Mouse Nptx2 Conditional Knockout Project (CRISPR/Cas9)
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Neuronal Pentraxin 2: a Synapse-Derived CSF Biomarker in Genetic Frontotemporal Dementia
J Neurol Neurosurg Psychiatry: first published as 10.1136/jnnp-2019-322493 on 9 April 2020. Downloaded from Neurodegeneration ORIGINAL RESEARCH Neuronal pentraxin 2: a synapse- derived CSF biomarker in genetic frontotemporal dementia Emma L van der Ende ,1 Meifang Xiao,2 Desheng Xu,2 Jackie M Poos ,1 Jessica L Panman,1,3 Lize C Jiskoot ,1,4 Lieke H Meeter,1 Elise GP Dopper,1 Janne M Papma,1 Carolin Heller ,5 Rhian Convery ,4 Katrina Moore,4 Martina Bocchetta ,4 Mollie Neason,4 Georgia Peakman,4 David M Cash,4 Charlotte E Teunissen,6 Caroline Graff,7,8 Matthis Synofzik,9,10 Fermin Moreno,11 Elizabeth Finger ,12 Raquel Sánchez- Valle,13 Rik Vandenberghe,14 Robert Laforce Jr,15 Mario Masellis,16 Maria Carmela Tartaglia,17 James B Rowe ,18 Christopher R Butler,19 Simon Ducharme,20 Alex Gerhard,21,22 Adrian Danek,23 Johannes Levin,23,24,25 Yolande AL Pijnenburg,26 Markus Otto ,27 Barbara Borroni ,28 Fabrizio Tagliavini,29 Alexandre de Mendonca,30 Isabel Santana,31 Daniela Galimberti,32,33 Harro Seelaar,1 Jonathan D Rohrer,4 Paul F Worley,2,34 John C van Swieten ,1 on behalf of the Genetic Frontotemporal Dementia Initiative (GENFI) ► Additional material is ABSTRACT INTRODUCTION published online only. To view Introduction Synapse dysfunction is emerging as an Frontotemporal dementia (FTD), a common form please visit the journal online (http:// dx. doi. org/ 10. 1136/ early pathological event in frontotemporal dementia of early-onset dementia, has an autosomal dominant jnnp- 2019- 322493). (FTD), however biomarkers are lacking. We aimed inheritance in 20%–30% of patients, most often to investigate the value of cerebrospinal fluid (CSF) due to mutations in granulin (GRN), chromosome For numbered affiliations see neuronal pentraxins (NPTXs), a family of proteins 9 open reading frame 72 (C9orf72) or microtubule- end of article. -
Regulation of Synapse Development by Activity Dependent Transcription in Inhibitory Neurons
Regulation of Synapse Development by Activity Dependent Transcription in Inhibitory Neurons The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Mardinly, Alan Robert. 2013. Regulation of Synapse Development by Activity Dependent Transcription in Inhibitory Neurons. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11151534 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 2013 Alan Robert Mardinly All rights reserved Dissertation Advisor: Professor Michael E. Greenberg Alan Robert Mardinly Regulation of Synapse Development by Activity Dependent Transcription in Inhibitory Neurons Abstract Neuronal activity and subsequent calcium influx activates a signaling cascade that causes transcription factors in the nucleus to rapidly induce an early-response program of gene expression. This early-response program is composed of transcriptional regulators that in turn induce transcription of late-response genes, which are enriched for regulators of synaptic development and plasticity that act locally at the synapse. The main focus of this thesis is to describe the activity-induced transcriptional program in inhibitory neurons and identify its functional roles. We find strong similarity of the early-induced transcription factors induced by activity in excitatory and inhibitory neurons, but significant differences in the late-response genes. This finding suggests that commonly induced transcription factors may regulate distinct sets of target genes to perform cell-type specific functional roles. -
Genome-Wide Identification and Characterization of Functional Neuronal Activity–Dependent Enhancers
ART ic LE S Genome-wide identification and characterization of functional neuronal activity–dependent enhancers Athar N Malik1–3,7, Thomas Vierbuchen1,7, Martin Hemberg4, Alex A Rubin1, Emi Ling1,5, Cameron H Couch1, Hume Stroud1, Ivo Spiegel1, Kyle Kai-How Farh1,6, David A Harmin1 & Michael E Greenberg1 Experience-dependent gene transcription is required for nervous system development and function. However, the DNA regulatory elements that control this program of gene expression are not well defined. Here we characterize the enhancers that function across the genome to mediate activity-dependent transcription in mouse cortical neurons. We find that the subset of enhancers enriched for monomethylation of histone H3 Lys4 (H3K4me1) and binding of the transcriptional coactivator CREBBP (also called CBP) that shows increased acetylation of histone H3 Lys27 (H3K27ac) after membrane depolarization of cortical neurons functions to regulate activity-dependent transcription. A subset of these enhancers appears to require binding of FOS, which was previously thought to bind primarily to promoters. These findings suggest that FOS functions at enhancers to control activity- dependent gene programs that are critical for nervous system function and provide a resource of functional cis-regulatory elements that may give insight into the genetic variants that contribute to brain development and disease. In the nervous system, sensory experience promotes both the refine- There is still a striking gap in our understanding of how early ment and maturation of synaptic connections and the subsequent mod- response transcription factors such as FOS, C-JUN, NR4A1 and EGR1 ification of neural circuits during learning, memory and behavior1–6. -
REVIEW ARTICLE the Genetics of Autism
REVIEW ARTICLE The Genetics of Autism Rebecca Muhle, BA*; Stephanie V. Trentacoste, BA*; and Isabelle Rapin, MD‡ ABSTRACT. Autism is a complex, behaviorally de- tribution of a few well characterized X-linked disorders, fined, static disorder of the immature brain that is of male-to-male transmission in a number of families rules great concern to the practicing pediatrician because of an out X-linkage as the prevailing mode of inheritance. The astonishing 556% reported increase in pediatric preva- recurrence rate in siblings of affected children is ϳ2% to lence between 1991 and 1997, to a prevalence higher than 8%, much higher than the prevalence rate in the general that of spina bifida, cancer, or Down syndrome. This population but much lower than in single-gene diseases. jump is probably attributable to heightened awareness Twin studies reported 60% concordance for classic au- and changing diagnostic criteria rather than to new en- tism in monozygotic (MZ) twins versus 0 in dizygotic vironmental influences. Autism is not a disease but a (DZ) twins, the higher MZ concordance attesting to ge- syndrome with multiple nongenetic and genetic causes. netic inheritance as the predominant causative agent. By autism (the autistic spectrum disorders [ASDs]), we Reevaluation for a broader autistic phenotype that in- mean the wide spectrum of developmental disorders cluded communication and social disorders increased characterized by impairments in 3 behavioral domains: 1) concordance remarkably from 60% to 92% in MZ twins social interaction; 2) language, communication, and and from 0% to 10% in DZ pairs. This suggests that imaginative play; and 3) range of interests and activities. -
Human Lectins, Their Carbohydrate Affinities and Where to Find Them
biomolecules Review Human Lectins, Their Carbohydrate Affinities and Where to Review HumanFind Them Lectins, Their Carbohydrate Affinities and Where to FindCláudia ThemD. Raposo 1,*, André B. Canelas 2 and M. Teresa Barros 1 1, 2 1 Cláudia D. Raposo * , Andr1 é LAQVB. Canelas‐Requimte,and Department M. Teresa of Chemistry, Barros NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829‐516 Caparica, Portugal; [email protected] 12 GlanbiaLAQV-Requimte,‐AgriChemWhey, Department Lisheen of Chemistry, Mine, Killoran, NOVA Moyne, School E41 of ScienceR622 Co. and Tipperary, Technology, Ireland; canelas‐ [email protected] NOVA de Lisboa, 2829-516 Caparica, Portugal; [email protected] 2* Correspondence:Glanbia-AgriChemWhey, [email protected]; Lisheen Mine, Tel.: Killoran, +351‐212948550 Moyne, E41 R622 Tipperary, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +351-212948550 Abstract: Lectins are a class of proteins responsible for several biological roles such as cell‐cell in‐ Abstract:teractions,Lectins signaling are pathways, a class of and proteins several responsible innate immune for several responses biological against roles pathogens. such as Since cell-cell lec‐ interactions,tins are able signalingto bind to pathways, carbohydrates, and several they can innate be a immuneviable target responses for targeted against drug pathogens. delivery Since sys‐ lectinstems. In are fact, able several to bind lectins to carbohydrates, were approved they by canFood be and a viable Drug targetAdministration for targeted for drugthat purpose. delivery systems.Information In fact, about several specific lectins carbohydrate were approved recognition by Food by andlectin Drug receptors Administration was gathered for that herein, purpose. plus Informationthe specific organs about specific where those carbohydrate lectins can recognition be found by within lectin the receptors human was body. -
Pan-Cancer Transcriptome Analysis Reveals a Gene Expression
Modern Pathology (2016) 29, 546–556 546 © 2016 USCAP, Inc All rights reserved 0893-3952/16 $32.00 Pan-cancer transcriptome analysis reveals a gene expression signature for the identification of tumor tissue origin Qinghua Xu1,6, Jinying Chen1,6, Shujuan Ni2,3,4,6, Cong Tan2,3,4,6, Midie Xu2,3,4, Lei Dong2,3,4, Lin Yuan5, Qifeng Wang2,3,4 and Xiang Du2,3,4 1Canhelp Genomics, Hangzhou, Zhejiang, China; 2Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; 3Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; 4Institute of Pathology, Fudan University, Shanghai, China and 5Pathology Center, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China Carcinoma of unknown primary, wherein metastatic disease is present without an identifiable primary site, accounts for ~ 3–5% of all cancer diagnoses. Despite the development of multiple diagnostic workups, the success rate of primary site identification remains low. Determining the origin of tumor tissue is, thus, an important clinical application of molecular diagnostics. Previous studies have paved the way for gene expression-based tumor type classification. In this study, we have established a comprehensive database integrating microarray- and sequencing-based gene expression profiles of 16 674 tumor samples covering 22 common human tumor types. From this pan-cancer transcriptome database, we identified a 154-gene expression signature that discriminated the origin of tumor tissue with an overall leave-one-out cross-validation accuracy of 96.5%. The 154-gene expression signature was first validated on an independent test set consisting of 9626 primary tumors, of which 97.1% of cases were correctly classified. -
Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity
New Research Development Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience- Dependent Cortical Plasticity Milo R. Smith1,2,3,4,5,6,7,8, Poromendro Burman1,3,4,5,8, Masato Sadahiro1,3,4,5,6,8, Brian A. Kidd,2,7 Joel T. Dudley,2,7 and Hirofumi Morishita1,3,4,5,8 DOI:http://dx.doi.org/10.1523/ENEURO.0240-16.2016 1Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 2Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 3Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 4Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 5Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 6Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 7Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, and 8Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029 Visual Abstract Throughout childhood and adolescence, periods of heightened neuroplasticity are critical for the development of healthy brain function and behavior. Given the high prevalence of neurodevelopmental disorders, such as autism, identifying disruptors of developmental plasticity represents an essential step for developing strategies for prevention and intervention. Applying a novel computational approach that systematically assessed connections between 436 transcriptional signatures of disease and multiple signatures of neuroplasticity, we identified inflammation as a common pathological process central to a diverse set of diseases predicted to dysregulate Significance Statement During childhood and adolescence, heightened neuroplasticity allows the brain to reorganize and adapt to its environment. -
The Neuronal Pentraxin-2 Pathway Is an Unrecognized Target in Human Neuroblastoma Which Also Offers Prognostic Value in Patients
Author Manuscript Published OnlineFirst on August 20, 2015; DOI: 10.1158/0008-5472.CAN-15-0649 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. The neuronal pentraxin-2 pathway is an unrecognized target in human neuroblastoma which also offers prognostic value in patients Alice Bartolini1, Daniela Di Paolo2, Alessio Noghero3, Daniele Murgia4, Angela R. Sementa4, Michele Cilli5, Renata Pasqualini6,7, Wadih Arap6,8, Federico Bussolino3,9, Mirco Ponzoni2, Fabio Pastorino2,§ and Serena Marchiò1,9,§ 1Laboratory of Tumor Microenvironment and 3Laboratory of Vascular Oncology, Candiolo Cancer Institute-IRCCS, Candiolo, Italy; 2Laboratory of Oncology and 4Department of Pathology, Istituto G Gaslini, Genova, Italy; 5Animal Facility, IRCCS Azienda Ospedaliera Universitaria San Martino- IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy; 6University of New Mexico Cancer Center and Divisions of 7Molecular Medicine, and 8Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM; 9University of Torino, Department of Oncology, Candiolo, Italy. §F. Pastorino and S. Marchiò contributed equally to this work Running title: Targeting the NPTX2/NPTXR pathway in neuroblastoma Keywords: Neuroblastoma, tumor microenvironment, neuronal pentraxins, target therapy The authors declare no conflict of interest. Correspondence: Serena Marchiò, Laboratory of Tumor Microenvironment, Candiolo Cancer Institute-IRCCS, S.p. 142 Km 3.95, 10060 Candiolo, Italy: [email protected]. Fabio Pastorino, Laboratory of Oncology, G Gaslini Institute, Via G Gaslini 5, 16147 Genoa, Italy: [email protected]. Word count: 2775; Number of Figures: 4; Number of Supplementary Figures: 4 1 Downloaded from cancerres.aacrjournals.org on October 3, 2021. -
Blood Biomarkers for Memory: Toward Early Detection of Risk for Alzheimer Disease, Pharmacogenomics, and Repurposed Drugs
Molecular Psychiatry (2020) 25:1651–1672 https://doi.org/10.1038/s41380-019-0602-2 IMMEDIATE COMMUNICATION Blood biomarkers for memory: toward early detection of risk for Alzheimer disease, pharmacogenomics, and repurposed drugs 1,2,3 1 1 1,3,4 1 1 1 3 A. B. Niculescu ● H. Le-Niculescu ● K. Roseberry ● S. Wang ● J. Hart ● A. Kaur ● H. Robertson ● T. Jones ● 3 3,5 5 2 1 1,4 4 A. Strasburger ● A. Williams ● S. M. Kurian ● B. Lamb ● A. Shekhar ● D. K. Lahiri ● A. J. Saykin Received: 25 March 2019 / Revised: 25 September 2019 / Accepted: 11 November 2019 / Published online: 2 December 2019 © The Author(s) 2019. This article is published with open access Abstract Short-term memory dysfunction is a key early feature of Alzheimer’s disease (AD). Psychiatric patients may be at higher risk for memory dysfunction and subsequent AD due to the negative effects of stress and depression on the brain. We carried out longitudinal within-subject studies in male and female psychiatric patients to discover blood gene expression biomarkers that track short term memory as measured by the retention measure in the Hopkins Verbal Learning Test. These biomarkers were subsequently prioritized with a convergent functional genomics approach using previous evidence in the field implicating them in AD. The top candidate biomarkers were then tested in an independent cohort for ability to predict state short-term memory, 1234567890();,: 1234567890();,: and trait future positive neuropsychological testing for cognitive impairment. The best overall evidence was for a series of new, as well as some previously known genes, which are now newly shown to have functional evidence in humans as blood biomarkers: RAB7A, NPC2, TGFB1, GAP43, ARSB, PER1, GUSB, and MAPT. -
Analysis of DNA Methylation Sites Used for Forensic Age Prediction and Their Correlation with Human Aging
Silva DSBS, et al., J Forensic Leg Investig Sci 2021, 7: 054 DOI: 10.24966/FLIS-733X/100054 HSOA Journal of Forensic, Legal & Investigative Sciences Research Article Analysis of DNA Methylation Introduction DNA samples left behind in crime scenes are often used for Sites used for Forensic Age identification purposes by comparing them to reference samples or to a forensic database. In cases where there is no match, investigators may Prediction and their Correlation turn to alternative approaches using advanced technologies to gain valuable leads on phenotypic traits (externally visible characteristics) with Human Aging of the person who had left the DNA material. Previous studies have found that phenotypes can be predicted by using information obtained from different DNA markers, such as single nucleotide Silva DSBS1* and Karantenislis G2 polymorphisms (SNPs), insertion/deletion polymorphisms (InDel), and epigenetic markers [1-11]. It is well established that epigenetic 1Department of Chemistry, Hofstra University, Hempstead-NY, USA modifications are major regulators in the translation of genotype 2John F Kennedy High School, Bellmore-NY, USA to phenotype. Epigenetic regulation encompasses various levels of gene expression and involves modifications of DNA, histones, RNA and chromatin, with functional consequences for the human Abstract genome [12-14]. DNA methylation is the most well-characterized epigenetic modification. It is usually associated with transcriptional Phenotype-related features, such as age, are linked to repression and it involves the addition of a methyl group (– CH3) in genetic components through regulatory pathways and epigenetic the cytosine of CpG dinucleotides. Differences in DNA methylation modifications, such as DNA methylation, are major regulators in levels in specific regions of the genome can affect the expression of the translation of genotype to phenotype. -
Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. -
Identification of Novel Cerebrospinal Fluid Biomarker Candidates for Dementia with Lewy Bodies: a Proteomic Approach Inger Van Steenoven1*† , Marleen J
Steenoven et al. Molecular Neurodegeneration (2020) 15:36 https://doi.org/10.1186/s13024-020-00388-2 RESEARCH ARTICLE Open Access Identification of novel cerebrospinal fluid biomarker candidates for dementia with Lewy bodies: a proteomic approach Inger van Steenoven1*† , Marleen J. A. Koel-Simmelink2†, Leonie J. M. Vergouw3, Betty M. Tijms1, Sander R. Piersma4, Thang V. Pham4, Claire Bridel2, Gian-Luca Ferri5, Cristina Cocco5, Barbara Noli5, Paul F. Worley6,7, Mei-Fang Xiao6, Desheng Xu6, Patrick Oeckl8, Markus Otto8, Wiesje M. van der Flier1,9, Frank Jan de Jong3, Connie R. Jimenez4, Afina W. Lemstra1 and Charlotte E. Teunissen2 Abstract Background: Diagnosis of dementia with Lewy bodies (DLB) is challenging, largely due to a lack of diagnostic tools. Cerebrospinal fluid (CSF) biomarkers have been proven useful in Alzheimer’s disease (AD) diagnosis. Here, we aimed to identify novel CSF biomarkers for DLB using a high-throughput proteomic approach. Methods: We applied liquid chromatography/tandem mass spectrometry with label-free quantification to identify biomarker candidates to individual CSF samples from a well-characterized cohort comprising patients with DLB (n = 20) and controls (n = 20). Validation was performed using (1) the identical proteomic workflow in an independent cohort (n = 30), (2) proteomic data from patients with related neurodegenerative diseases (n = 149) and (3) orthogonal techniques in an extended cohort consisting of DLB patients and controls (n = 76). Additionally, we utilized random forest analysis to identify the subset of candidate markers that best distinguished DLB from all other groups. Results: In total, we identified 1995 proteins. In the discovery cohort, 69 proteins were differentially expressed in DLB compared to controls (p < 0.05).