DOCSLIB.ORG

Host and MTB Genome Encoded Mirna Markers for Diagnosis Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Host and MTB Genome Encoded Mirna Markers for Diagnosis Of Tuberculosis 116 (2019) 37–43 Contents lists available at ScienceDirect Tuberculosis journal homepage: www.elsevier.com/locate/tube Diagnostics Host and MTB genome encoded miRNA markers for diagnosis of tuberculosis T Sanjiban Chakrabartya, Ajay Kumarb, Kuthethur Raviprasada, Sandeep Mallyac, ∗∗ ∗ Kapaettu Satyamoorthya, , Kiran Chawlab, a Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, India b Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India c Department of Bioinformatics, School of Life Sciences, Manipal Academy of Higher Education, Manipal, India ABSTRACT MicroRNAs (miRNAs) are a class of noncoding RNA molecules which are involved in various cellular and physiological processes. Previously, studies have identified several miRNAs that are potential diagnostic biomarkers for various infectious diseases including tuberculosis. We have performed small RNA sequencing using the Ion Torrent PGM platform in extra pulmonary tuberculosis (EPTB) subject's serum samples to identify circulating miRNAs during mycobacterium tuberculosis (MTB) infection. Our analysis identified 20 circulating miRNAs upregulated and 5 miRNAs downregulated during MTB infection in patient's serum. In addition, we have identified 6 MTB genome encoded miRNAs upregulated in EPTB patient's serum samples. Taqman based qRT-PCR analysis of host-genome encoded (hsa-miR-146a-5p and hsa-miR-125b-5p) and MTB genome encoded (MTB-miR5) miRNAs showed increased expression in a cohort of 52 healthy, pulmonary tuberculosis (PTB) and extra pulmonary tuberculosis (EPTB) patients serum samples. Our study identified for the first time a panel of host and MTB genome specificdifferentially expressed circulating miRNAs in serum samples of an Indian patient cohort with tuberculosis infection with a potential as a non-invasive diagnostic biomarker for tuberculosis infection. 1. Introduction to the limitations in conventional methods for diagnosis of TB, re- searchers in the past have emphasized the need for development of Despite advancement in pulmonary medicine in past few decades, diagnostic tests based on host biomarkers that can be used for assess- tuberculosis (TB) globally continues to be the major cause of mortality ment of disease status and monitoring of treatment outcomes [5,6]. and morbidity due to an infectious agent. According to World Health Major challenge for developing an ideal biomarker is to ensure that the Organization (WHO) report 10.4 million people fell ill with TB in 2016; discovered biomarker is a stable molecule, abundantly present in body 6.3 million among them were new cases and 0.49 million had multidrug fluids, can be easily recovered, offers high sensitivity and specificity resistant TB. In 2016, TB accounted for 1.3 million deaths alone and with translational potential as a point of care test. In the above context, 0.37 million deaths among HIV co-infected people [1]. Although, early human MicroRNAs (miRNA), a class of non-coding highly conserved diagnosis and appropriate treatment can prevent most TB related single stranded small RNAs of approximately 18–25 nucleotides in deaths, limited availability of a reliable tool for diagnosis of TB remains length that modulate the expression of genes involved in development, one of the major obstacles in controlling the spread of this epidemic. cell differentiation, proliferation, and apoptosis are promising candi- Current standards of TB diagnosis are based on detection of pathogens dates for use as a biomarker [7–10]. Recently, researchers have high- in the sample thus rely heavily on bacterial load which makes the di- lighted the importance of miRNAs in diagnosis of infectious diseases agnosis even challenging especially in smear negative pulmonary TB [11–13]. A preliminary study on circulating miRNAs in patients with cases, extrapulmonary TB and paediatric TB cases where bacterial load active pulmonary TB reported 59 upregulated and 33 downregulated is often low [2–4]. Various methods are employed for the diagnosis of signatures when compared to non-TB controls [14]. Another study EPTB such as radiology, smear microscopy, culture identification, his- identified miR-3179 and miR-147 overexpression during TB infections topathology, tuberculin skin test (TST), serological assays, all these in patients sputum as compared to controls [15]. It has been reported methods have limitations such as suboptimal sensitivity or specificity that miRNA-144 is highly expressed in peripheral blood mono nuclear and time delays whereas, tests based on DNA amplification or inter- cell while miRNA-361-5P, miRNA-889, and miRNA-576-3p were sig- feron-γ release are expensive. MTB is known to modulate host cellular nificantly upregulated in serum samples of active TB patients [16]. microenvironment including immune mechanism and apoptosis. Owing Further, six serum micro RNAs hsa-miR-378, hsa-miR-483- 5p, hsa-miR- ∗ Corresponding author. Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, India. ∗∗ Corresponding author. Department of Cell and Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India. E-mail addresses: [email protected] (K. Satyamoorthy), [email protected] (K. Chawla). https://doi.org/10.1016/j.tube.2019.04.002 Received 26 November 2018; Received in revised form 26 February 2019; Accepted 16 April 2019 1472-9792/ © 2019 Published by Elsevier Ltd. S. Chakrabarty, et al. Tuberculosis 116 (2019) 37–43 22, hsa-miR-29c, hsa-miR-101 and hsa-miR-320b have been identified 2.5. Small RNA sequencing as specific markers to discriminate pulmonary TB from healthy controls [17]. Thus, it is evident that further exploration of miRNAs may be The small RNA sequencing was performed in pooled control (n = 2) useful to unravel information on pathophysiology of TB and discovery and pooled extra pulmonary tuberculosis (EPTB) serum samples of specific markers for its diagnosis. Recent reports have suggested that (n = 2). In brief, total RNA from the samples were enriched for small serum derived miRNAs are extremely stable under harsh conditions and RNAs using Total RNA-Seq Kit v2 (ThermoFisher Scientific). The useful as non-invasive biomarkers for early diagnosis of various in- quality and quantity of samples enriched for small RNA were analyzed fectious diseases [17]. In the present study, we performed small RNA using the Agilent small RNA kit (Agilent Technologies, Santa Clara, sequencing and Taqman based qRT-PCR based serum miRNA profiling California, USA) in 2100 Bioanalyzer Instrument. Samples were then of subjects with pulmonary and extrapulmonary tuberculosis in com- barcoded and used for library construction using Total RNA-Seq Kit v2. parison with healthy control. Our study identified a panel of serum Amplification of the templates was performed using Ion OneTouch™ 2 derived circulating host as well as pathogen derived miRNAs which are system and Ion OneTouch™ ES (ThermoFisher Scientific). Enriched differentially expressed during tuberculosis infection. products were loaded onto an Ion 318 chip and run on an Ion PGM system™ (ThermoFisher Scientific). 2. Materials and methods 2.6. Computational and statistical analysis 2.1. Ethical statement BAM files of pooled control and pooled EPTB samples were up- Our study was approved by Kasturba Medical College and Kasturba loaded in CAP-miRSeq pipeline for read pre-processing, alignment, Hospital Institutional Ethics committee, Manipal Academy of Higher distribution of RNA types, and differential miRNA expression analysis Education, Manipal, India. Written informed consent was obtained from [18]. LogFC (log2fold change) > 1 and < -1 were assigned to up- and all subjects prior to their enrolment in the study. down regulated miRNAs with FDR (False Discovery Rate) < 0.05. Targets were predicted using miRDB (Score ≥80) [19], PITA 2.2. Study groups (Score ≤−10) [20], and DIANA microT v4 (Score≥0.9) [21]. Pathway analysis was performed using DIANA miRPath v3.0 [22]. ROC analysis The present study was conducted on 52 individuals divided into was performed for miRNA expression to analyse the diagnostic accu- three groups. Group 1 included 15 TB patients diagnosed based on racy, against pulmonary TB and extra pulmonary TB using MedCalc clinical signs, radiological findings smear microscopy, culture and nu- software. cleic acid amplification tests. Group 2 included 22 Extrapulmonary TB patients diagnosed based 2.7. MTB genome encoded miRNA analysis on clinical signs, radiological/CT findings, MRI, smear microscopy, culture, histopathological findings and nucleic acid amplification tests. The unmapped reads after aligning to the human genome (GRCh37/ Group 3 included 15 normal healthy individuals without any symptoms hg19) were extracted and mapped to Mycobacterium tuberculosis (MTB) of Tuberculosis. (H37Rv). We further identified all small RNA sequencing reads that aligned to MTB genome as potential miRNAs. To validate the same, we 2.3. Sample collection extracted 500 flanking upstream and downstream bases from the mapped coordinates and used a SVM based method to predict pre- Samples from TB and extra pulmonary TB patients were collected miRNAs in the fasta sequence ab-initio. Pre-miRNAs residing between prior to anti-tubercular therapy. Five millilitres of venous blood was 450 and 550 were identified and with a criterion of minimum free withdrawn in a sterile vacutainer from each participant
Load more

Recommended publications
  • Doctoral Thesis Genetics of Male Infertility
    DOCTORAL THESIS GENETICS OF MALE INFERTILITY: MOLECULAR STUDY OF NON-SYNDROMIC CRYPTORCHIDISM AND SPERMATOGENIC IMPAIRMENT Deborah Grazia Lo Giacco November 2013 Genetics of male infertility: molecular study of non-syndromic cryptorchidism and spermatogenic impairment Thesis presented by Deborah Grazia Lo Giacco To fulfil the PhD degree at Universitat Autònoma de Barcelona Thesis realized under the direction of Dr. Elisabet Ars Criach and Prof. Csilla Krausz at the laboratory of Molecular Biology of Fundació Puigvert, Barcelona Thesis ascribed to the Department of Cellular Biology, Physiology and Immunology, Medicine School of Universitat Autònoma de Barcelona PhD in Cellular Biology Dr. Elisabet Ars Criach Prof. Csilla Krausz Dr. Carme Nogués Sanmiquel Director of the thesis Director of the thesis Tutor of the thesis Deborah Grazia Lo Giacco Ph.D Candidate A mis padres Agradecimientos Esta tesis es un esfuerzo en el cual, directa o indirectamente, han participado varias personas, leyendo, opinando, corrigiendo, teniéndo paciencia, dando ánimo, acompañando en los momentos de crisis y en los momentos de felicidad. Antes de todo quisiera agradecer a mis directoras de tesis, la Dra Csilla Krausz y la Dra Elisabet Ars, por su dedicación costante y continua a este trabajo de investigación y por sus observaciones y siempre acertados consejos. Gracias por haber sido mentores y amigas, gracias por transmitirme vuestro entusiasmo y por todo lo que he aprendido de vosotras. Mi más profundo agradecimiento a la Sra Esperança Marti por haber creído en el valor de nuestro trabajo y haber hecho que fuera posible. Quisiera agradecer al Dr. Eduard Ruiz-Castañé por su apoyo y ayuda constante, y a todos los médicos del Servicio de Andrología: Dr.
    [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]
  • Mir‑128‑3P Serves As an Oncogenic Microrna in Osteosarcoma Cells by Downregulating ZC3H12D
    ONCOLOGY LETTERS 21: 152, 2021 miR‑128‑3p serves as an oncogenic microRNA in osteosarcoma cells by downregulating ZC3H12D MAOSHU ZHU1*, YULONG WU2*, ZHAOWEI WANG3, MINGHUA LIN4, BIN SU5, CHUNYANG LI6, FULONG LIANG7 and XINJIANG CHEN6 Departments of 1Central Laboratory, 2Urinary Surgery, 3Gynecology, 4Pathology, 5Pharmacy, 6Orthopedics and 7Neurology, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China Received August 30, 2019; Accepted November 24, 2020 DOI: 10.3892/ol.2020.12413 Abstract. Osteosarcoma is the second leading cause of miR‑128‑3p‑mediated molecular pathway and how it is associ‑ cancer‑associated mortality worldwide in children and ated with osteosarcoma development. adolescents. ZC3H12D has been shown to negatively regulate Toll‑like receptor signaling and serves as a possible tumor Introduction suppressor gene. MicroRNAs (miRNAs/miRs) are known to play an important role in the proliferation of human osteo‑ As the most commonly occurring primary malignant bone sarcoma cells. However, whether miRNAs can affect tumor tumor, osteosarcoma accounts for >10% of all solid tumors development by regulating the expression of ZC3H12D has worldwide (1‑3). Osteosarcoma is the second leading cause of not yet been investigated. The aim of the present study was cancer‑associated mortality worldwide and primarily affects to investigate the role of miR128‑3p in regulating ZC3H12D young individuals, including children and adolescents (4,5). expression, as well as its function in tumor cell proliferation, Owing to advancements in surgical technology and combined apoptosis, and metastasis. Reverse transcription‑quantitative therapeutic strategies, the 5‑year overall survival rate of osteo‑ PCR, western blotting and dual luciferase reporter assays were sarcoma has increased to 60‑70% (6).
    [Show full text]
  • A Turner Syndrome Patient Carrying a Mosaic Distal X Chromosome Marker
    Hindawi Publishing Corporation Case Reports in Genetics Volume 2014, Article ID 597314, 5 pages http://dx.doi.org/10.1155/2014/597314 Case Report A Turner Syndrome Patient Carrying a Mosaic Distal X Chromosome Marker Roberto L. P. Mazzaschi,1 Juliet Taylor,2 Stephen P. Robertson,3 Donald R. Love,1,4 and Alice M. George1 1 Diagnostic Genetics, LabPlus, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand 2 Genetic Health Service New Zealand-Northern Hub, Auckland City Hospital, Private Bag 92024, Auckland 1142, New Zealand 3 Department of Paediatrics and Child Health, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand 4 School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand Correspondence should be addressed to Alice M. George; [email protected] Received 31 December 2013; Accepted 5 February 2014; Published 17 March 2014 Academic Editors: M. Fenger, G. Vogt, and X. Wang Copyright © 2014 Roberto L. P. Mazzaschi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A skin sample from a 17-year-old female was received for routine karyotyping with a set of clinical features including clonic seizures, cardiomyopathy, hepatic adenomas, and skeletal dysplasia. Conventional karyotyping revealed a mosaic Turner syndrome karyotype with a cell line containing a small marker of X chromosome origin. This was later confirmed on peripheral blood cultures by conventional G-banding, fluorescence in situ hybridisation and microarray analysis.
    [Show full text]
  • 2842-2852-Microrna-Mrna and P-P Interaction Analysis in Pancreatic
    Eur opean Rev iew for Med ical and Pharmacol ogical Sci ences 2016; 20: 2842-2852 Integrative microRNA-mRNA and protein-protein interaction analysis in pancreatic neuroendocrine tumors H.-Q. ZHOU 1,2 , Q.-C. CHEN 2, Z.-T. QIU 2, W.-L. TAN 1, C.-Q. MO 3, S.-W. GAO 1 1Department of Anesthesia, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Chin a 2Sun Yat-sen University School of Medicine, Guangzhou, China 3Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China Abstract. – OBJECTIVE : Pancreatic neuroen - Key Words: docrine tumors are relatively rare pancreatic microRNA, mRNA, Pancreatic neuroendocrine tu - neoplasms over the world. Investigations of the mors, Protein-protein interaction network. molecular biology of PNETs are insufficient for nowadays. We aimed to explore the expression of microRNA and messenger RNA and regulato - ry processes underlying pancreatic neuroen - Introduction docrine tumors. MATERIALS AND METHODS: The messenger RNA and microRNA expression profile of Pancreatic neuroendocrine tumors (PNETs), GSE43796 were downloaded, including 6 sam - also called islet cell tumors, are relatively rare ples with pancreatic neuroendocrine tumors and pancreatic neoplasms, arising from the endocrine 5 healthy samples. First, the Limma package was tissues rather than glandular epithelium of the utilized to distinguish the differentially ex - pancreas. With secreting a variety of peptide hor - pressed messenger RNA and microRNA sepa - mones, PNETs are terminologically divided as rately. Then we used microRNA Walk databases to predict the target genes of the differentially insulinoma, gastrinoma, glucagonoma, somato - expressed microRNAs (DE-microRNAs), and se - statinoma and vasoactive intestinal peptide tu - lected differentially expressed target genes mors (VIPoma), resulting in numbers of clinical whose expression was reversely correlated with syndromes.
    [Show full text]
  • A Temporally Controlled Sequence of X-Chromosome Inactivation and Reactivation Defines Female Mouse in Vitro Germ Cells with Meiotic Potential
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.11.455976; this version posted August 11, 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-NC 4.0 International license. A temporally controlled sequence of X-chromosome inactivation and reactivation defines female mouse in vitro germ cells with meiotic potential Jacqueline Severino1†, Moritz Bauer1,9†, Tom Mattimoe1, Niccolò Arecco1, Luca Cozzuto1, Patricia Lorden2, Norio Hamada3, Yoshiaki Nosaka4,5,6, So Nagaoka4,5,6, Holger Heyn2, Katsuhiko Hayashi7, Mitinori Saitou4,5,6 and Bernhard Payer1,8* Abstract The early mammalian germ cell lineage is characterized by extensive epigenetic reprogramming, which is required for the maturation into functional eggs and sperm. In particular, the epigenome needs to be reset before parental marks can be established and then transmitted to the next generation. In the female germ line, reactivation of the inactive X- chromosome is one of the most prominent epigenetic reprogramming events, and despite its scale involving an entire chromosome affecting hundreds of genes, very little is known about its kinetics and biological function. Here we investigate X-chromosome inactivation and reactivation dynamics by employing a tailor-made in vitro system to visualize the X-status during differentiation of primordial germ cell-like cells (PGCLCs) from female mouse embryonic stem cells (ESCs). We find that the degree of X-inactivation in PGCLCs is moderate when compared to somatic cells and characterized by a large number of genes escaping full inactivation.
    [Show full text]
  • Patterns of Molecular Evolution of an Avian Neo-Sex Chromosome
    Patterns of Molecular Evolution of an Avian Neo-sex Chromosome Irene Pala,*,1 Dennis Hasselquist,1 Staffan Bensch,1 and Bengt Hansson*,1 1Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden *Corresponding author: E-mail: [email protected]; [email protected]. Associate editor: Yoko Satta Abstract Newer parts of sex chromosomes, neo-sex chromosomes, offer unique possibilities for studying gene degeneration and sequence evolution in response to loss of recombination and population size decrease. We have recently described a neo-sex chromosome Downloaded from https://academic.oup.com/mbe/article/29/12/3741/1005710 by guest on 28 September 2021 system in Sylvioidea passerines that has resulted from a fusion between the first half (10 Mb) of chromosome 4a and the ancestral Research article sex chromosomes. In this study, we report the results of molecular analyses of neo-Z and neo-W gametologs and intronic parts of neo-Z and autosomal genes on the second half of chromosome 4a in three species within different Sylvioidea lineages (Acrocephalidea, Timaliidae, and Alaudidae). In line with hypotheses of neo-sex chromosome evolution, we observe 1) lower genetic diversity of neo-Z genes compared with autosomal genes, 2) moderate synonymous and weak nonsynonymous sequence divergence between neo-Z and neo-W gametologs, and 3) lower GC content on neo-W than neo-Z gametologs. Phylogenetic reconstruction of eight neo-Z and neo-W gametologs suggests that recombination continued after the split of Alaudidae from the rest of the Sylvioidea lineages (i.e., after 42.2 Ma) and with some exceptions also after the split of Acrocephalidea and Timaliidae (i.e., after 39.4 Ma).
    [Show full text]
  • The Development of a Statistical Model to Study How the Deletion of PD-1 Promotes Anti-Tumor Immunity
    The Development of a Statistical Model to Study How the Deletion of PD-1 Promotes Anti-Tumor Immunity The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Diallo, Alos Burgess. 2021. The Development of a Statistical Model to Study How the Deletion of PD-1 Promotes Anti-Tumor Immunity. Master's thesis, Harvard University Division of Continuing Education. Citable link https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37367694 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA The Development of a Statistical Model to Study How the Deletion of PD-1 Promotes Anti-Tumor Immunity Alos Diallo A Thesis in the Field of Bioinformatics for the Degree of Master of Liberal Arts in Extension Studies Harvard University March 2021 1 2 Copyright 2021 [Alos Diallo] Abstract T-cells are an essential component to the immune system, but they do not act alone and are instead a component in the body’s immune system. PD-1 and its ligands PD-L1 and PD-L2 play an important role in the regulation of T-cells which are incredibly important to the treatment of cancer. Tumors have been able to hijack the PD-1 inhibitory pathway to evade our body’s immune response. PD-1 pathway blockade, therefore, can serve as an important approach for cancer immunotherapy.
    [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]
  • Global Patterns of Changes in the Gene Expression Associated with Genesis of Cancer a Dissertation Submitted in Partial Fulfillm
    Global Patterns Of Changes In The Gene Expression Associated With Genesis Of Cancer A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at George Mason University By Ganiraju Manyam Master of Science IIIT-Hyderabad, 2004 Bachelor of Engineering Bharatiar University, 2002 Director: Dr. Ancha Baranova, Associate Professor Department of Molecular & Microbiology Fall Semester 2009 George Mason University Fairfax, VA Copyright: 2009 Ganiraju Manyam All Rights Reserved ii DEDICATION To my parents Pattabhi Ramanna and Veera Venkata Satyavathi who introduced me to the joy of learning. To friends, family and colleagues who have contributed in work, thought, and support to this project. iii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Ancha Baranova, whose tolerance, patience, guidance and encouragement helped me throughout the study. This dissertation would not have been possible without her ever ending support. She is very sincere and generous with her knowledge, availability, compassion, wisdom and feedback. I would also like to thank Dr. Vikas Chandhoke for funding my research generously during my doctoral study at George Mason University. Special thanks go to Dr. Patrick Gillevet, Dr. Alessandro Giuliani, Dr. Maria Stepanova who devoted their time to provide me with their valuable contributions and guidance to formulate this project. Thanks to the faculty of Molecular and Micro Biology (MMB) department, Dr. Jim Willett and Dr. Monique Vanhoek in embedding valuable thoughts to this dissertation by being in my dissertation committee. I would also like to thank the present and previous doctoral program directors, Dr. Daniel Cox and Dr. Geraldine Grant, for facilitating, allowing, and encouraging me to work in this project.
    [Show full text]
  • A Second Generation Human Haplotype Map of Over 3.1 Million Snps the International Hapmap Consortium1
    doi: 10.1038/nature06258 SUPPLEMENTARY INFORMATION A second generation human haplotype map of over 3.1 million SNPs The International HapMap Consortium1 Supplementary material S1 The density of common SNPs in the Phase II HapMap and the assembled human genome S2 Analysis of data quality S2.1 Analysis of amplicon structure to genotyping error S2.2 Analysis of genotype discordance from overlap with Seattle SNPs S2.3 Analysis of genotype discordance from fosmid end sequences S2.4 Analysis of monomorphism/polymorphism discrepancies S2.5 Interchromosomal LD S3. Analysis of population stratification S4. Analysis of relatedness S5. Segmental analysis of relatedness S6. Analysis of homozygosity S7. Perlegen genotyping protocols Supplementary tables Legends to supplementary figures 1 See end of manuscript for Consortium details www.nature.com/nature 1 doi: 10.1038/nature06258 SUPPLEMENTARY INFORMATION Supplementary text 1. The density of common SNPs in the Phase II HapMap and the assembled human genome. To estimate the fraction of all common variants on the autosomes that have been successfully genotyped in the consensus Phase II HapMap we note that in YRI (release 21) there are 2,334,980 SNPs with MAF≥0.05. Across the autosomes, the completed reference sequence assembled in contigs is 2.68 billion bp. Assuming that the allele frequency distribution in the YRI is well approximated by that of a simple coalescent model and using an estimate of the population mutation rate of θ = 1.2 per kb for African populations1,2 the expected number of variants with MAF≥0.05 in a sample of 120 chromosomes is 114 = θ E(S MAF≥5% ) L ∑ /1 i i=6 where L is the total length of the sequence3.
    [Show full text]
  • Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing
    ARTICLE Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing Yong-hui Jiang,1,18 Ryan K.C. Yuen,2,18 Xin Jin,3,4,5,18 Mingbang Wang,3,18 Nong Chen,3 Xueli Wu,3 Jia Ju,3 Junpu Mei,3 Yujian Shi,3 Mingze He,3 Guangbiao Wang,3 Jieqin Liang,3 Zhe Wang,3 Dandan Cao,3 Melissa T. Carter,6 Christina Chrysler,7 Irene E. Drmic,7 Jennifer L. Howe,2 Lynette Lau,2 Christian R. Marshall,2,8 Daniele Merico,2 Thomas Nalpathamkalam,2 Bhooma Thiruvahindrapuram,2 Ann Thompson,7 Mohammed Uddin,2 Susan Walker,2 Jun Luo,9 Evdokia Anagnostou,10 Lonnie Zwaigenbaum,11 Robert H. Ring,12 Jian Wang,3 Clara Lajonchere,12 Jun Wang,3,13,14,15,16 Andy Shih,12 Peter Szatmari,7 Huanming Yang,3 Geraldine Dawson,12,17 Yingrui Li,3,* and Stephen W. Scherer2,8,* Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo muta- tions in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations).
    [Show full text]