DOCSLIB.ORG

UCLA UCLA Electronic Theses and Dissertations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
UCLA UCLA Electronic Theses and Dissertations UCLA UCLA Electronic Theses and Dissertations Title Global and Local Regulation of Gene Expression in the Human Brain Permalink https://escholarship.org/uc/item/83g7t3g1 Author Hartl, Christopher Publication Date 2019 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Global and Local Regulation of Gene Expression in the Human Brain A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Bioinformatics by Christopher Hartl 2019 © Copyright by Christopher Hartl 2019 ABSTRACT OF THE DISSERTATION Global and Local Regulation of Gene Expression in the Human Brain by Christopher Hartl Doctor of Philosophy in Bioinformatics University of California, Los Angeles, 2019 Professor Daniel H. Geschwind, Chair Neuropsychiatric disorders are behavioral conditions marked by intellectual, social, or emotional deficits that can be linked to diseases of the nervous system. Autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BP), major depressive disorder (MDD), and attention deficit and hyperactivity disorder (ADHD) are common, heritable diseases each with a prevalence exceeding 1% of the population, none of which can be characterized by discernable anatomical or neurological pathologies. Genetic association studies have identified mutations in hundreds of genes that contribute to risk for at least one of these disorders, and have shown that a substantial fraction of the genetic liability is shared between many of these neuropsychiatric diseases. It has long been hoped that with enough genetic evidence we will identify the biological pathways, developmental time points, and brain regions that, when disrupted, give rise to neuropsychiatric disorders. However, the cellular and functional complexity of the human ii brain, as well as the genetic complexity of neuropsychiatric disease, make it difficult to search for such convergence. In this thesis, I investigate global and local transcriptional regulation within and across 12 regions of the human brain in order to investigate the regional specificity of neuropsychiatric disorders. I develop novel bioinformatics methods – ranging from data processing to network construction – to identify whether the transcriptional regulation of a set of genes is shared or specific. I hypothesize that local, region-specific transcriptional regulation corresponds directly to cell types and processes that are specific to, or far more prevalent in, a given region; that cross-regional transcriptional regulation corresponds to cell types that show little heterogeneity across brain regions; and that genetic disruption of region-specific transcriptional programs results in regional susceptibility. I use a systems-biology approach to summarize transcriptional regulation into reproducibly co-expressed gene sets (“co-expression modules”), which can be analyzed statistically to identify common functions, pathways, and cell types. I then integrate data from genetic association studies to ascertain gene sets conferring outsized risk for neuropsychiatric disorders, thereby implicating the corresponding pathways for further investigation in disease etiology. Finally, I use the network structure itself to investigate the genetic architecture of ASD and SCZ in terms of omnigenics and network polygenics. Chapter 1 presents the biological background for the studies and summarizes some of the major studies of neuropsychiatric disorders along with their principal methods and conclusions. In chapter 2, utilizing my multi-regional co-expression approach, I identify 12 brain-wide, 114 region-specific, and 50 cross-regional co-expression modules. Nearly 40% of expressed genes fall into brain-wide modules and correspond to major cell classes and conserved biological iii processes, while region-specific modules comprise 25% of expressed genes and correspond to region-specific cell types. The detailed study in chapter 3 demonstrates that neuropsychiatric risk concentrates in both brain wide and multi-regional modules, implicating major core cell types in disease etiology but not region-specific susceptibility. Chapter 4 presents a new and more general framework for defining genetic networks. Using this framework, I show that the network pattern of ASD-associated rare loss-of-function mutations, as well as the large number of significant targets for trans master regulators in BP and SCZ, support a classical polygenic architecture with thousands of directly causal genes. These results suggest that a nontrivial component of risk for neuropsychiatric disease comes from the global polygenic disruption of neuronal function and neuronal maturation. iv The dissertation of Christopher Lee Hartl is approved. Michael Gandal Jason Ernst Bogdan Pasaniuc Daniel H. Geschwind, Committee Chair University of California, Los Angeles 2019 v Table of Contents Chapter 1 Systems biology approaches to neuropsychiatric disease ....................................... 1 1.1 Systems biology approaches to neuropsychiatric disease ..................................................... 2 1.1a Systems biology has implicated neuron-related pathways across neuropsychiatric disease ...... 3 1.1b Brain co-expression network analysis: an overview and 15-year summary ................................ 7 1.2 Heritability and etiology of complex neuropsychiatric disorders ........................................ 19 1.2a Heritability and genetic complexity of common neuropsychiatric disease ............................... 21 1.2b Quantitative genetics: partitioning risk into regulatory elements and cell types ..................... 24 1.3c Gene networks and genetic architecture: the omnigenetic model versus systems biology ...... 28 1.3 Conclusions .............................................................................................................................. 29 Chapter 2 The human brain co-expression network atlas ....................................................... 32 2.1 Abstract .................................................................................................................................... 33 2.2 Introduction ............................................................................................................................. 34 2.3 Results ...................................................................................................................................... 35 2.3a Estimating and validating co-expression from brain RNA-seq data ........................................... 35 2.3b Identifying and verifying specific and shared network modules ............................................... 40 2.3c Methodology has little impact on identified region-level and whole-brain modules ................ 44 2.3d Hierarchical networks elucidate sources of regional and global brain co-expression ............... 51 2.3e Cell-type-specific lncRNA and isoforms in the human brain ...................................................... 56 2.3f Region-specific upregulation: increased protein turnover in subcortical brain regions ............ 65 2.4 Discussion ................................................................................................................................ 68 2.5 Methods ................................................................................................................................... 70 Chapter 3 Linking neuropsychiatric disease to regional brain processes ................................. 90 3.1 Abstract .................................................................................................................................... 91 3.2 Introduction ............................................................................................................................. 91 3.3a Qualifying regional specificity of previously-identified neuropsychiatric disorder co-expression networks ............................................................................................................................................ 92 3.3b Convergence of molecular signatures of neuropsychiatric disease onto brain-wide neuronal modules ............................................................................................................................................. 97 3.3c Neuropsychiatric disease risk enriches in cortical and cerebellar modules which are differentially co-expressed in ASD brains ........................................................................................ 101 3.4 Discussion .............................................................................................................................. 105 3.5 Methods ................................................................................................................................. 106 Chapter 4 Network genetic architecture and the omnigenic disease model ......................... 109 4.1 Abstract .................................................................................................................................. 109 4.2 Introduction ........................................................................................................................... 109 4.3 Results .................................................................................................................................... 111 4.3a Likely high-penetrance ASD mutations do not exhibit omnigenic network enrichments ....... 111 4.3b Co-expression
Load more

Recommended publications
  • Mayr, Annu Rev Genet 2017
    GE51CH09-Mayr ARI 12 October 2017 10:21 Annual Review of Genetics Regulation by 3-Untranslated Regions Christine Mayr Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; email: [email protected] Annu. Rev. Genet. 2017. 51:171–94 Keywords First published as a Review in Advance on August noncoding RNA, regulatory RNA, alternative 3-UTRs, alternative 30, 2017 polyadenylation, cotranslational protein complex formation, cellular The Annual Review of Genetics is online at organization, mRNA localization, RNA-binding proteins, cooperativity, genet.annualreviews.org accessibility of regulatory elements https://doi.org/10.1146/annurev-genet-120116- 024704 Abstract Copyright c 2017 by Annual Reviews. 3 -untranslated regions (3 -UTRs) are the noncoding parts of mRNAs. Com- All rights reserved pared to yeast, in humans, median 3-UTR length has expanded approx- imately tenfold alongside an increased generation of alternative 3-UTR isoforms. In contrast, the number of coding genes, as well as coding region length, has remained similar. This suggests an important role for 3-UTRs in the biology of higher organisms. 3-UTRs are best known to regulate ANNUAL REVIEWS Further diverse fates of mRNAs, including degradation, translation, and localiza- Click here to view this article's tion, but they can also function like long noncoding or small RNAs, as has Annu. Rev. Genet. 2017.51:171-194. Downloaded from www.annualreviews.org online features: • Download figures as PPT slides been shown for whole 3 -UTRs as well as for cleaved fragments. Further- • Navigate linked references • Download citations more, 3 -UTRs determine the fate of proteins through the regulation of Access provided by Memorial Sloan-Kettering Cancer Center on 11/30/17.
    [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]
  • Dissertation
    Regulation of gene silencing: From microRNA biogenesis to post-translational modifications of TNRC6 complexes DISSERTATION zur Erlangung des DOKTORGRADES DER NATURWISSENSCHAFTEN (Dr. rer. nat.) der Fakultät Biologie und Vorklinische Medizin der Universität Regensburg vorgelegt von Johannes Danner aus Eggenfelden im Jahr 2017 Das Promotionsgesuch wurde eingereicht am: 12.09.2017 Die Arbeit wurde angeleitet von: Prof. Dr. Gunter Meister Johannes Danner Summary ‘From microRNA biogenesis to post-translational modifications of TNRC6 complexes’ summarizes the two main projects, beginning with the influence of specific RNA binding proteins on miRNA biogenesis processes. The fate of the mature miRNA is determined by the incorporation into Argonaute proteins followed by a complex formation with TNRC6 proteins as core molecules of gene silencing complexes. miRNAs are transcribed as stem-loop structured primary transcripts (pri-miRNA) by Pol II. The further nuclear processing is carried out by the microprocessor complex containing the RNase III enzyme Drosha, which cleaves the pri-miRNA to precursor-miRNA (pre-miRNA). After Exportin-5 mediated transport of the pre-miRNA to the cytoplasm, the RNase III enzyme Dicer cleaves off the terminal loop resulting in a 21-24 nt long double-stranded RNA. One of the strands is incorporated in the RNA-induced silencing complex (RISC), where it directly interacts with a member of the Argonaute protein family. The miRNA guides the mature RISC complex to partially complementary target sites on mRNAs leading to gene silencing. During this process TNRC6 proteins interact with Argonaute and recruit additional factors to mediate translational repression and target mRNA destabilization through deadenylation and decapping leading to mRNA decay.
    [Show full text]
  • Genomic and Transcriptomic Investigations Into the Feed Efficiency Phenotype of Beef Cattle
    Provided by the author(s) and NUI Galway in accordance with publisher policies. Please cite the published version when available. Title Genomic and transcriptomic investigations into the feed efficiency phenotype of beef cattle Author(s) Higgins, Marc Publication Date 2019-03-06 Publisher NUI Galway Item record http://hdl.handle.net/10379/15008 Downloaded 2021-09-25T18:07:39Z Some rights reserved. For more information, please see the item record link above. Genomic and Transcriptomic Investigations into the Feed Efficiency Phenotype of Beef Cattle Marc Higgins, B.Sc., M.Sc. A thesis submitted for the Degree of Doctor of Philosophy to the Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway. Supervisor: Dr. Derek Morris Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway. Supervisor: Dr. Sinéad Waters Teagasc, Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange. Submitted November 2018 Table of Contents Declaration ................................................................................................................ vii Funding .................................................................................................................... viii Acknowledgements .................................................................................................... ix Abstract ......................................................................................................................
    [Show full text]
  • This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G
    This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Identification and characterisation of novel factors involved in the nonsense-mediated mRNA decay (NMD) pathway Angela Casadio Thesis presented for the degree of Doctor of Philosophy The University of Edinburgh 2016 Declaration I declare that this thesis is of my own composition. The work presented in this thesis is my own, unless otherwise stated, and has not been presented for any other degree or professional qualification. Angela Casadio ii Acknowledgements First and foremost, I would like to thank my supervisor Javier for making this possible. I have really enjoyed working on a field I knew little about when I started my project, I’ve learnt a lot in the past four years and I will treasure the experience! A huge thank you goes to Dasa for all the help and good advice she gave me during the course of my PhD.
    [Show full text]
  • Clinical Impact of Copy Number Variation Changes in Bladder Cancer Samples
    EXPERIMENTAL AND THERAPEUTIC MEDICINE 22: 901, 2021 Clinical impact of copy number variation changes in bladder cancer samples VICTORIA SPASOVA1, BORIS MLADENOV2, SIMEON RANGELOV3, ZORA HAMMOUDEH1, DESISLAVA NESHEVA1, DIMITAR SERBEZOV1, RADA STANEVA1,4, SAVINA HADJIDEKOVA1,4, MIHAIL GANEV1, LUBOMIR BALABANSKI1,5, RADOSLAVA VAZHAROVA5,6, CHAVDAR SLAVOV3, DRAGA TONCHEVA1 and OLGA ANTONOVA1 1Department of Medical Genetics, Medical University‑Sofia, 1431 Sofia;2 Department of Urology, UMBALSM N.I. Pirogov, 1606 Sofia; 3Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia; 4Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia; 5Medical Genetics Laboratory, GARH Malinov, 1680 Sofia; 6Department of Biology, Medical Genetics and Microbiology, Faculty of Medicine, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria Received November 30, 2019; Accepted February 18, 2021 DOI: 10.3892/etm.2021.10333 Abstract. The aim of the present study was to detect copy uroepithelial tumours may lay a foundation for implementing number variations (CNVs) related to tumour progression and molecular CNV profiling of bladder tumours as part of a metastasis of urothelial carcinoma through whole‑genome routine progression risk estimation strategy, thus expanding scanning. A total of 30 bladder cancer samples staged from the personalized therapeutic approach. pTa to pT4 were included in the study. DNA was extracted from freshly frozen tissue via standard phenol‑chloroform extraction Introduction and CNV analysis was performed on two alternative platforms (CytoChip Oligo aCGH, 4x44K and Infinium OncoArray‑500K The most successful approach to treating a disease has BeadChip; Illumina, Inc.). Data were analysed with BlueFuse always been etiological therapy. In the case of bladder Multi software and Karyostudio, respectively.
    [Show full text]
  • The PIWI Protein Aubergine Recruits Eif3 to Activate Translation in the Germ Plasm
    www.nature.com/cr www.cell-research.com ARTICLE OPEN The PIWI protein Aubergine recruits eIF3 to activate translation in the germ plasm Anne Ramat1, Maria-Rosa Garcia-Silva1, Camille Jahan1, Rima Naït-Saïdi1, Jérémy Dufourt 1,5, Céline Garret1, Aymeric Chartier1, Julie Cremaschi1, Vipul Patel1, Mathilde Decourcelle 2, Amandine Bastide3, François Juge 4 and Martine Simonelig 1 Piwi-interacting RNAs (piRNAs) and PIWI proteins are essential in germ cells to repress transposons and regulate mRNAs. In Drosophila, piRNAs bound to the PIWI protein Aubergine (Aub) are transferred maternally to the embryo and regulate maternal mRNA stability through two opposite roles. They target mRNAs by incomplete base pairing, leading to their destabilization in the soma and stabilization in the germ plasm. Here, we report a function of Aub in translation. Aub is required for translational activation of nanos mRNA, a key determinant of the germ plasm. Aub physically interacts with the poly(A)-binding protein (PABP) and the translation initiation factor eIF3. Polysome gradient profiling reveals the role of Aub at the initiation step of translation. In the germ plasm, PABP and eIF3d assemble in foci that surround Aub-containing germ granules, and Aub acts with eIF3d to promote nanos translation. These results identify translational activation as a new mode of mRNA regulation by Aub, highlighting the versatility of PIWI proteins in mRNA regulation. Cell Research (2020) 30:421–435; https://doi.org/10.1038/s41422-020-0294-9 1234567890();,: INTRODUCTION directly interacts with the Oskar (Osk) protein that is specifically Translational control is a widespread mechanism to regulate synthesized at the posterior pole of oocytes and embryos and gene expression in many biological contexts.
    [Show full text]
  • A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
    Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase.
    [Show full text]
  • 13300 CNOT3 (E1L9S) Rabbit Mab
    Revision 1 C 0 2 - t CNOT3 (E1L9S) Rabbit mAb a e r o t S Orders: 877-616-CELL (2355) [email protected] 0 Support: 877-678-TECH (8324) 0 3 Web: [email protected] 3 www.cellsignal.com 1 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source/Isotype: UniProt ID: Entrez-Gene Id: WB, IP H Endogenous 105 Rabbit IgG O75175 4849 Product Usage Information 4. Zheng, X. et al. (2012) Stem Cells 30, 910-22. 5. Takahashi, A. et al. (2012) Biochem Biophys Res Commun 419, 268-73. Application Dilution 6. Venturini, G. et al. (2012) PLoS Genet 8, e1003040. 7. De Keersmaecker, K. et al. (2013) Nat Genet 45, 186-90. Western Blotting 1:1000 Immunoprecipitation 1:50 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% sodium azide. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity CNOT3 (E1L9S) Rabbit mAb recognizes endogenous levels of total CNOT3 protein. Species Reactivity: Human Species predicted to react based on 100% sequence homology: Mouse, Rat Source / Purification Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues surrounding Leu638 of human CNOT3 protein. Background The evolutionarily conserved CCR4-NOT (CNOT) complex regulates mRNA metabolism in eukaryotic cells (1). This regulation occurs at different levels of mRNA synthesis and degradation, including transcription initiation, elongation, deadenylation, and degradation (1). Multiple components, including CNOT1, CNOT2, CNOT3, CNOT4, CNOT6, CNOT6L, CNOT7, CNOT8, CNOT9, and CNOT10 have been identified in this complex (2).
    [Show full text]
  • The Changing Chromatome As a Driver of Disease: a Panoramic View from Different Methodologies
    The changing chromatome as a driver of disease: A panoramic view from different methodologies Isabel Espejo1, Luciano Di Croce,1,2,3 and Sergi Aranda1 1. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain 2. Universitat Pompeu Fabra (UPF), Barcelona, Spain 3. ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain *Corresponding authors: Luciano Di Croce ([email protected]) Sergi Aranda ([email protected]) 1 GRAPHICAL ABSTRACT Chromatin-bound proteins regulate gene expression, replicate and repair DNA, and transmit epigenetic information. Several human diseases are highly influenced by alterations in the chromatin- bound proteome. Thus, biochemical approaches for the systematic characterization of the chromatome could contribute to identifying new regulators of cellular functionality, including those that are relevant to human disorders. 2 SUMMARY Chromatin-bound proteins underlie several fundamental cellular functions, such as control of gene expression and the faithful transmission of genetic and epigenetic information. Components of the chromatin proteome (the “chromatome”) are essential in human life, and mutations in chromatin-bound proteins are frequently drivers of human diseases, such as cancer. Proteomic characterization of chromatin and de novo identification of chromatin interactors could thus reveal important and perhaps unexpected players implicated in human physiology and disease. Recently, intensive research efforts have focused on developing strategies to characterize the chromatome composition. In this review, we provide an overview of the dynamic composition of the chromatome, highlight the importance of its alterations as a driving force in human disease (and particularly in cancer), and discuss the different approaches to systematically characterize the chromatin-bound proteome in a global manner.
    [Show full text]
  • Comprehensive Analysis of DNA Methylation and Prediction of Response to Neoadjuvanttherapy in Locally Advanced Rectal Cancer
    cancers Article Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer Luisa Matos do Canto 1,2 , Mateus Camargo Barros-Filho 2,3 , Cláudia Aparecida Rainho 4 , Diogo Marinho 5, Bruna Elisa Catin Kupper 6, Maria Dirlei Ferreira de Souza Begnami 7, Cristovam Scapulatempo-Neto 8, Birgitte Mayland Havelund 9,10, Jan Lindebjerg 10,11 , Fabio Albuquerque Marchi 2 , Jan Baumbach 12, Samuel Aguiar Jr. 6 and Silvia Regina Rogatto 1,10,13,* 1 Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; [email protected] 2 International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; mfi[email protected] (M.C.B.-F.); [email protected] (F.A.M.) 3 Department of Head and Neck Surgery, Hospital das Clinicas HCFMUSP, Sao Paulo 01246-903, Brazil 4 Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University (Unesp), Botucatu 18618-689, Brazil; [email protected] 5 Institute of Biological Psychiatry, Psykiatrisk Center Sct. Hans, 4000 Roskilde, Denmark; [email protected] 6 Colorectal Cancer Service, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; [email protected] (B.E.C.K.); [email protected] (S.A.J.) 7 Department of Pathology, Sírio-Libanês Hospital, Sao Paulo 01308-050, Brazil; [email protected] 8 Molecular Oncology Research Center, Barretos – 14784-400, and Diagnósticos da América (DASA), Barueri
    [Show full text]
  • LCM-Seq Reveals Unique Transcriptional Adaptation Mechanisms of Resistant Neurons and Identifies Protective Pathways in Spinal Muscular Atrophy
    Downloaded from genome.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Research LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy Susanne Nichterwitz,1 Jik Nijssen,1,4 Helena Storvall,2,3,4 Christoph Schweingruber,1 Laura Helen Comley,1 Ilary Allodi,1 Mirjam van der Lee,1 Qiaolin Deng,3,5 Rickard Sandberg,2,3 and Eva Hedlund1,6 1Department of Neuroscience, 2Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; 3Ludwig Institute for Cancer Research, Karolinska Institutet, 171 77 Stockholm, Sweden Somatic motor neurons are selectively vulnerable in spinal muscular atrophy (SMA), which is caused by a deficiency of the ubiquitously expressed survival of motor neuron protein. However, some motor neuron groups, including oculomotor and trochlear (ocular), which innervate eye muscles, are for unknown reasons spared. To reveal mechanisms of vulnerability and resistance in SMA, we investigate the transcriptional dynamics in discrete neuronal populations using laser capture micro- dissection coupled with RNA sequencing (LCM-seq). Using gene correlation network analysis, we reveal a TRP53-mediated stress response that is intrinsic to all somatic motor neurons independent of their vulnerability, but absent in relatively re- sistant red nucleus and visceral motor neurons. However, the temporal and spatial expression analysis across neuron types shows that the majority of SMA-induced modulations are cell type–specific. Using Gene Ontology and protein network analyses, we show that ocular motor neurons present unique disease-adaptation mechanisms that could explain their resil- ience. Specifically, ocular motor neurons up-regulate (1) Syt1, Syt5, and Cplx2, which modulate neurotransmitter release; (2) the neuronal survival factors Gdf15, Chl1, and Lif; (3) Aldh4, that protects cells from oxidative stress; and (4) the caspase inhibitor Pak4.
    [Show full text]