Disruption of Interneuron Neurogenesis in Premature Newborns and Reversal with Estrogen Treatment
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Interaction Network of Immune‑Associated Genes Affecting the Prognosis of Patients with Glioblastoma
EXPERIMENTAL AND THERAPEUTIC MEDICINE 21: 61, 2021 Interaction network of immune‑associated genes affecting the prognosis of patients with glioblastoma XIAOHONG HOU1*, JIALIN CHEN2*, QIANG ZHANG1, YINCHUN FAN1, CHENGMING XIANG1, GUIYIN ZHOU1, FANG CAO1 and SHENGTAO YAO1 1Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University;2 Department of Neonatology, The First People' s Hospital of Zunyi Affiliated to Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China Received October 15, 2019; Accepted October 6, 2020 DOI: 10.3892/etm.2020.9493 Abstract. Glioblastoma multiforme (GBM) is a common and immune genes of interest. The interaction network of malignant tumor type of the nervous system. The purpose immune‑regulatory genes constructed in the present study of the present study was to establish a regulatory network of enhances the current understanding of mechanisms associated immune‑associated genes affecting the prognosis of patients with poor prognosis of patients with GBM. The risk score with GBM. The GSE4290, GSE50161 and GSE2223 datasets model established in the present study may be used to evaluate from the Gene Expression Omnibus database were screened the prognosis of patients with GBM. to identify common differentially expressed genes (co‑DEGs). A functional enrichment analysis indicated that the co‑DEGs Introduction were mainly enriched in cell communication, regulation of enzyme activity, immune response, nervous system, cytokine Glioblastoma multiforme (GBM) is one of the most malig‑ signaling in immune system and the AKT signaling pathway. nant tumor types of the central nervous system, with short The co‑DEGs accumulated in immune response were then median survival and poor prognosis. -
Selective Estrogen Receptor Modulators: Discrimination of Agonistic Versus Antagonistic Activities by Gene Expression Profiling in Breast Cancer Cells
[CANCER RESEARCH 64, 1522–1533, February 15, 2004] Selective Estrogen Receptor Modulators: Discrimination of Agonistic versus Antagonistic Activities by Gene Expression Profiling in Breast Cancer Cells Jonna Frasor,1 Fabio Stossi,1 Jeanne M. Danes,1 Barry Komm,2 C. Richard Lyttle,2 and Benita S. Katzenellenbogen1 1Department of Molecular and Integrative Physiology, University of Illinois and College of Medicine, Urbana, Illinois, and 2Women’s Health Research Institute, Wyeth Research, Collegeville, Pennsylvania ABSTRACT tures in these women; however, some detrimental side effects such as an increased risk of endometrial cancer, stroke, and pulmonary embolism Selective estrogen receptor modulators (SERMs) such as tamoxifen are were also associated with tamoxifen treatment (7). Ral was examined in effective in the treatment of many estrogen receptor-positive breast cancers the Multiple Outcomes of Raloxifene Evaluation trial and found to be and have also proven to be effective in the prevention of breast cancer in women at high risk for the disease. The comparative abilities of tamoxifen effective in reducing the incidence of osteoporosis in postmenopausal versus raloxifene in breast cancer prevention are currently being compared in women, as well as the incidence of breast cancer but, unlike tamoxifen, the Study of Tamoxifen and Raloxifene trial. To better understand the actions without the increased risk of endometrial cancer (8, 9). On the basis of the of these compounds in breast cancer, we have examined their effects on the positive outcome of these trials, the Study of Tamoxifen and Raloxifene expression of ϳ12,000 genes, using Affymetrix GeneChip microarrays, with trial was begun in 1999 to directly compare the effects of these two quantitative PCR verification in many cases, categorizing their actions as SERMs, tamoxifen and Ral, in prevention of breast cancer (10, 11). -
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. -
Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart
RESEARCH ARTICLE Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart Chung-Il An1☯*, Yasunori Ichihashi2☯¤a¤b*, Jie Peng3, Neelima R. Sinha2, Nobuko Hagiwara1* 1 Division of Cardiovascular Medicine, Department of Internal Medicine, University of California Davis, Davis, California, United States of America, 2 Department of Plant Biology, University of California Davis, Davis, California, United States of America, 3 Department of Statistics, University of California Davis, Davis, California, United States of America ☯ These authors contributed equally to this work. a11111 ¤a Current address: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan ¤b Current address: JST, PRESTO, Kawaguchi, Saitama, Japan * [email protected] (CA); [email protected] (YI); [email protected] (NH) Abstract OPEN ACCESS The postnatal heart undergoes highly coordinated developmental processes culminating in Citation: An C-I, Ichihashi Y, Peng J, Sinha NR, the complex physiologic properties of the adult heart. The molecular mechanisms of postna- Hagiwara N (2016) Transcriptome Dynamics and tal heart development remain largely unexplored despite their important clinical implications. Potential Roles of Sox6 in the Postnatal Heart. To gain an integrated view of the dynamic changes in gene expression during postnatal PLoS ONE 11(11): e0166574. doi:10.1371/journal. heart development at the organ level, time-series transcriptome analyses of the postnatal pone.0166574 hearts of neonatal through adult mice (P1, P7, P14, P30, and P60) were performed using a Editor: Katherine Yutzey, Cincinnati Children's newly developed bioinformatics pipeline. We identified functional gene clusters by principal Hospital Medical Center, UNITED STATES component analysis with self-organizing map clustering which revealed organized, discrete Received: July 16, 2016 gene expression patterns corresponding to biological functions associated with the neona- Accepted: October 31, 2016 tal, juvenile and adult stages of postnatal heart development. -
Characterisation of Keratan Sulfate Phosphoglycan
DIPLOMARBEIT Titel der Diplomarbeit Verification of Dscam expression in rat microglia angestrebter akademischer Grad Magister der Naturwissenschaften (Mag. rer.nat.) Verfasser: Roland Prielhofer Matrikel-Nummer: 0400857 Studienrichtung: A490 - Molekulare Biologie Betreuerin Univ.-Doz. Dr. Monika Bradl (Medizinische Universität Wien) Wien, August 2009 Table of contents: Abstract Zusammenfassung 1. Introduction ........................................................................................................ - 1 - 2. Material and Methods ..................................................................................... - 7 - 2.1. Cell biology ................................................................................................... - 7 - 2.1.1. Media ............................................................................................................. - 7 - 2.1.2. Model organisms ........................................................................................... - 8 - 2.1.3. Preparation of primary mixed glial cell cultures ........................................... - 8 - 2.1.4. BD PuraMatrix™ peptide hydrogel .............................................................. - 9 - 2.1.5. Isolation of microglia from adult lewis rat spinal cords ................................ - 10 - 2.1.6. Lymphocyte isolation .................................................................................... - 11 - 2.1.7. Phase-contrast microscopy and imaging ....................................................... - 11 - -
Prox1regulates the Subtype-Specific Development of Caudal Ganglionic
The Journal of Neuroscience, September 16, 2015 • 35(37):12869–12889 • 12869 Development/Plasticity/Repair Prox1 Regulates the Subtype-Specific Development of Caudal Ganglionic Eminence-Derived GABAergic Cortical Interneurons X Goichi Miyoshi,1 Allison Young,1 Timothy Petros,1 Theofanis Karayannis,1 Melissa McKenzie Chang,1 Alfonso Lavado,2 Tomohiko Iwano,3 Miho Nakajima,4 Hiroki Taniguchi,5 Z. Josh Huang,5 XNathaniel Heintz,4 Guillermo Oliver,2 Fumio Matsuzaki,3 Robert P. Machold,1 and Gord Fishell1 1Department of Neuroscience and Physiology, NYU Neuroscience Institute, Smilow Research Center, New York University School of Medicine, New York, New York 10016, 2Department of Genetics & Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, 3Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan, 4Laboratory of Molecular Biology, Howard Hughes Medical Institute, GENSAT Project, The Rockefeller University, New York, New York 10065, and 5Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Neurogliaform (RELNϩ) and bipolar (VIPϩ) GABAergic interneurons of the mammalian cerebral cortex provide critical inhibition locally within the superficial layers. While these subtypes are known to originate from the embryonic caudal ganglionic eminence (CGE), the specific genetic programs that direct their positioning, maturation, and integration into the cortical network have not been eluci- dated. Here, we report that in mice expression of the transcription factor Prox1 is selectively maintained in postmitotic CGE-derived cortical interneuron precursors and that loss of Prox1 impairs the integration of these cells into superficial layers. Moreover, Prox1 differentially regulates the postnatal maturation of each specific subtype originating from the CGE (RELN, Calb2/VIP, and VIP). -
Supplemental Tables4.Pdf
Yano_Supplemental_Table_S4 Gene ontology – Biological process 1 of 9 Fold List Pop Pop GO Term Count % PValue Bonferroni Benjamini FDR Genes Total Hits Total Enrichment DLC1, CADM1, NELL2, CLSTN1, PCDHGA8, CTNNB1, NRCAM, APP, CNTNAP2, FERT2, RAPGEF1, PTPRM, MPDZ, SDK1, PCDH9, PTPRS, VEZT, NRXN1, MYH9, GO:0007155~cell CTNNA2, NCAM1, NCAM2, DDR1, LSAMP, CNTN1, 50 5.61 2.14E-08 510 311 7436 2.34 4.50E-05 4.50E-05 3.70E-05 adhesion ROR2, VCAN, DST, LIMS1, TNC, ASTN1, CTNND2, CTNND1, CDH2, NEO1, CDH4, CD24A, FAT3, PVRL3, TRO, TTYH1, MLLT4, LPP, NLGN1, PCDH19, LAMA1, ITGA9, CDH13, CDON, PSPC1 DLC1, CADM1, NELL2, CLSTN1, PCDHGA8, CTNNB1, NRCAM, APP, CNTNAP2, FERT2, RAPGEF1, PTPRM, MPDZ, SDK1, PCDH9, PTPRS, VEZT, NRXN1, MYH9, GO:0022610~biological CTNNA2, NCAM1, NCAM2, DDR1, LSAMP, CNTN1, 50 5.61 2.14E-08 510 311 7436 2.34 4.50E-05 4.50E-05 3.70E-05 adhesion ROR2, VCAN, DST, LIMS1, TNC, ASTN1, CTNND2, CTNND1, CDH2, NEO1, CDH4, CD24A, FAT3, PVRL3, TRO, TTYH1, MLLT4, LPP, NLGN1, PCDH19, LAMA1, ITGA9, CDH13, CDON, PSPC1 DCC, ENAH, PLXNA2, CAPZA2, ATP5B, ASTN1, PAX6, ZEB2, CDH2, CDH4, GLI3, CD24A, EPHB1, NRCAM, GO:0006928~cell CTTNBP2, EDNRB, APP, PTK2, ETV1, CLASP2, STRBP, 36 4.04 3.46E-07 510 205 7436 2.56 7.28E-04 3.64E-04 5.98E-04 motion NRG1, DCLK1, PLAT, SGPL1, TGFBR1, EVL, MYH9, YWHAE, NCKAP1, CTNNA2, SEMA6A, EPHA4, NDEL1, FYN, LRP6 PLXNA2, ADCY5, PAX6, GLI3, CTNNB1, LPHN2, EDNRB, LPHN3, APP, CSNK2A1, GPR45, NRG1, RAPGEF1, WWOX, SGPL1, TLE4, SPEN, NCAM1, DDR1, GRB10, GRM3, GNAQ, HIPK1, GNB1, HIPK2, PYGO1, GO:0007166~cell RNF138, ROR2, CNTN1, -
Accompanies CD8 T Cell Effector Function Global DNA Methylation
Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer, Benjamin G. Barwick, Benjamin A. Youngblood, Rafi Ahmed and Jeremy M. Boss This information is current as of October 1, 2021. J Immunol 2013; 191:3419-3429; Prepublished online 16 August 2013; doi: 10.4049/jimmunol.1301395 http://www.jimmunol.org/content/191/6/3419 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130139 Material 5.DC1 References This article cites 81 articles, 25 of which you can access for free at: http://www.jimmunol.org/content/191/6/3419.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer,* Benjamin G. Barwick,* Benjamin A. Youngblood,*,† Rafi Ahmed,*,† and Jeremy M. -
Supplemental Materials and Methods
Supplemental Material for: Transcriptional silencing of γ-globin by BCL11A involves long-range interactions and cooperation with SOX6 Jian Xu, Vijay G. Sankaran, Min Ni, Tobias F. Menne, Rishi V. Puram, Woojin Kim, Stuart H. Orkin* *To whom correspondence should be addressed. E-mail: [email protected] Supplemental Materials and Methods Flow cytometry Cells at various stages of differentiation were analyzed by flow cytometry using FACSCalibur (BD Biosciences, San Jose, CA). Live cells were identified and gated by exclusion of 7-amino-actinomycin D (7-AAD; BD Pharmingen). The cells were analyzed for expression of cell surface receptors with antibodies specific for CD34, CD45, CD71, CD235, and CD36 conjugated to phycoerythrin (PE), fluorescein isothiocyanate (FITC), or allophycocyanin (APC; BD Pharmingen). Data were analyzed using FlowJo software (Ashland, OR). Cytology Cytocentrifuge preparations were stained with May-Grunwald-Giemsa as previously described (Sankaran et al. 2008). Real-time RT-PCR Real-time quantitative RT-PCR was performed using the iQ SYBR Green Supermix (Bio- Rad). The following primers were used for real-time RT-PCR: human and mouse BCL11A-XL (forward, 5’-ATGCGAGCTGTGCAACTATG-3’; reverse, 5’- GTAAACGTCCTTCCCCACCT-3’), human and mouse BCL11A-L (forward, 5’- CAGCTCAAAAGAGGGCAGAC-3’; reverse, 5’-GAGCTTCCATCCGAAAACTG-3’), and human BCL11A exon 1 and 2 (common between all known isoforms; forward, 5’- AACCCCAGCACTTAAGCAAA-3’; reverse, 5’-GGAGGTCATGATCCCCTTCT-3’). Supplemental Figure Legends Supplemental Figure 1. Expression of BCL11A isoforms in human and mouse erythroid cells. (A) Schematic diagram of human BCL11A isoforms (Liu et al. 2006). The antibodies used for ChIP experiments and their corresponding epitopes are indicated. Locations of primers used for RT-PCR analysis of all BCL11A isoforms (forward and reverse primers indicated by arrowheads), XL and L isoforms are indicated. -
Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice. -
A Set of Regulatory Genes Co-Expressed in Embryonic Human Brain Is Implicated in Disrupted Speech Development
Molecular Psychiatry https://doi.org/10.1038/s41380-018-0020-x ARTICLE A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development 1 1 1 2 3 Else Eising ● Amaia Carrion-Castillo ● Arianna Vino ● Edythe A. Strand ● Kathy J. Jakielski ● 4,5 6 7 8 9 Thomas S. Scerri ● Michael S. Hildebrand ● Richard Webster ● Alan Ma ● Bernard Mazoyer ● 1,10 4,5 6,11 6,12 13 Clyde Francks ● Melanie Bahlo ● Ingrid E. Scheffer ● Angela T. Morgan ● Lawrence D. Shriberg ● Simon E. Fisher 1,10 Received: 22 September 2017 / Revised: 3 December 2017 / Accepted: 2 January 2018 © The Author(s) 2018. This article is published with open access Abstract Genetic investigations of people with impaired development of spoken language provide windows into key aspects of human biology. Over 15 years after FOXP2 was identified, most speech and language impairments remain unexplained at the molecular level. We sequenced whole genomes of nineteen unrelated individuals diagnosed with childhood apraxia of speech, a rare disorder enriched for causative mutations of large effect. Where DNA was available from unaffected parents, CHD3 SETD1A WDR5 fi 1234567890();,: we discovered de novo mutations, implicating genes, including , and . In other probands, we identi ed novel loss-of-function variants affecting KAT6A, SETBP1, ZFHX4, TNRC6B and MKL2, regulatory genes with links to neurodevelopment. Several of the new candidates interact with each other or with known speech-related genes. Moreover, they show significant clustering within a single co-expression module of genes highly expressed during early human brain development. This study highlights gene regulatory pathways in the developing brain that may contribute to acquisition of proficient speech. -
Cortical Foxp2 Supports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression
bioRxiv preprint doi: https://doi.org/10.1101/624973; this version posted May 2, 2019. 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-ND 4.0 International license. Cortical Foxp2 supports behavioral flexibility and developmental dopamine D1 receptor expression Marissa Co, Stephanie L. Hickey, Ashwinikumar Kulkarni, Matthew Harper, Genevieve Konopka* Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA *Correspondence: [email protected] Contact information Genevieve Konopka, Ph.D. Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., ND4.300, Dallas, TX 75390-9111 TEL: 214-648-5135, FAX: 214-648-1801, Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/624973; this version posted May 2, 2019. 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-ND 4.0 International license. Abstract FoxP2 encodes a forkhead box transcription factor required for the development of neural circuits underlying language, vocalization, and motor-skill learning. Human genetic studies have associated FOXP2 variation with neurodevelopmental disorders (NDDs), and within the cortex, it is coexpressed and interacts with other NDD-associated transcription factors. Cortical Foxp2 is required in mice for proper social interactions, but its role in other NDD-relevant behaviors and molecular pathways is unknown.