Tissue-Specific Transcriptome for Poeciliopsis Prolifica Reveals
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Comparative Gene Expression Profiling of Stromal Cell Matrices
ell Res C ea m rc te h S & f o T h l Journal of Tiwari et al., J Stem Cell Res Ther 2013, 3:4 e a r n a r p u DOI: 10.4172/2157-7633.1000152 y o J ISSN: 2157-7633 Stem Cell Research & Therapy Research Article Open Access Comparative Gene Expression Profiling of Stromal Cell Matrices that Support Expansion of Hematopoietic Stem/Progenitor Cells Abhilasha Tiwari1,2, Christophe Lefevre2, Mark A Kirkland2*, Kevin Nicholas2 and Gopal Pande1* 1CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India 2Deakin University, Waurn Ponds, Geelong, VIC, Australia Abstract The bone marrow microenvironment maintains a stable balance between self-renewal and differentiation of hematopoietic stem/progenitor cells (HSPCs). This microenvironment, also termed the “hematopoietic niche”, is primarily composed of stromal cells and their extracellular matrices (ECM) that jointly regulate HSPC functions. Previously, we have demonstrated that umbilical cord blood derived HSPCs can be maintained and expanded on stromal cell derived acellular matrices that mimic the complexity of the hematopoietic niche. The results indicated that matrices prepared at 20% O2 with osteogenic medium (OGM) were best suited for expanding committed HSPCs, whereas, matrices prepared at 5% O2 without OGM were better for primitive progenitors. Based upon these results we proposed that individual constituents of these matrices could be responsible for regulation of specific HSPC functions. To explore this hypothesis, we have performed comparative transcriptome profiling of these matrix producing cells, which identified differential expression of both known niche regulators, such as Wnt4, Angpt2, Vcam and Cxcl12, as well as genes not previously associated with HSPC regulation, such as Depp. -
Sorbonne Université́
Sorbonne Université́ École Doctorale ED515 – Complexité́ du vivant INSERM UMRS 933 : Physiopathologie des maladies génétiques d'expression pédiatrique Mécanismes physiopathologiques impliqués dans la différenciation du tractus génital masculin Matthieu Peycelon Thèse de Doctorat de Génétique Humaine Dirigée par Pr. Jean-Pierre Siffroi Présentée et soutenue publiquement le 19 décembre 2019 Devant un jury composé de : Brigitte BENZACKEN PU-PH Université Paris 13 Rapporteur Anne-Françoise SPINOIT Professeur Université de Gand Rapporteur Irène NETCHINE PU-PH Université Paris 6 Examinateur Nicolas KALFA PU-PH Université de Montpellier Examinateur Alaa EL GHONEIMI PU-PH Université Paris 7 Président Jean-Pierre SIFFROI PU-PH Université Paris 6 Directeur de thèse Sorbonne Université́ École Doctorale ED515 – Complexité́ du vivant INSERM UMRS 933 : Physiopathologie des maladies génétiques d'expression pédiatrique Mécanismes physiopathologiques impliqués dans la différenciation du tractus génital masculin Matthieu Peycelon Thèse de Doctorat de Génétique Humaine Dirigée par Pr. Jean-Pierre Siffroi Présentée et soutenue publiquement le 19 décembre 2019 Devant un jury composé de : Brigitte BENZACKEN PU-PH Université Paris 13 Rapporteur Anne-Françoise SPINOIT Professeur Université de Gand Rapporteur Irène NETCHINE PU-PH Université Paris 6 Examinateur Nicolas KALFA PU-PH Université de Montpellier Examinateur Alaa EL GHONEIMI PU-PH Université Paris 7 Président Jean-Pierre SIFFROI PU-PH Université Paris 6 Directeur de thèse Ce travail de thèse a été réalisé́ sous la direction du Professeur Jean-Pierre Siffroi, au sein de l’unité́ mixte de recherche INSERM / Sorbonne Université UMR_S933 dirigée par le Professeur Serge Amselem. Adresse : Département de Génétique Médicale, Hôpital Armand Trousseau ; 26 avenue du Docteur Arnold Netter, 75012, Paris. -
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. -
TET2 Binds the Androgen Receptor and Loss Is Associated with Prostate Cancer
Oncogene (2016), 1–12 © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 0950-9232/16 www.nature.com/onc ORIGINAL ARTICLE TET2 binds the androgen receptor and loss is associated with prostate cancer ML Nickerson1,14, S Das2,KMIm3, S Turan1, SI Berndt4,HLi1,5,HLou1,5, SA Brodie4,6, JN Billaud7, T Zhang8, AJ Bouk4,6, D Butcher9, Z Wang4, L Sun10, K Misner1,WTan1,5, A Esnakula11, D Esposito12, WY Huang4, RN Hoover4, MA Tucker4, JR Keller10, J Boland4,6, K Brown8, SK Anderson1, LE Moore4, WB Isaacs13, SJ Chanock4, M Yeager4,6, M Dean1,14 and T Andresson2 Genetic alterations associated with prostate cancer (PCa) may be identified by sequencing metastatic tumour genomes to identify molecular markers at this lethal stage of disease. Previously, we characterized somatic alterations in metastatic tumours in the methylcytosine dioxygenase ten-eleven translocation 2 (TET2), which is altered in 5–15% of myeloid, kidney, colon and PCas. Genome-wide association studies previously identified non-coding risk variants associated with PCa and melanoma. We perform fine-mapping of PCa risk across TET2 using genotypes from the PEGASUS case-control cohort and identify six new risk variants in introns 1 and 2. Oligonucleotides containing two risk variants are bound by the transcription factor octamer-binding protein 1 (Oct1/POU2F1) and TET2 and Oct1 expression are positively correlated in prostate tumours. TET2 is expressed in normal prostate tissue and reduced in a subset of tumours from the Cancer Genome Atlas (TCGA). Small interfering RNA-mediated TET2 knockdown (KD) increases LNCaP cell proliferation, migration and wound healing, verifying loss drives a cancer phenotype. -
C10ORF10/DEPP, a Transcriptional Target of FOXO3, Regulates ROS
Salcher et al. Molecular Cancer 2014, 13:224 http://www.molecular-cancer.com/content/13/1/224 RESEARCH Open Access C10ORF10/DEPP, a transcriptional target of FOXO3, regulates ROS-sensitivity in human neuroblastoma Stefan Salcher2,4, Judith Hagenbuchner2,4, Kathrin Geiger4, Maximilian A Seiter1,4, Johannes Rainer3,4, Reinhard Kofler3,4, Martin Hermann5, Ursula Kiechl-Kohlendorfer2, Michael J Ausserlechner1,4* and Petra Obexer2,4* Abstract Background: FOXO transcription factors control cellular levels of reactive oxygen species (ROS) which critically contribute to cell survival and cell death in neuroblastoma. In the present study we investigated the regulation of C10orf10/DEPP by the transcription factor FOXO3. As a physiological function of C10orf10/DEPP has not been described so far we analyzed its effects on cellular ROS detoxification and death sensitization in human neuroblastoma cells. Methods: The effect of DEPP on cellular ROS was measured by catalase activity assay and live cell fluorescence microscopy using the ROS-sensitive dye reduced MitoTracker Red CM-H2XROS. The cellular localization of DEPP was determined by confocal microscopy of EYFP-tagged DEPP, fluorescent peroxisomal- and mitochondrial probes and co-immunoprecipitation of the PEX7 receptor. Results: We report for the first time that DEPP regulates ROS detoxification and localizes to peroxisomes and mitochondria in neuroblastoma cells. FOXO3-mediated apoptosis involves a biphasic ROS accumulation. Knockdown of DEPP prevented the primary and secondary ROS wave during FOXO3 activation and attenuated FOXO3- and H2O2-induced apoptosis. Conditional overexpression of DEPP elevates cellular ROS levels and sensitizes to H2O2 and etoposide-induced cell death. In neuronal cells, cellular ROS are mainly detoxified in peroxisomes by the enzyme CAT/catalase. -
Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders
177 Arch Neuropsychitry 2020;57:177−191 RESEARCH ARTICLE https://doi.org/10.29399/npa.24890 Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders Hakan GÜRKAN1 , Emine İkbal ATLI1 , Engin ATLI1 , Leyla BOZATLI2 , Mengühan ARAZ ALTAY2 , Sinem YALÇINTEPE1 , Yasemin ÖZEN1 , Damla EKER1 , Çisem AKURUT1 , Selma DEMİR1 , Işık GÖRKER2 1Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey 2Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey ABSTRACT Introduction: Aneuploids, copy number variations (CNVs), and single in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown nucleotide variants in specific genes are the main genetic causes of significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients developmental delay (DD) and intellectual disability disorder (IDD). were reported. In 6 patients, one or more pathogenic CNVs were These genetic changes can be detected using chromosome analysis, determined. Therefore, the diagnostic efficiency of CMA was found to chromosomal microarray (CMA), and next-generation DNA sequencing be 31.7% (39/123). techniques. Therefore; In this study, we aimed to investigate the Conclusion: Today, genetic analysis is still not part of the routine in the importance of CMA in determining the genomic etiology of unexplained evaluation of IDD patients who present to psychiatry clinics. A genetic DD and IDD in 123 patients. diagnosis from CMA can eliminate genetic question marks and thus Method: For 123 patients, chromosome analysis, DNA fragment analysis alter the clinical management of patients. Approximately one-third and microarray were performed. Conventional G-band karyotype of the positive CMA findings are clinically intervenable. -
Genetic Findings As the Potential Basis of Personalized Pharmacotherapy in Phelan-Mcdermid Syndrome
G C A T T A C G G C A T genes Review Genetic Findings as the Potential Basis of Personalized Pharmacotherapy in Phelan-McDermid Syndrome Brianna Dyar 1, Erika Meaddough 1, Sara M. Sarasua 1, Curtis Rogers 2, Katy Phelan 3 and Luigi Boccuto 1,* 1 Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; [email protected] (B.D.); [email protected] (E.M.); [email protected] (S.M.S.) 2 Greenwood Genetic Center, Greenwood, SC 29649, USA; [email protected] 3 Florida Cancer Specialists & Research Institute, Fort Myers, FL 33905, USA; kphelan@flcancer.com * Correspondence: [email protected] Abstract: Phelan-McDermid syndrome (PMS) is a genetic disorder often characterized by autism or autistic-like behavior. Most cases are associated with haploinsufficiency of the SHANK3 gene resulting from deletion of the gene at 22q13.3 or from a pathogenic variant in the gene. Treatment of PMS often targets SHANK3, yet deletion size varies from <50 kb to >9 Mb, potentially encompassing dozens of genes and disrupting regulatory elements altering gene expression, inferring the potential for multiple therapeutic targets. Repurposed drugs have been used in clinical trials investigating therapies for PMS: insulin-like growth factor 1 (IGF-1) for its effect on social and aberrant behaviors, intranasal insulin for improvements in cognitive and social ability, and lithium for reversing regression and stabilizing behavior. The pharmacogenomics of PMS is complicated by the CYP2D6 enzyme which metabolizes antidepressants and antipsychotics often used for treatment. The gene coding for Citation: Dyar, B.; Meaddough, E.; CYP2D6 maps to 22q13.2 and is lost in individuals with deletions larger than 8 Mb. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
The Expression of Decidual Protein Induced by Progesterone
G C A T T A C G G C A T genes Article The Expression of Decidual Protein Induced by Progesterone (DEPP) Is Controlled by Three Distal Consensus Hypoxia Responsive Element (HRE) in Hypoxic Retinal Epithelial Cells Katrin Klee 1,2, Federica Storti 1, Jordi Maggi 2,3 , Vyara Todorova 1,4, Duygu Karademir 1,2, Wolfgang Berger 2,3,4, Marijana Samardzija 1 and Christian Grimm 1,2,4,* 1 Department of Ophthalmology, Lab for Retinal Cell Biology, University of Zurich, 8952 Schlieren, Switzerland; [email protected] (K.K.); [email protected] (F.S.); [email protected] (V.T.); [email protected] (D.K.); [email protected] (M.S.) 2 Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland; [email protected] (J.M.); [email protected] (W.B.) 3 Institute of Medical Molecular Genetic, University of Zurich, 8952 Schlieren, Switzerland 4 Neuroscience Center, University of Zurich, 8006 Zurich, Switzerland * Correspondence: [email protected]; Tel.: +41-43-253-3001 Received: 19 November 2019; Accepted: 14 January 2020; Published: 18 January 2020 Abstract: Hypoxia affects the development and/or progression of several retinopathies. Decidual protein induced by progesterone (DEPP) has been identified as a hypoxia-responsive gene that may be part of cellular pathways such as autophagy and connected to retinal diseases. To increase our understanding of DEPP regulation in the eye, we defined its expression pattern in mouse and human retina and retinal pigment epithelium (RPE). Interestingly, DEPP expression was increased in an age-dependent way in the central human RPE. -
Gene Expression Analysis of Endometrium Reveals Progesterone Resistance and Candidate Susceptibility Genes in Women with Endometriosis
0013-7227/07/$15.00/0 Endocrinology 148(8):3814–3826 Printed in U.S.A. Copyright © 2007 by The Endocrine Society doi: 10.1210/en.2006-1692 Gene Expression Analysis of Endometrium Reveals Progesterone Resistance and Candidate Susceptibility Genes in Women with Endometriosis Richard O. Burney,* Said Talbi,* Amy E. Hamilton, Kim Chi Vo, Mette Nyegaard, Camran R. Nezhat, Bruce A. Lessey, and Linda C. Giudice Downloaded from https://academic.oup.com/endo/article-abstract/148/8/3814/2502189 by guest on 14 June 2020 Department of Obstetrics and Gynecology (R.O.B., M.N., C.R.N.), Stanford University, Stanford, California 94305; Department of Obstetrics, Gynecology, and Reproductive Sciences (S.T., A.E.H., K.C.V., L.C.G.), University of California, San Francisco, San Francisco, California 94143-0138; and Department of Obstetrics and Gynecology (B.A.L.), University Medical Group, Greenville Hospital System, Greenville, South Carolina 29605 The identification of molecular differences in the endome- enhanced cellular survival and persistent expression of genes trium of women with endometriosis is an important step to- involved in DNA synthesis and cellular mitosis in the setting ward understanding the pathogenesis of this condition and of endometriosis. Comparative gene expression analysis of toward developing novel strategies for the treatment of asso- progesterone-regulated genes in secretory phase endome- ciated infertility and pain. In this study, we conducted global trium confirmed the observation of attenuated progesterone gene expression analysis of endometrium from women with response. Additionally, interesting candidate susceptibility and without moderate/severe stage endometriosis and com- genes were identified that may be associated with this disor- pared the gene expression signatures across various phases of der, including FOXO1A, MIG6, and CYP26A1. -
Transcriptomics of Early Human Development
TRANSCRIPTOMICS OF EARLY HUMAN DEVELOPMENT NAHENIWELA HERATH MUDIYANSELAGE WISHVA BANDARA HERATH NATIONAL UNIVERSITY OF SINGAPORE 2011 TRANSCRIPTOMICS OF EARLY HUMAN DEVELOPMENT NAHENIWELA HERATH MUDIYANSELAGE WISHVA BANDARA HERATH BSc. (Hons.), Grad. Chem. A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY NUS GRADUATE SCHOOL FOR INTEGRATIVE SCIENCES AND ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2011 Acknowledgement My phD journey was an extremely eventful one. I was trained as a microbiologist and a chemist, then became a biochemist working on proteomics and ended up doing my thesis project as a developmental / molecular biologist on transcriptomics. Without the help of several special people this thesis would not have been possible. I would like to thank... Dr. Paul Robson, my supervisor, for giving me the opportunity to work under him, for his advice, insights and guidance throughout the project and for creating a stress-free environment in the lab which is a pleasure to work in. Prof. Justine Burley, for her kindness and support when I needed it the most. My wife Dulani, for being by my side, through thick and thin. Thank you! The trophoblast differentiation protocol which I use extensively in my thesis was first described by Dr. Luo Wenlong. Dr. Mikael Huss helped me with bioinformatic analysis and helped me learn python programming, Mr. Audi Harsono helped me in validating RNA-Seq data, Ms. Woon Chow Thai ran the microarrays, Ms. Jameelah Sheik Mohamed taught me stem cell culture and Dr. Guo Guoji helped me extract mouse embryo samples. I would also like to acknowledge NUS Graduate School for Integrative Sciences and Engineering (NGS) for my scholarship and the Genome Institute of Singapore (GIS) where I carried out my research. -
DNA Methylation Epi-Signature Is Associated with Two Molecularly
Schenkel et al. Clin Epigenet (2021) 13:2 https://doi.org/10.1186/s13148-020-00990-7 RESEARCH Open Access DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome L. C. Schenkel1,2, E. Aref‑Eshghi1, K. Rooney1, J. Kerkhof1, M. A. Levy1, H. McConkey1, R. C. Rogers4, K. Phelan5, S. M. Sarasua6, L. Jain3,6, R. Pauly3, L. Boccuto3,6, B. DuPont3, G. Cappuccio7,8, N. Brunetti‑Pierri7,8, C. E. Schwartz3* and B. Sadikovic1,2* Abstract Background: Phelan‑McDermid syndrome is characterized by a range of neurodevelopmental phenotypes with incomplete penetrance and variable expressivity. It is caused by a variable size and breakpoint microdeletions in the distal long arm of chromosome 22, referred to as 22q13.3 deletion syndrome, including the SHANK3 gene. Genetic defects in a growing number of neurodevelopmental genes have been shown to cause genome‑wide disruptions in epigenomic profles referred to as epi‑signatures in afected individuals. Results: In this study we assessed genome‑wide DNA methylation profles in a cohort of 22 individuals with Phelan‑ McDermid syndrome, including 11 individuals with large (2 to 5.8 Mb) 22q13.3 deletions, 10 with small deletions (< 1 Mb) or intragenic variants in SHANK3 and one mosaic case. We describe a novel genome‑wide DNA methylation epi‑signature in a subset of individuals with Phelan‑McDermid syndrome. Conclusion: We identifed the critical region including the BRD1 gene as responsible for the Phelan‑McDermid syndrome epi‑signature. Metabolomic profles of individuals with the DNA methylation epi‑signature showed sig‑ nifcantly diferent metabolomic profles indicating evidence of two molecularly and phenotypically distinct clinical subtypes of Phelan‑McDermid syndrome.