Accumulation of Cd11c+CD163+ Adipose Tissue Macrophages Through Upregulation of Intracellular 11Β-HSD1 in Human Obesity
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Article Genetic Control of Gonadal Sex Determination and Development STEVANT, Isabelle, NEF, Serge Abstract Sex determination is the process by which the bipotential gonads develop as either testes or ovaries. With two distinct potential outcomes, the gonadal primordium offers a unique model for the study of cell fate specification and how distinct cell populations diverge from multipotent progenitors. This review focuses on recent advances in our understanding of the genetic programs and epigenetic mechanisms that regulate gonadal sex determination and the regulation of cell fate commitment in the bipotential gonads. We rely primarily on mouse data to illuminate the complex and dynamic genetic programs controlling cell fate decision and sex-specific cell differentiation during gonadal formation and gonadal sex determination. Reference STEVANT, Isabelle, NEF, Serge. Genetic Control of Gonadal Sex Determination and Development. Trends in Genetics, 2019 PMID : 30902461 DOI : 10.1016/j.tig.2019.02.004 Available at: http://archive-ouverte.unige.ch/unige:115790 Disclaimer: layout of this document may differ from the published version. 1 / 1 Trends in Genetics Genetic control of sex determination and gonad development --Manuscript Draft-- Manuscript Number: TIGS-D-18-00173R1 Article Type: Review Keywords: sex determination; ovary; testis; lineage specification; gene expression; epigenetic regulation Corresponding Author: Serge Nef geneva, SWITZERLAND First Author: Isabelle Stévant Order of Authors: Isabelle Stévant Serge Nef Abstract: Sex determination is the process by which the bipotential gonads develop as either testes or ovaries. With two distinct potential outomes, the gonadal primordium offers a unique model for the study of cell fate specification and how distinct cell populations diverge from multipotent progenitors. -
Hormone Therapy Use and Breast Tissue DNA
http://www.diva-portal.org This is the published version of a paper published in Epigenetics. Citation for the original published paper (version of record): Harlid, S., Xu, Z., Kirk, E., Wilson, L E., Troester, M A. et al. (2019) Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study Epigenetics, 14(2): 146-157 https://doi.org/10.1080/15592294.2019.1580111 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-157445 EPIGENETICS 2019, VOL. 14, NO. 2, 146–157 https://doi.org/10.1080/15592294.2019.1580111 RESEARCH PAPER Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study Sophia Harlid a,b, Zongli Xuc, Erin Kirkd, Lauren E. Wilson c,e, Melissa A. Troesterd, and Jack A. Taylor a,c aEpigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; bDepartment of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden; cEpidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; dDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; eDepartment of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA ABSTRACT ARTICLE HISTORY Hormone therapy (HT) is associated with increased risk of breast cancer, strongly dependent on Received 4 September 2018 type, duration, and recency of use. HT use could affect cancer risk by changing breast tissue Revised 21 December 2018 transcriptional programs. -
The Genomic Response to Retinal Disease and Injury: Evidence for Endothelin Signaling from Photoreceptors to Glia
4540 • The Journal of Neuroscience, May 4, 2005 • 25(18):4540–4549 Neurobiology of Disease The Genomic Response to Retinal Disease and Injury: Evidence for Endothelin Signaling from Photoreceptors to Glia Amir Rattner1 and Jeremy Nathans1,2 1Department of Molecular Biology and Genetics and 2Departments of Neuroscience and Ophthalmology and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Regardless of proximal cause, photoreceptor injury or disease almost invariably leads to the activation of Muller cells, the principal glial cells in the retina. This observation implies the existence of signaling systems that inform Muller cells of the health status of photorecep- tors. It further suggests that diverse types of photoreceptor damage elicit a limited range of biochemical responses. Using the mouse retina, we show by microarray, RNA blot, and in situ hybridization that the genomic responses to both light damage and inherited photoreceptor degeneration involve a relatively small number of genes and that the genes activated by these two insults overlap substan- tially with one another and with the genes activated by retinal detachment. Among the induced transcripts, those coding for endothelin2 (Edn2) are unusual in that they are localized to photoreceptors and are also highly induced in all of the tested models of photoreceptor disease or injury. Acute light damage also leads to a Ͼ10-fold increase in endothelin receptor B (Ednrb) in Muller cells 24 h after injury. These observations suggest that photoreceptor-derived EDN2 functions as a general stress signal, that EDN2 signals to Muller cells by binding to EDNRB, and that Muller cells can increase their sensitivity to EDN2 as part of the injury response. -
The Role of the Mtor Pathway in Developmental Reprogramming Of
THE ROLE OF THE MTOR PATHWAY IN DEVELOPMENTAL REPROGRAMMING OF HEPATIC LIPID METABOLISM AND THE HEPATIC TRANSCRIPTOME AFTER EXPOSURE TO 2,2',4,4'- TETRABROMODIPHENYL ETHER (BDE-47) An Honors Thesis Presented By JOSEPH PAUL MCGAUNN Approved as to style and content by: ________________________________________________________** Alexander Suvorov 05/18/20 10:40 ** Chair ________________________________________________________** Laura V Danai 05/18/20 10:51 ** Committee Member ________________________________________________________** Scott C Garman 05/18/20 10:57 ** Honors Program Director ABSTRACT An emerging hypothesis links the epidemic of metabolic diseases, such as non-alcoholic fatty liver disease (NAFLD) and diabetes with chemical exposures during development. Evidence from our lab and others suggests that developmental exposure to environmentally prevalent flame-retardant BDE47 may permanently reprogram hepatic lipid metabolism, resulting in an NAFLD-like phenotype. Additionally, we have demonstrated that BDE-47 alters the activity of both mTOR complexes (mTORC1 and 2) in hepatocytes. The mTOR pathway integrates environmental information from different signaling pathways, and regulates key cellular functions such as lipid metabolism, innate immunity, and ribosome biogenesis. Thus, we hypothesized that the developmental effects of BDE-47 on liver lipid metabolism are mTOR-dependent. To assess this, we generated mice with liver-specific deletions of mTORC1 or mTORC2 and exposed these mice and their respective controls perinatally to -
Mice Subjected to Ap2-Cre Mediated Ablation of Microsomal Triglyceride Transfer Protein Are Resistant to High Fat Diet Induced Obesity Ahmed Bakillah1,2* and M
Bakillah and Hussain Nutrition & Metabolism (2016) 13:1 DOI 10.1186/s12986-016-0061-6 RESEARCH Open Access Mice subjected to aP2-Cre mediated ablation of microsomal triglyceride transfer protein are resistant to high fat diet induced obesity Ahmed Bakillah1,2* and M. Mahmood Hussain1,2,3 Abstract Background: Microsomal triglyceride transfer protein (MTP) is essential for the assembly of lipoproteins. MTP has been shown on the surface of lipid droplets of adipocytes; however its function in adipose tissue is not well defined. We hypothesized that MTP may play critical role in adipose lipid droplet formation and expansion. Methods: Plasmids mediated overexpression and siRNA mediated knockdown of Mttp gene were performed in 3T3-L1 pre-adipocytes to evaluate the effects of MTP on cell differentiation and triglyceride accumulation. Adipose- specific knockdown of MTP was achieved in mice bybreeding MTP floxed (Mttpfl/fl) mice with aP2-Cre recombinase transgenic mice. Adipose-specific MTP deficient (A-Mttp-/-) mice were fed 60 % high-fat diet (HFD), and the effects of MTP knockdown on body weight, body fat composition, plasma and tissues lipid composition, glucose metabolism, lipogenesis and intestinal absorption was studied. Lipids were measured in total fasting plasma and size fractionated plasma using colorimetric assays. Gene expression was investigated by Real-Time quantitative PCR. All data was assessed using t-test, ANOVA. Results: MTP expression increased during early differentiation in 3T3-L1 cells, and declined later. The increases in MTP expression preceded PPARγ expression. MTP overexpression enhanced lipid droplets formation, and knockdown attenuated cellular lipid accumulation. These studies indicated that MTP positively affects adipogenesis. -
Supplementary Table S1. Upregulated Genes Differentially
Supplementary Table S1. Upregulated genes differentially expressed in athletes (p < 0.05 and 1.3-fold change) Gene Symbol p Value Fold Change 221051_s_at NMRK2 0.01 2.38 236518_at CCDC183 0.00 2.05 218804_at ANO1 0.00 2.05 234675_x_at 0.01 2.02 207076_s_at ASS1 0.00 1.85 209135_at ASPH 0.02 1.81 228434_at BTNL9 0.03 1.81 229985_at BTNL9 0.01 1.79 215795_at MYH7B 0.01 1.78 217979_at TSPAN13 0.01 1.77 230992_at BTNL9 0.01 1.75 226884_at LRRN1 0.03 1.74 220039_s_at CDKAL1 0.01 1.73 236520_at 0.02 1.72 219895_at TMEM255A 0.04 1.72 201030_x_at LDHB 0.00 1.69 233824_at 0.00 1.69 232257_s_at 0.05 1.67 236359_at SCN4B 0.04 1.64 242868_at 0.00 1.63 1557286_at 0.01 1.63 202780_at OXCT1 0.01 1.63 1556542_a_at 0.04 1.63 209992_at PFKFB2 0.04 1.63 205247_at NOTCH4 0.01 1.62 1554182_at TRIM73///TRIM74 0.00 1.61 232892_at MIR1-1HG 0.02 1.61 204726_at CDH13 0.01 1.6 1561167_at 0.01 1.6 1565821_at 0.01 1.6 210169_at SEC14L5 0.01 1.6 236963_at 0.02 1.6 1552880_at SEC16B 0.02 1.6 235228_at CCDC85A 0.02 1.6 1568623_a_at SLC35E4 0.00 1.59 204844_at ENPEP 0.00 1.59 1552256_a_at SCARB1 0.02 1.59 1557283_a_at ZNF519 0.02 1.59 1557293_at LINC00969 0.03 1.59 231644_at 0.01 1.58 228115_at GAREM1 0.01 1.58 223687_s_at LY6K 0.02 1.58 231779_at IRAK2 0.03 1.58 243332_at LOC105379610 0.04 1.58 232118_at 0.01 1.57 203423_at RBP1 0.02 1.57 AMY1A///AMY1B///AMY1C///AMY2A///AMY2B// 208498_s_at 0.03 1.57 /AMYP1 237154_at LOC101930114 0.00 1.56 1559691_at 0.01 1.56 243481_at RHOJ 0.03 1.56 238834_at MYLK3 0.01 1.55 213438_at NFASC 0.02 1.55 242290_at TACC1 0.04 1.55 ANKRD20A1///ANKRD20A12P///ANKRD20A2/// -
ARHGEF4 (NM 015320) 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 RC215591 ARHGEF4 (NM_015320) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: ARHGEF4 (NM_015320) Human Tagged ORF Clone Tag: Myc-DDK Symbol: ARHGEF4 Synonyms: ASEF; ASEF1; GEF4; SMIM39; STM6 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin 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 / 5 ARHGEF4 (NM_015320) Human Tagged ORF Clone – RC215591 ORF Nucleotide >RC215591 representing NM_015320 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGCCCTGGGAAGAACCAGCAGGTGAGAAGCCCAGTTGCTCTCACAGTCAGAAGGCATTCCACATGGAGC CTGCCCAGAAGCCCTGCTTCACCACTGACATGGTGACATGGGCCCTCCTCTGCATCTCTGCAGAGACTGT GCGTGGGGAGGCTCCTTCACAGCCTAGGGGCATCCCTCACCGCTCGCCCGTCAGTGTGGATGACCTGTGG CTGGAGAAGACACAGAGAAAGAAGTTGCAGAAGCAGGCCCACATCGAAAGGAGGCTGCACATAGGGGCAG TGCACAAAGATGGAGTCAAGTGCTGGAGAAAGACGATCATTACCTCTCCAGAGTCTTTGAATCTCCCTAG AAGAAGCCATCCACTCTCCCAGAGTGCTCCAACGGGACTGAACCACATGGGCTGGCCAGAGCACACACCA GGCACTGCCATGCCTGATGGAGCTCTGGACACAGCTGTCTGCGCTGACGAAGTGGGGAGCGAGGAGGACC TGTATGATGACCTGCACAGCTCCAGCCACCACTACAGCCACCCTGGAGGGGGTGGGGAGCAGCTGGCTAT CAATGAGCTCATCAGCGATGGCAGTGTGGTCTGCGCTGAAGCACTCTGGGACCATGTCACCATGGACGAC -
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. -
Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002) -
(Arhgef4) Deficiency Enhances Spatial and Object Recognition Memory
https://doi.org/10.5607/en20049 Exp Neurobiol. 2020 Oct;29(5):334-343. pISSN 1226-2560 • eISSN 2093-8144 Short Communication Rho Guanine Nucleotide Exchange Factor 4 (Arhgef4) Deficiency Enhances Spatial and Object Recognition Memory Ki-Seo Yoo1, Kina Lee1, Yong-Seok Lee2, Won-Jong Oh3 and Hyong Kyu Kim1* 1Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, 2Department of Physiology, Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, 3Neurovascular Unit Research Group, Korea Brain Research Institute, Daegu 41062, Korea Guanine nucleotide exchange factors (GEFs) play multiple functional roles in neurons. In a previous study, we reported that Arhgef4 (Rho guanine nucleotide exchange factor 4) functioned as a negative regulator of the excitatory synaptic function by sequestering postsynaptic density protein 95 (PSD-95). However, the role of Arhgef4 in behavior has not been examined. We performed comprehensive behavioral tests in knockout (KO) mice to investigate of the effects of Arhgef4 deficiency. We found that the expressed PSD-95 particle size was significantly increased in hippocampal neuronal cultures from Arhgef4 KO mice, which is consistent with the previous in vitro findings. Arhgef4 KO mice exhibited general motor activity and anxiety-like behavior comparable to those of the wild type littermates. However, spatial memory and object recognition memory were signifi- cantly enhanced in the Arhgef4 KO mice. Taken together, these data confirm the role of Arhgef4 as a negative synaptic regulator at the behavioral level. Key words: Arhgef4, PSD-95, Spatial memory, Recognition INTRODUCTION tin, a GEF of inhibitory synapses selectively activating the small GTPase Cdc42, results in a reduced capability of spatial learning Rho guanine nucleotide exchange factors (GEFs) are involved in and enhances anxiety-like behavior in collybistin-deficient mice the activation of Rho family GTPases by accelerating the exchange [4]. -
Fucosyltransferase Genes on Porcine Chromosome 6Q11 Are Closely Linked to the Blood Group Inhibitor (S) and Escherichia Coli F18 Receptor (ECF18R) Loci
Mammalian Genome 8, 736–741 (1997). © Springer-Verlag New York Inc. 1997 Two a(1,2) fucosyltransferase genes on porcine Chromosome 6q11 are closely linked to the blood group inhibitor (S) and Escherichia coli F18 receptor (ECF18R) loci E. Meijerink,1 R. Fries,1,*P.Vo¨geli,1 J. Masabanda,1 G. Wigger,1 C. Stricker,1 S. Neuenschwander,1 H.U. Bertschinger,2 G. Stranzinger1 1Institute of Animal Science, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zurich, Switzerland 2Institute of Veterinary Bacteriology, University of Zurich, CH 8057 Zurich, Switzerland Received: 17 February 1997 / Accepted: 30 May 1997 Abstract. The Escherichia coli F18 receptor locus (ECF18R) has fimbriae F107, has been shown to be genetically controlled by the been genetically mapped to the halothane linkage group on porcine host and is inherited as a dominant trait (Bertschinger et al. 1993) Chromosome (Chr) 6. In an attempt to obtain candidate genes for with B being the susceptibility allele and b the resistance allele. this locus, we isolated 5 cosmids containing the a(1,2)fucosyl- The genetic locus for this E. coli F18 receptor (ECF18R) has been transferase genes FUT1, FUT2, and the pseudogene FUT2P from mapped to porcine Chr 6 (SSC6), based on its close linkage to the a porcine genomic library. Mapping by fluorescence in situ hy- S locus and other loci of the halothane (HAL) linkage group (Vo¨- bridization placed all these clones in band q11 of porcine Chr 6 geli et al. 1996). The epistatic S locus suppresses the phenotypic (SSC6q11). Sequence analysis of the cosmids resulted in the char- expression of the A-0 blood group system when being SsSs (Vo¨geli acterization of an open reading frame (ORF), 1098 bp in length, et al. -
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