elle M Weeks4, Minxian Wang3,4, George Hindy10, Wei Zhou4,11,12,9, Christopher Grace6,7, 6 Carolina Roselli3, Nicholas A Marston13, Frederick K Kamanu13, Ida Surakka14, Loreto Muñoz 7 Venegas15,16, Paul Sherliker17, Satoshi Koyama18, Kazuyoshi Ishigaki19, Bjørn O Åsvold20,21,22, 8 Michael R Brown23, Ben Brumpton20,21, Paul S de Vries23, Olga Giannakopoulou8, Panagiota 9 Giardoglou24, Daniel F Gudbjartsson25,26, Ulrich Güldener27, Syed M. Ijlal Haider15, Anna 10 Helgadottir25, Maysson Ibrahim28, Adnan Kastrati27,29, Thorsten Kessler27,29, Ling Li27, Lijiang 11 Ma30,31, Thomas Meitinger32,33,29, Sören Mucha15, Matthias Munz15, Federico Murgia28, Jonas B 12 Nielsen34,20, Markus M Nöthen35, Shichao Pang27, Tobias Reinberger15, Gudmar Thorleifsson25, 13 Moritz von Scheidt27,29, Jacob K Ulirsch4,11,36, EPIC-CVD Consortium, Biobank Japan, David O 14 Arnar25,37,38, Deepak S Atri39,3, Noël P Burtt4, Maria C Costanzo4, Jason Flannick40, Rajat M 15 Gupta39,3,4, Kaoru Ito18, Dong-Keun Jang4,
    [Show full text]
  • UNIVERSITY of CALIFORNIA, SAN DIEGO Measuring
    UNIVERSITY OF CALIFORNIA, SAN DIEGO Measuring and Correlating Blood and Brain Gene Expression Levels: Assays, Inbred Mouse Strain Comparisons, and Applications to Human Disease Assessment A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Biomedical Sciences by Mary Elizabeth Winn Committee in charge: Professor Nicholas J Schork, Chair Professor Gene Yeo, Co-Chair Professor Eric Courchesne Professor Ron Kuczenski Professor Sanford Shattil 2011 Copyright Mary Elizabeth Winn, 2011 All rights reserved. 2 The dissertation of Mary Elizabeth Winn is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2011 iii DEDICATION To my parents, Dennis E. Winn II and Ann M. Winn, to my siblings, Jessica A. Winn and Stephen J. Winn, and to all who have supported me throughout this journey. iv TABLE OF CONTENTS Signature Page iii Dedication iv Table of Contents v List of Figures viii List of Tables x Acknowledgements xiii Vita xvi Abstract of Dissertation xix Chapter 1 Introduction and Background 1 INTRODUCTION 2 Translational Genomics, Genome-wide Expression Analysis, and Biomarker Discovery 2 Neuropsychiatric Diseases, Tissue Accessibility and Blood-based Gene Expression 4 Mouse Models of Human Disease 5 Microarray Gene Expression Profiling and Globin Reduction 7 Finding and Accessible Surrogate Tissue for Neural Tissue 9 Genetic Background Effect Analysis 11 SPECIFIC AIMS 12 ENUMERATION OF CHAPTERS
    [Show full text]
  • MEF2I JCI-Final-5-30
    Supplemental Materials. 1. Extended Experimental Procedures 2. Supplemental Figure 1. qPCR of cardiac growth-associated genes. 3. Supplemental Figure 2. Echocardiographic measurements - TAC prevention model. 4. Supplemental Figure 3. Additional echocardiographic measurements - reversal model. 5. Supplemental Figure 4. HDAC5 nuclear localization. 6. Supplemental Table 1. Human clinical samples. 7. Supplemental Table 2. Blood chemistries of 8MI treated mice. 8. Supplemental Table 3. Annotations of hypertrophy-associated genes normalized by 8MI. 9. Supplemental Table 4. Ingenuity pathways and networks. 10.Supplemental Table 5. Gene Set Enrichment Analysis. Extended Experimental Procedures Reagents Antibodies were obtained from the following vendors: anti-MEF2 and anti-HDAC4 from Santa Cruz Biotechnology (Santa Cruz, California, USA), anti-GATA4 and anti-acetyl-lysine from Upstate (Charlottesville, Virginia, USA), anti-actin from Chemicon (Danvers, Massachusetts, USA), anti-HDAC5 and anti–p(S498)-HDAC5 were from Millipore and Abcam respectively. Trichostatin A (TSA) was purchased from Selleck Chemicals and MC1568 was provided by Sigma. The Amersham ECL Western detection system (GE Healthcare Bio-Sciences, Piscataway, New Jersey, USA) was used for chemiluminescence visualization of immunoblots. Reagents for real-time polymerase chain reaction (PCR) including Master Mix® and primers with TaqMan® probes were obtained from Applied Biosystems (Foster City, California, USA). RNA extraction was performed using Trizol (Molecular Research Center, Inc, Cincinnati, Ohio, USA). Rhodamine-conjugated phalloidin and wheat germ agglutinin (WGA) were purchased from Invitrogen (Carlsbad, California, USA). Myocyte cell culture Primary neonatal rat ventricular cardiomyocyte cultures were prepared from the hearts of 1- 3 day-old neonatal rat pups (Charles River, Wilmington, Massachusetts, USA) as previously described {Bishopric, 1991 #920}, by sequential digestion in a trypsin-containing calcium- free buffer and trituration.
    [Show full text]
  • Transcriptome Profiling Reveals the Complexity of Pirfenidone Effects in IPF
    ERJ Express. Published on August 30, 2018 as doi: 10.1183/13993003.00564-2018 Early View Original article Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska, Anna Gungl, Jochen Wilhelm, Leigh M. Marsh, Helene Thekkekara Puthenparampil, Katharina Sinn, Miroslava Didiasova, Walter Klepetko, Djuro Kosanovic, Ralph T. Schermuly, Lukasz Wujak, Benjamin Weiss, Liliana Schaefer, Marc Schneider, Michael Kreuter, Andrea Olschewski, Werner Seeger, Horst Olschewski, Malgorzata Wygrecka Please cite this article as: Kwapiszewska G, Gungl A, Wilhelm J, et al. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF. Eur Respir J 2018; in press (https://doi.org/10.1183/13993003.00564-2018). This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Copyright ©ERS 2018 Copyright 2018 by the European Respiratory Society. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska1,2, Anna Gungl2, Jochen Wilhelm3†, Leigh M. Marsh1, Helene Thekkekara Puthenparampil1, Katharina Sinn4, Miroslava Didiasova5, Walter Klepetko4, Djuro Kosanovic3, Ralph T. Schermuly3†, Lukasz Wujak5, Benjamin Weiss6, Liliana Schaefer7, Marc Schneider8†, Michael Kreuter8†, Andrea Olschewski1,
    [Show full text]
  • A Systems Immunology Approach Identifies the Collective Impact of Five Mirs in Th2 Inflammation Supplementary Information
    A systems immunology approach identifies the collective impact of five miRs in Th2 inflammation Supplementary information Ayşe Kılıç, Marc Santolini, Taiji Nakano, Matthias Schiller, Mizue Teranishi,Pascal Gellert, Yuliya Ponomareva, Thomas Braun, Shizuka Uchida, Scott T. Weiss, Amitabh Sharma and Harald Renz Corresponding Author: Harald Renz, MD Institute of Laboratory Medicine Philipps University Marburg 35043 Marburg, Germany Phone +49 6421 586 6235 [email protected] 1 Kılıç A et. al. 2018 A B C D PBS OVA chronic PAS PAS (cm H2O*s/ml (cm Raw Sirius Red Sirius Supplementary figure 1: Characteristic phenotype of the acute and chronic allergic airway inflammatory response in the OVA-induced mouse model. (a) Total and differential cell counts determined in BAL and cytospins show a dominant influx of eosinophils. (b) Serum titers of OVA-specific immunoglobulins are elevated. (c) Representative measurement of airway reactivity to increasing methacholine (Mch) responsiveness measured by head-out body plethysmography. (d) Representative lung section staining depicting airway inflammation and mucus production (PAS, original magnification x 10) and airway remodeling (SiriusRed; original magnification x 20). Data are presented as mean ± SEM and are representative for at least 3 independent experiments with n=8-10 animals per group. Statistical analyses have been performed with one-way ANOVA and Tukey’s post-test and show *p<0.05, **p<0.01 and ***p<0.001. 2 Kılıç A et. al. 2018 lymphocytes A lung activated CD4+-cells CD4+-T-cell-subpopulations SSC FSC ST2 live CD69 CD4 CXCR3 B spleen Naive CD4+- T cells DAPI FSC single cells SSC CD62L CD4 CD44 FSC FSC-W Supplementary figure 2.
    [Show full text]