Genetic Variants Associated with Anxiety and Stress-Related Disorders a Genome-Wide Association Study and Mouse-Model Study
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
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. -
The MIS12 Complex Is a Protein Interaction Hub for Outer Kinetochore Assembly
JCB: Article The MIS12 complex is a protein interaction hub for outer kinetochore assembly Arsen Petrovic,1 Sebastiano Pasqualato,1 Prakash Dube,3 Veronica Krenn,1 Stefano Santaguida,1 Davide Cittaro,4 Silvia Monzani,1 Lucia Massimiliano,1 Jenny Keller,1 Aldo Tarricone,1 Alessio Maiolica,1 Holger Stark,3 and Andrea Musacchio1,2 1Department of Experimental Oncology, European Institute of Oncology (IEO) and 2Research Unit of the Italian Institute of Technology, Italian Foundation for Cancer Research Institute of Molecular Oncology–IEO Campus, I-20139 Milan, Italy 33D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, and Göttingen Center for Microbiology, University of Göttingen, 37077 Göttingen, Germany 4Consortium for Genomic Technologies, I-20139 Milan, Italy inetochores are nucleoprotein assemblies responsi axis of 22 nm. Through biochemical analysis, cross- ble for the attachment of chromosomes to spindle linking–based methods, and negative-stain electron mi K microtubules during mitosis. The KMN network, croscopy, we investigated the reciprocal organization of a crucial constituent of the outer kinetochore, creates an the subunits of the MIS12 complex and their contacts with interface that connects microtubules to centromeric chro the rest of the KMN network. A highlight of our findings matin. The NDC80, MIS12, and KNL1 complexes form the is the identification of the NSL1 subunit as a scaffold core of the KMN network. We recently reported the struc supporting interactions of the MIS12 complex with the tural organization of the human NDC80 complex. In this NDC80 and KNL1 complexes. Our analysis has important study, we extend our analysis to the human MIS12 com implications for understanding kinetochore organization in plex and show that it has an elongated structure with a long different organisms. -
The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid
The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid Leukemia Cells Supported Only by Exogenous Cytokines Is Associated with a Patient Subset with Adverse Outcome Annette K. Brenner, Elise Aasebø, Maria Hernandez-Valladares, Frode Selheim, Frode Berven, Ida-Sofie Grønningsæter, Sushma Bartaula-Brevik and Øystein Bruserud Supplementary Material S2 of S31 Table S1. Detailed information about the 68 AML patients included in the study. # of blasts Viability Proliferation Cytokine Viable cells Change in ID Gender Age Etiology FAB Cytogenetics Mutations CD34 Colonies (109/L) (%) 48 h (cpm) secretion (106) 5 weeks phenotype 1 M 42 de novo 241 M2 normal Flt3 pos 31.0 3848 low 0.24 7 yes 2 M 82 MF 12.4 M2 t(9;22) wt pos 81.6 74,686 low 1.43 969 yes 3 F 49 CML/relapse 149 M2 complex n.d. pos 26.2 3472 low 0.08 n.d. no 4 M 33 de novo 62.0 M2 normal wt pos 67.5 6206 low 0.08 6.5 no 5 M 71 relapse 91.0 M4 normal NPM1 pos 63.5 21,331 low 0.17 n.d. yes 6 M 83 de novo 109 M1 n.d. wt pos 19.1 8764 low 1.65 693 no 7 F 77 MDS 26.4 M1 normal wt pos 89.4 53,799 high 3.43 2746 no 8 M 46 de novo 26.9 M1 normal NPM1 n.d. n.d. 3472 low 1.56 n.d. no 9 M 68 MF 50.8 M4 normal D835 pos 69.4 1640 low 0.08 n.d. -
Congenital Microcephaly
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Sussex Research Online American Journal of Medical Genetics Part C (Seminars in Medical Genetics) ARTICLE Congenital Microcephaly DIANA ALCANTARA AND MARK O'DRISCOLL* The underlying etiologies of genetic congenital microcephaly are complex and multifactorial. Recently, with the exponential growth in the identification and characterization of novel genetic causes of congenital microcephaly, there has been a consolidation and emergence of certain themes concerning underlying pathomechanisms. These include abnormal mitotic microtubule spindle structure, numerical and structural abnormalities of the centrosome, altered cilia function, impaired DNA repair, DNA Damage Response signaling and DNA replication, along with attenuated cell cycle checkpoint proficiency. Many of these processes are highly interconnected. Interestingly, a defect in a gene whose encoded protein has a canonical function in one of these processes can often have multiple impacts at the cellular level involving several of these pathways. Here, we overview the key pathomechanistic themes underlying profound congenital microcephaly, and emphasize their interconnected nature. © 2014 Wiley Periodicals, Inc. KEY WORDS: cell division; mitosis; DNA replication; cilia How to cite this article: Alcantara D, O'Driscoll M. 2014. Congenital microcephaly. Am J Med Genet Part C Semin Med Genet 9999:1–16. INTRODUCTION mid‐gestation although glial cell division formation of the various cortical layers. and consequent brain volume enlarge- Furthermore, differentiating and devel- Congenital microcephaly, an occipital‐ ment does continue after birth [Spalding oping neurons must migrate to their frontal circumference of equal to or less et al., 2005]. Impaired neurogenesis is defined locations to construct the com- than 2–3 standard deviations below the therefore most obviously reflected clini- plex architecture and laminar layered age‐related population mean, denotes cally as congenital microcephaly. -
Real-Time Dynamics of Plasmodium NDC80 Reveals Unusual Modes of Chromosome Segregation During Parasite Proliferation Mohammad Zeeshan1,*, Rajan Pandey1,*, David J
© 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2021) 134, jcs245753. doi:10.1242/jcs.245753 RESEARCH ARTICLE SPECIAL ISSUE: CELL BIOLOGY OF HOST–PATHOGEN INTERACTIONS Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation Mohammad Zeeshan1,*, Rajan Pandey1,*, David J. P. Ferguson2,3, Eelco C. Tromer4, Robert Markus1, Steven Abel5, Declan Brady1, Emilie Daniel1, Rebecca Limenitakis6, Andrew R. Bottrill7, Karine G. Le Roch5, Anthony A. Holder8, Ross F. Waller4, David S. Guttery9 and Rita Tewari1,‡ ABSTRACT eukaryotic organisms to proliferate, propagate and survive. During Eukaryotic cell proliferation requires chromosome replication and these processes, microtubular spindles form to facilitate an equal precise segregation to ensure daughter cells have identical genomic segregation of duplicated chromosomes to the spindle poles. copies. Species of the genus Plasmodium, the causative agents of Chromosome attachment to spindle microtubules (MTs) is malaria, display remarkable aspects of nuclear division throughout their mediated by kinetochores, which are large multiprotein complexes life cycle to meet some peculiar and unique challenges to DNA assembled on centromeres located at the constriction point of sister replication and chromosome segregation. The parasite undergoes chromatids (Cheeseman, 2014; McKinley and Cheeseman, 2016; atypical endomitosis and endoreduplication with an intact nuclear Musacchio and Desai, 2017; Vader and Musacchio, 2017). Each membrane and intranuclear mitotic spindle. To understand these diverse sister chromatid has its own kinetochore, oriented to facilitate modes of Plasmodium cell division, we have studied the behaviour movement to opposite poles of the spindle apparatus. During and composition of the outer kinetochore NDC80 complex, a key part of anaphase, the spindle elongates and the sister chromatids separate, the mitotic apparatus that attaches the centromere of chromosomes to resulting in segregation of the two genomes during telophase. -
Molecular Genetics of Microcephaly Primary Hereditary: an Overview
brain sciences Review Molecular Genetics of Microcephaly Primary Hereditary: An Overview Nikistratos Siskos † , Electra Stylianopoulou †, Georgios Skavdis and Maria E. Grigoriou * Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; [email protected] (N.S.); [email protected] (E.S.); [email protected] (G.S.) * Correspondence: [email protected] † Equal contribution. Abstract: MicroCephaly Primary Hereditary (MCPH) is a rare congenital neurodevelopmental disorder characterized by a significant reduction of the occipitofrontal head circumference and mild to moderate mental disability. Patients have small brains, though with overall normal architecture; therefore, studying MCPH can reveal not only the pathological mechanisms leading to this condition, but also the mechanisms operating during normal development. MCPH is genetically heterogeneous, with 27 genes listed so far in the Online Mendelian Inheritance in Man (OMIM) database. In this review, we discuss the role of MCPH proteins and delineate the molecular mechanisms and common pathways in which they participate. Keywords: microcephaly; MCPH; MCPH1–MCPH27; molecular genetics; cell cycle 1. Introduction Citation: Siskos, N.; Stylianopoulou, Microcephaly, from the Greek word µικρoκεϕαλi´α (mikrokephalia), meaning small E.; Skavdis, G.; Grigoriou, M.E. head, is a term used to describe a cranium with reduction of the occipitofrontal head circum- Molecular Genetics of Microcephaly ference equal, or more that teo standard deviations -
Discovery of Novel Putative Tumor Suppressors from CRISPR Screens Reveals Rewired 2 Lipid Metabolism in AML Cells 3 4 W
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.08.332023; this version posted August 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Discovery of novel putative tumor suppressors from CRISPR screens reveals rewired 2 lipid metabolism in AML cells 3 4 W. Frank Lenoir1,2, Micaela Morgado2, Peter C DeWeirdt3, Megan McLaughlin1,2, Audrey L 5 Griffith3, Annabel K Sangree3, Marissa N Feeley3, Nazanin Esmaeili Anvar1,2, Eiru Kim2, Lori L 6 Bertolet2, Medina Colic1,2, Merve Dede1,2, John G Doench3, Traver Hart2,4,* 7 8 9 1 - The University of Texas MD Anderson Cancer Center UTHealth Graduate School of 10 Biomedical Sciences; The University of Texas MD Anderson Cancer Center, Houston, TX 11 12 2 - Department of Bioinformatics and Computational Biology, The University of Texas MD 13 Anderson Cancer Center, Houston, TX, USA 14 15 3 - Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA 16 17 4 - Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 18 Houston, TX, USA 19 20 21 22 23 * - Corresponding author: [email protected] 24 25 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.08.332023; this version posted August 20, 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. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
FAM82A2 (RMDN3) (NM 018145) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC209526L3 FAM82A2 (RMDN3) (NM_018145) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: FAM82A2 (RMDN3) (NM_018145) Human Tagged ORF Clone Tag: Myc-DDK Symbol: RMDN3 Synonyms: FAM82A2; FAM82C; ptpip51; RMD-3; RMD3 Vector: pLenti-C-Myc-DDK-P2A-Puro (PS100092) E. coli Selection: Chloramphenicol (34 ug/mL) Cell Selection: Puromycin ORF Nucleotide The ORF insert of this clone is exactly the same as(RC209526). Sequence: Restriction Sites: SgfI-MluI Cloning Scheme: ACCN: NM_018145 ORF Size: 1410 bp This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 FAM82A2 (RMDN3) (NM_018145) Human Tagged ORF Clone – RC209526L3 OTI Disclaimer: Due to the inherent nature of this plasmid, standard methods to replicate additional amounts of DNA in E. coli are highly likely to result in mutations and/or rearrangements. Therefore, OriGene does not guarantee the capability to replicate this plasmid DNA. Additional amounts of DNA can be purchased from OriGene with batch-specific, full-sequence verification at a reduced cost. Please contact our customer care team at [email protected] or by calling 301.340.3188 option 3 for pricing and delivery. The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. -
Bub1 Positions Mad1 Close to KNL1 MELT Repeats to Promote Checkpoint Signalling
ARTICLE Received 14 Dec 2016 | Accepted 3 May 2017 | Published 12 June 2017 DOI: 10.1038/ncomms15822 OPEN Bub1 positions Mad1 close to KNL1 MELT repeats to promote checkpoint signalling Gang Zhang1, Thomas Kruse1, Blanca Lo´pez-Me´ndez1, Kathrine Beck Sylvestersen1, Dimitriya H. Garvanska1, Simone Schopper1, Michael Lund Nielsen1 & Jakob Nilsson1 Proper segregation of chromosomes depends on a functional spindle assembly checkpoint (SAC) and requires kinetochore localization of the Bub1 and Mad1/Mad2 checkpoint proteins. Several aspects of Mad1/Mad2 kinetochore recruitment in human cells are unclear and in particular the underlying direct interactions. Here we show that conserved domain 1 (CD1) in human Bub1 binds directly to Mad1 and a phosphorylation site exists in CD1 that stimulates Mad1 binding and SAC signalling. Importantly, fusion of minimal kinetochore-targeting Bub1 fragments to Mad1 bypasses the need for CD1, revealing that the main function of Bub1 is to position Mad1 close to KNL1 MELTrepeats. Furthermore, we identify residues in Mad1 that are critical for Mad1 functionality, but not Bub1 binding, arguing for a direct role of Mad1 in the checkpoint. This work dissects functionally relevant molecular interactions required for spindle assembly checkpoint signalling at kinetochores in human cells. 1 The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark. Correspondence and requests for materials should be addressed to G.Z. -
The Genome of Schmidtea Mediterranea and the Evolution Of
OPEN ArtICLE doi:10.1038/nature25473 The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms Markus Alexander Grohme1*, Siegfried Schloissnig2*, Andrei Rozanski1, Martin Pippel2, George Robert Young3, Sylke Winkler1, Holger Brandl1, Ian Henry1, Andreas Dahl4, Sean Powell2, Michael Hiller1,5, Eugene Myers1 & Jochen Christian Rink1 The planarian Schmidtea mediterranea is an important model for stem cell research and regeneration, but adequate genome resources for this species have been lacking. Here we report a highly contiguous genome assembly of S. mediterranea, using long-read sequencing and a de novo assembler (MARVEL) enhanced for low-complexity reads. The S. mediterranea genome is highly polymorphic and repetitive, and harbours a novel class of giant retroelements. Furthermore, the genome assembly lacks a number of highly conserved genes, including critical components of the mitotic spindle assembly checkpoint, but planarians maintain checkpoint function. Our genome assembly provides a key model system resource that will be useful for studying regeneration and the evolutionary plasticity of core cell biological mechanisms. Rapid regeneration from tiny pieces of tissue makes planarians a prime De novo long read assembly of the planarian genome model system for regeneration. Abundant adult pluripotent stem cells, In preparation for genome sequencing, we inbred the sexual strain termed neoblasts, power regeneration and the continuous turnover of S. mediterranea (Fig. 1a) for more than 17 successive sib- mating of all cell types1–3, and transplantation of a single neoblast can rescue generations in the hope of decreasing heterozygosity. We also developed a lethally irradiated animal4. Planarians therefore also constitute a a new DNA isolation protocol that meets the purity and high molecular prime model system for stem cell pluripotency and its evolutionary weight requirements of PacBio long-read sequencing12 (Extended Data underpinnings5.