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Molecular Mechanisms Underlying Noncoding Risk Variations in Psychiatric Genetic Studies
OPEN Molecular Psychiatry (2017) 22, 497–511 www.nature.com/mp REVIEW Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies X Xiao1,2, H Chang1,2 and M Li1 Recent large-scale genetic approaches such as genome-wide association studies have allowed the identification of common genetic variations that contribute to risk architectures of psychiatric disorders. However, most of these susceptibility variants are located in noncoding genomic regions that usually span multiple genes. As a result, pinpointing the precise variant(s) and biological mechanisms accounting for the risk remains challenging. By reviewing recent progresses in genetics, functional genomics and neurobiology of psychiatric disorders, as well as gene expression analyses of brain tissues, here we propose a roadmap to characterize the roles of noncoding risk loci in the pathogenesis of psychiatric illnesses (that is, identifying the underlying molecular mechanisms explaining the genetic risk conferred by those genomic loci, and recognizing putative functional causative variants). This roadmap involves integration of transcriptomic data, epidemiological and bioinformatic methods, as well as in vitro and in vivo experimental approaches. These tools will promote the translation of genetic discoveries to physiological mechanisms, and ultimately guide the development of preventive, therapeutic and prognostic measures for psychiatric disorders. Molecular Psychiatry (2017) 22, 497–511; doi:10.1038/mp.2016.241; published online 3 January 2017 RECENT GENETIC ANALYSES OF NEUROPSYCHIATRIC neurodevelopment and brain function. For example, GRM3, DISORDERS GRIN2A, SRR and GRIA1 were known to involve in the neuro- Schizophrenia, bipolar disorder, major depressive disorder and transmission mediated by glutamate signaling and synaptic autism are highly prevalent complex neuropsychiatric diseases plasticity. -
Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
The Epidermal Growth Factor Receptor Family As a Central Element for Cellular Signal Transduction and Diversification
Endocrine-Related Cancer (2001) 8 11–31 The epidermal growth factor receptor family as a central element for cellular signal transduction and diversification N Prenzel, O M Fischer, S Streit, S Hart and A Ullrich Max-Planck Institut fu¨r Biochemie, Department of Molecular Biology, Am Klopferspitz 18A, 82152 Martinsried, Germany (Requests for offprints should be addressed to A Ullrich; Email: [email protected]) Abstract Homeostasis of multicellular organisms is critically dependent on the correct interpretation of the plethora of signals which cells are exposed to during their lifespan. Various soluble factors regulate the activation state of cellular receptors which are coupled to a complex signal transduction network that ultimately generates signals defining the required biological response. The epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases represents both key regulators of normal cellular development as well as critical players in a variety of pathophysiological phenomena. The aim of this review is to give a broad overview of signal transduction networks that are controlled by the EGFR superfamily of receptors in health and disease and its application for target-selective therapeutic intervention. Since the EGFR and HER2 were recently identified as critical players in the transduction of signals by a variety of cell surface receptors, such as G-protein-coupled receptors and integrins, our special focus is the mechanisms and significance of the interconnectivity between heterologous signalling systems. Endocrine-Related Cancer (2001) 8 11–31 Introduction autophosphorylation of cytoplasmic tyrosine residues (reviewed in Ullrich & Schlessinger 1990, Heldin 1995, Cell surface receptors integrate a multitude of extracellular Alroy & Yarden 1997). -
Involvement of CRH Receptors in the Neuroprotective Action of R-Apomorphine in the Striatal 6-OHDA Rat Model
Neuroscience & Medicine, 2013, 4, 299-318 299 Published Online December 2013 (http://www.scirp.org/journal/nm) http://dx.doi.org/10.4236/nm.2013.44044 Involvement of CRH Receptors in the Neuroprotective Action of R-Apomorphine in the Striatal 6-OHDA Rat Model Mustafa Varçin1, Eduard Bentea1, Steven Roosens1, Yvette Michotte1, Sophie Sarre1,2* 1Department of Pharmaceutical Chemistry and Drug Analysis, Center for Neurosciences, Vrije Universiteit Brussel, Faculty of Medicine and Pharmacy, Brussels, Belgium; 2Belgian Pharmacists Association, Medicines Control Laboratory, Brussels, Belgium. Email: *[email protected] Received October 21st, 2013; revised November 20th, 2013; accepted December 10th, 2013 Copyright © 2013 Mustafa Varçin 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. ABSTRACT The dopamine D1-D2 receptor agonist, R-apomorphine, has been shown to be neuroprotective in different models of Parkinson’s disease. Different mechanisms of action for this effect have been proposed, but not verified in the striatal 6-hydroxydopamine rat model. In this study, the expression of a set of genes involved in 1) signaling, 2) growth and differentiation, 3) neuronal regeneration and survival, 4) apoptosis and 5) inflammation in the striatum was measured after a subchronic R-apomorphine treatment (10 mg/kg/day, subcutaneously, during 11 days) in the striatal 6-hydroxy- dopamine rat model. The expression of 84 genes was analysed by using the rat neurotrophins and receptors RT2 Pro- filer™ PCR array. The neuroprotective effects of R-apomorphine in the striatal 6-hydroxydopamine model were con- firmed by neurochemical and behavioural analysis. -
RET Controls Sympathetic Innervation
Development 128, 3963-3974 (2001) 3963 Printed in Great Britain © The Company of Biologists Limited 2001 DEV8811 RET signaling is essential for migration, axonal growth and axon guidance of developing sympathetic neurons Hideki Enomoto1, Peter A. Crawford1, Alexander Gorodinsky1, Robert O. Heuckeroth2,3, Eugene M. Johnson, Jr3 and Jeffrey Milbrandt1,* 1Departments of Pathology and Internal Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8118, St Louis, MO 63110, USA 2Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, Box 8116, St Louis, MO 63110, USA 3Department of Molecular Biology and Pharmacology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8113, St Louis, MO 63110, USA *Author for correspondence (e-mail: [email protected]) Accepted 26 July 2001 SUMMARY Sympathetic axons use blood vessels as an intermediate trunks and accelerated cell death of sympathetic neurons path to reach their final target tissues. The initial contact later in development. Artemin is expressed in blood vessels between differentiating sympathetic neurons and blood during periods of early sympathetic differentiation, and vessels occurs following the primary sympathetic chain can promote and attract axonal growth of the sympathetic formation, where precursors of sympathetic neurons ganglion in vitro. This analysis identifies RET and artemin migrate and project axons along or toward blood vessels. as central regulators of early sympathetic innervation. We demonstrate -
Regulation of Adipose Tissue Function and Metabolic Homeostasis
REGULATION OF ADIPOSE TISSUE FUNCTION AND METABOLIC HOMEOSTASIS by Guoxiao Wang A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in the University of Michigan 2014 Doctoral committee: Associate Professor Jiandie D. Lin, Chair Associate Professor Peter Dempsey Professor Ormond MacDougald Professor Liangyou Rui Professor Alan R. Saltiel © Guoxiao Wang 2014 DEDICATION To my parents and my husband, for their unconditional love ii ACKNOWLEDGEMENTS I would like to give special thanks to my mentor Jiandie Lin, who inspires confidence, enhances criticism and drives me forward. He bears all the virtues of a good mentor, always available to students despite the tremendous demands on his time. By actively doing research himself, he led us from the front and served as a role model. He has created a lab that is scientifically intense yet nurturing. He celebrates everybody’s success and respects individual difference, allowing us to “smell the rose”. I also would like to thank Siming Li, senior research staff in our lab, who has provided tremendous help from the start of my rotation and throughout my thesis research. I want to thank all my labmates, for the help I receive and friendship I enjoy. Thank you Xuyun Zhao and Zhuoxian Meng for help on our collaborative projects. Thank you Zhimin Chen and Yuanyuan Xiao for sharing resources and ideas that moves my project forward. Thank you Zoharit Cozacov for being such a terrific technician. And thank you Qi Yu and Lin Wang for providing common reagents to allow the lab to run smoothly. -
New Insights Into the Secretory Functions of Brown Adipose Tissue
243 2 Journal of J Villarroya et al. Secretory functions of brown 243:2 R19–R27 Endocrinology adipose tissue REVIEW New insights into the secretory functions of brown adipose tissue Joan Villarroya, Rubén Cereijo, Aleix Gavaldà-Navarro, Marion Peyrou, Marta Giralt and Francesc Villarroya Departament de Bioquímica i Biomedicina Molecular and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain CIBER Fisiopatología de la Obesidad y Nutrición, Barcelona, Catalonia, Spain Correspondence should be addressed to F Villarroya: [email protected] Abstract In recent years, an important secretory role of brown adipose tissue (BAT) has emerged, Key Words which is consistent, to some extent, with the earlier recognition of the important f brown adipose tissue secretory role of white fat. The so-called brown adipokines or ‘batokines’ may play an f brown adipokine autocrine role, which may either be positive or negative, in the thermogenic function f batokine of brown adipocytes. Additionally, there is a growing recognition of the signalling f thermogenesis molecules released by brown adipocytes that target sympathetic nerve endings (such as neuregulin-4 and S100b protein), vascular cells (e.g., bone morphogenetic protein-8b), and immune cells (e.g., C-X-C motif chemokine ligand-14) to promote the tissue remodelling associated with the adaptive BAT recruitment in response to thermogenic stimuli. Moreover, existing indications of an endocrine role of BAT are being confirmed through the release of brown adipokines acting on other distant tissues and organs; a recent example is the recognition that BAT-secreted fibroblast growth factor-21 and myostatin target the heart and skeletal muscle, respectively. -
HCC and Cancer Mutated Genes Summarized in the Literature Gene Symbol Gene Name References*
HCC and cancer mutated genes summarized in the literature Gene symbol Gene name References* A2M Alpha-2-macroglobulin (4) ABL1 c-abl oncogene 1, receptor tyrosine kinase (4,5,22) ACBD7 Acyl-Coenzyme A binding domain containing 7 (23) ACTL6A Actin-like 6A (4,5) ACTL6B Actin-like 6B (4) ACVR1B Activin A receptor, type IB (21,22) ACVR2A Activin A receptor, type IIA (4,21) ADAM10 ADAM metallopeptidase domain 10 (5) ADAMTS9 ADAM metallopeptidase with thrombospondin type 1 motif, 9 (4) ADCY2 Adenylate cyclase 2 (brain) (26) AJUBA Ajuba LIM protein (21) AKAP9 A kinase (PRKA) anchor protein (yotiao) 9 (4) Akt AKT serine/threonine kinase (28) AKT1 v-akt murine thymoma viral oncogene homolog 1 (5,21,22) AKT2 v-akt murine thymoma viral oncogene homolog 2 (4) ALB Albumin (4) ALK Anaplastic lymphoma receptor tyrosine kinase (22) AMPH Amphiphysin (24) ANK3 Ankyrin 3, node of Ranvier (ankyrin G) (4) ANKRD12 Ankyrin repeat domain 12 (4) ANO1 Anoctamin 1, calcium activated chloride channel (4) APC Adenomatous polyposis coli (4,5,21,22,25,28) APOB Apolipoprotein B [including Ag(x) antigen] (4) AR Androgen receptor (5,21-23) ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 (4) ARHGAP35 Rho GTPase activating protein 35 (21) ARID1A AT rich interactive domain 1A (SWI-like) (4,5,21,22,24,25,27,28) ARID1B AT rich interactive domain 1B (SWI1-like) (4,5,22) ARID2 AT rich interactive domain 2 (ARID, RFX-like) (4,5,22,24,25,27,28) ARID4A AT rich interactive domain 4A (RBP1-like) (28) ARID5B AT rich interactive domain 5B (MRF1-like) (21) ASPM Asp (abnormal -
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 -
Effects of Neuregulin 3 Genotype on Human Prefrontal Cortex Physiology
The Journal of Neuroscience, January 15, 2014 • 34(3):1051–1056 • 1051 Brief Communications Effects of Neuregulin 3 Genotype on Human Prefrontal Cortex Physiology Heike Tost,1,2 Joseph H. Callicott,1 Roberta Rasetti,1 Radhakrishna Vakkalanka,1,3 Venkata S. Mattay,1,3 Daniel R. Weinberger,1,3,4* and Amanda J. Law1,5* 1Clinical Brain Disorders Branch, Genes, Cognition, and Psychosis Program, National Institute of Mental Health, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, 2Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, 61859 Mannheim, Germany, 3Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, Maryland 21205, 4Departments of Psychiatry, Neurology, and Neuroscience and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, and 5Departments of Psychiatry and Cell and Developmental Biology, University of Colorado, School of Medicine, Aurora, Colorado 80045 The neuregulin 3 gene (NRG3) plays pleiotropic roles in neurodevelopment and is a putative susceptibility locus for schizophrenia. Specifically, the T allele of NRG3 rs10748842 has been associated with illness risk, altered cognitive function, and the expression of a novel splice isoform in prefrontal cortex (PFC), but the neural system effects are unexplored. Here, we report an association between rs10748842 and PFC physiology as measured by functional magnetic resonance imaging of human working memory performance, where a convincing link between increased genetic risk for schizophrenia and increased activation in some PFC areas has been established. In 410controlindividuals(195males,215females),wedetectedahighlysignificanteffectofNRG3genotypemanifestingasanunanticipated increase in ventrolateral PFC activation in nonrisk-associated C allele carriers. -
The Erbb Receptor Tyrosine Family As Signal Integrators
Endocrine-Related Cancer (2001) 8 151–159 The ErbB receptor tyrosine family as signal integrators N E Hynes, K Horsch, M A Olayioye and A Badache Friedrich Miescher Institute, PO Box 2543, CH-4002 Basel, Switzerland (Requests for offprints should be addressed to N E Hynes, Friedrich Miescher Institute, R-1066.206, Maulbeerstrasse 66, CH-4058 Basel, Switzerland. Email: [email protected]) (M A Olayioye is now at The Walter and Eliza Hall Institute of Medical Research, PO Royal Melbourne Hospital, Victoria 3050, Australia) Abstract ErbB receptor tyrosine kinases (RTKs) and their ligands have important roles in normal development and in human cancer. Among the ErbB receptors only ErbB2 has no direct ligand; however, ErbB2 acts as a co-receptor for the other family members, promoting high affinity ligand binding and enhancement of ligand-induced biological responses. These characteristics demonstrate the central role of ErbB2 in the receptor family, which likely explains why it is involved in the development of many human malignancies, including breast cancer. ErbB RTKs also function as signal integrators, cross-regulating different classes of membrane receptors including receptors of the cytokine family. Cross-regulation of ErbB RTKs and cytokines receptors represents another mechanism for controlling and enhancing tumor cell proliferation. Endocrine-Related Cancer (2001) 8 151–159 Introduction The EGF-related peptide growth factors The epidermal growth factor (EGF) or ErbB family of type ErbB receptors are activated by ligands, known as the I receptor tyrosine kinases (RTKs) has four members:EGF EGF-related peptide growth factors (reviewed in Peles & receptor, also termed ErbB1/HER1, ErbB2/Neu/HER2, Yarden 1993, Riese & Stern 1998). -
Sarcomeres Regulate Murine Cardiomyocyte Maturation Through MRTF-SRF Signaling
Sarcomeres regulate murine cardiomyocyte maturation through MRTF-SRF signaling Yuxuan Guoa,1,2,3, Yangpo Caoa,1, Blake D. Jardina,1, Isha Sethia,b, Qing Maa, Behzad Moghadaszadehc, Emily C. Troianoc, Neil Mazumdara, Michael A. Trembleya, Eric M. Smalld, Guo-Cheng Yuanb, Alan H. Beggsc, and William T. Pua,e,2 aDepartment of Cardiology, Boston Children’s Hospital, Boston, MA 02115; bDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215; cDivision of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115; dAab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642; and eHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 Edited by Janet Rossant, The Gairdner Foundation, Toronto, ON, Canada, and approved November 24, 2020 (received for review May 6, 2020) The paucity of knowledge about cardiomyocyte maturation is a Mechanisms that orchestrate ultrastructural and transcrip- major bottleneck in cardiac regenerative medicine. In develop- tional changes in cardiomyocyte maturation are beginning to ment, cardiomyocyte maturation is characterized by orchestrated emerge. Serum response factor (SRF) is a transcription factor that structural, transcriptional, and functional specializations that occur is essential for cardiomyocyte maturation (3). SRF directly acti- mainly at the perinatal stage. Sarcomeres are the key cytoskeletal vates key genes regulating sarcomere assembly, electrophysiology, structures that regulate the ultrastructural maturation of other and mitochondrial metabolism. This transcriptional regulation organelles, but whether sarcomeres modulate the signal trans- subsequently drives the proper morphogenesis of mature ultra- duction pathways that are essential for cardiomyocyte maturation structural features of myofibrils, T-tubules, and mitochondria.