Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition from Differentiation to Functional Maturation
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Expression Gene Network Analyses Reveal Molecular Mechanisms And
www.nature.com/scientificreports OPEN Diferential expression and co- expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken Eva Pampouille1,2, Christelle Hennequet-Antier1, Christophe Praud1, Amélie Juanchich1, Aurélien Brionne1, Estelle Godet1, Thierry Bordeau1, Fréderic Fagnoul2, Elisabeth Le Bihan-Duval1 & Cécile Berri1* The broiler industry is facing an increasing prevalence of breast myopathies, such as white striping (WS) and wooden breast (WB), and the precise aetiology of these occurrences remains poorly understood. To progress our understanding of the structural changes and molecular pathways involved in these myopathies, a transcriptomic analysis was performed using an 8 × 60 K Agilent chicken microarray and histological study. The study used pectoralis major muscles from three groups: slow-growing animals (n = 8), fast-growing animals visually free from defects (n = 8), or severely afected by both WS and WB (n = 8). In addition, a weighted correlation network analysis was performed to investigate the relationship between modules of co-expressed genes and histological traits. Functional analysis suggested that selection for fast growing and breast meat yield has progressively led to conditions favouring metabolic shifts towards alternative catabolic pathways to produce energy, leading to an adaptive response to oxidative stress and the frst signs of infammatory, regeneration and fbrosis processes. All these processes are intensifed in muscles afected by severe myopathies, in which new mechanisms related to cellular defences and remodelling seem also activated. Furthermore, our study opens new perspectives for myopathy diagnosis by highlighting fne histological phenotypes and genes whose expression was strongly correlated with defects. Te poultry industry relies on the production of fast-growing chickens, which are slaughtered at high weights and intended for cutting and processing. -
Comparative Mapping of Growth Habit, Plant Height, and Flowering Qtls in Two Interspecific Families of Leymus
Published online November 21, 2006 Comparative Mapping of Growth Habit, Plant Height, and Flowering QTLs in Two Interspecific Families of Leymus Steven R. Larson,* Xiaolei Wu, Thomas A. Jones, Kevin B. Jensen, N. Jerry Chatterton, Blair L. Waldron, Joseph G. Robins, B. Shaun Bushman, and Antonio J. Palazzo ABSTRACT Aggressive rhizomes and adaptation to poorly drained Leymus cinereus (Scribn. & Merr.) A´ .Lo¨ve and L. triticoides alkaline sites, primarily within the western USA, charac- (Buckley) Pilg. are tall caespitose and short rhizomatous perennial terize sod-forming L. triticoides (0.3–0.7 m). Conversely, Triticeae grasses, respectively. Circumference of rhizome spreading, L. cinereus is a tall (up to 2 m) conspicuous bunchgrass proportion of bolting culms, anthesis date, and plant height were eval- adapted to deep well-drained soils from Saskatchewan to uated in two mapping families derived from two interspecific hybrids of British Columbia, south to California, northern Arizona, L. cinereus Acc:636 and L. triticoides Acc:641 accessions, backcrossed and New Mexico, and east to South Dakota and Minne- to one L. triticoides tester. Two circumference, two bolting, and two sota. Most populations of L. cinereus and L. triticoides are height QTLs were homologous between families. Two circumference, allotetraploids; however, octoploid forms of L. cinereus seven bolting, all five anthesis date, and five height QTLs were family are typical in the Pacific Northwest. Basin wildrye, and specific. Thus, substantial QTL variation was apparent within and be- octoploid giant wildrye [L. condensatus (J. Presl) A´ . tween natural source populations of these species. Two of the four circumference QTLs were detected in homoeologous regions of linkage Lo¨ve], are the largest cool-season bunch grasses native to groups 3a and 3b in both families, indicating that one gene may control western North America. -
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. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
ATP8B1 Gene Atpase Phospholipid Transporting 8B1
ATP8B1 gene ATPase phospholipid transporting 8B1 Normal Function The ATP8B1 gene (also known as FIC1) provides instructions for making a protein that is found throughout the body. It is thought to control the distribution of certain fat molecules known as aminophospholipids on the inner surface of liver cell membranes. Based on this role, the ATP8B1 protein is sometimes known as an aminophospholipid translocase. In particular, this protein performs its function in the membranes of liver cells that transport fat-digesting acids called bile acids into bile, and it likely plays a role in maintaining an appropriate balance of bile acids. This process, known as bile acid homeostasis, is critical for the normal secretion of bile and the proper functioning of liver cells. Health Conditions Related to Genetic Changes Benign recurrent intrahepatic cholestasis Mutations in the ATP8B1 gene can cause benign recurrent intrahepatic cholestasis type 1 (BRIC1). People with BRIC1 have occasional episodes of impaired bile secretion that lead to severe itching (pruritus), and yellowing of the skin and whites of the eyes ( jaundice). Most ATP8B1 gene mutations that cause BRIC1 change single protein building blocks (amino acids) in the ATP8B1 protein. These mutations likely alter the structure or function of the ATP8B1 protein only moderately. Through unknown mechanisms, mutations in the ATP8B1 gene result in the buildup of bile acids in liver cells, which leads to the signs and symptoms of BRIC1. It is unclear what causes the episodes to begin or end. On occasion, people with BRIC1 have been later diagnosed with a more severe condition called progressive familial intrahepatic cholestasis ( described below) when their symptoms worsened. -
Taqman® Openarray® Pharmacogenomics (Pgx) Panel
PRODUCT OVERVIEW TaqMan® OpenArray® Pharmacogenomics (PGx) Panel TaqMan® OpenArray® Pharmacogenomics (PGx) Panel Genotyping analysis of drug metabolism enzymes and associated transport proteins The TaqMan® OpenArray® Trusted TaqMan® performance samples, studies, and labs. Assays Pharmacogenomics (PGx) Panel is Each TaqMan® DME Genotyping were selected for optimal relevance a powerful tool to help researchers Assay contains two allele-specific to current pharmacogenomics study human genetic variation probes and a primer pair to detect studies and organized for a simplified in relation to drug action and its the specific SNP target. Both the workflow. potential application to medical probes and primers uniquely align ® ® treatment. within the genome, enabling the The TaqMan OpenArray PGx TaqMan® genotyping technology to Panel provides valuable data for ® ® The TaqMan OpenArray PGx provide superior specificity. It is this the study of drug interactions in Panel was developed for quick and specificity that allows these assays several research areas. Targeted easy screening of known high- to detect targets residing in highly genes relate to areas of study such value target genes associated with homologous gene families that may as cardiovascular (CYP2D6, CYP2C19, drug metabolism enzymes and include pseudogenes. TaqMan® Drug NAT1, NAT2), analgesics (CYP2C9, associated transport proteins. Metabolism Enzyme Genotyping CYP2D6), rheumatology (CYP2C9, The panel consists of 158 drug Assays were developed using a high TPMT), neurology (CYP2C19, CYP2D6), metabolism enzyme (DME) assays level of bioinformatics and wet-lab and musculoskeletal (CYP2C19). A derived from the PharmaADME stringency. All assays have passed total of 29 genes are covered across Core Marker Set (Table 1). The performance tests involving 180 158 unique assays. -
Research Article Identification of ATP8B1 As a Tumor Suppressor Gene for Colorectal Cancer and Its Involvement in Phospholipid Homeostasis
Hindawi BioMed Research International Volume 2020, Article ID 2015648, 16 pages https://doi.org/10.1155/2020/2015648 Research Article Identification of ATP8B1 as a Tumor Suppressor Gene for Colorectal Cancer and Its Involvement in Phospholipid Homeostasis Li Deng,1,2 Geng-Ming Niu,1 Jun Ren,1 and Chong-Wei Ke 1 1Department of General Surgery, The Fifth People’s Hospital of Shanghai, Fudan University, Shanghai, China 2Department of General Surgery, The Shanghai Public Health Clinical Center, Fudan University, Shanghai, China Correspondence should be addressed to Chong-Wei Ke; [email protected] Received 5 May 2020; Revised 16 July 2020; Accepted 17 August 2020; Published 29 September 2020 Academic Editor: Luis Loura Copyright © 2020 Li Deng 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. Homeostasis of membrane phospholipids plays an important role in cell oncogenesis and cancer progression. The flippase ATPase class I type 8b member 1 (ATP8B1), one of the P4-ATPases, translocates specific phospholipids from the exoplasmic to the cytoplasmic leaflet of membranes. ATP8B1 is critical for maintaining the epithelium membrane stability and polarity. However, the prognostic values of ATP8B1 in colorectal cancer (CRC) patients remain unclear. We analyzed transcriptomics, genomics, and clinical data of CRC samples from The Cancer Genome Atlas (TCGA). ATP8B1 was the only potential biomarker of phospholipid transporters in CRC. Its prognostic value was also validated with the data from the Gene Expression Omnibus (GEO). Compared to the normal group, the expression of ATP8B1 was downregulated in the tumor group and the CRC cell lines, which declined with disease progression. -
A Case of Congenital Central Hypothyroidism Caused by a Novel Variant (Gln1255ter) in IGSF1 Gene
Türkkahraman D et al. A Novel Variant in IGSF1 Gene CASE REPORT DO I: 10.4274/jcrpe.galenos.2020.2020.0149 J Clin Res Pediatr Endocrinol 2021;13(3):353-357 A Case of Congenital Central Hypothyroidism Caused by a Novel Variant (Gln1255Ter) in IGSF1 Gene Doğa Türkkahraman1, Nimet Karataş Torun2, Nadide Cemre Randa3 1University of Health Sciences Turkey, Antalya Training and Research Hospital, Clinic of Pediatric Endocrinology, Antalya, Turkey 2University of Healty Sciences Turkey, Antalya Training and Research Hospital, Clinic of Pediatrics, Antalya, Turkey 3University of Healty Sciences Turkey, Antalya Training and Research Hospital, Clinic of Medical Genetics, Antalya, Turkey What is already known on this topic? Mutations in the immunoglobulin superfamily, member 1 (IGSF1) gene that mainly regulates pituitary thyrotrope function lead to X-linked hypothyroidism characterized by congenital hypothyroidism of central origin and testicular enlargement. The clinical features associated with IGSF1 mutations are variable, but prolactin and/or growth hormone deficiency, and discordance between timing of testicular growth and rise of serum testosterone levels could be seen. What this study adds? Genetic analysis revealed a novel c.3763C>T variant in the IGSF1 gene. To our knowledge, this is the first reported case of IGSF1 deficiency from Turkey. Additionally, as in our case, early testicular enlargement but delayed testosterone rise should be evaluated in all boys with central hypothyroidism, as macro-orchidism is usually seen in adulthood. Abstract Loss-of-function mutations in the immunoglobulin superfamily, member 1 (IGSF1) gene cause X-linked central hypothyroidism, and therefore its mutation affects mainly males. Central hypothyroidism in males is the hallmark of the disorder, however some patients additionally present with hypoprolactinemia, transient and partial growth hormone deficiency, early/normal timing of testicular enlargement but delayed testosterone rise in puberty, and adult macro-orchidism. -
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 -
MECHANISMS in ENDOCRINOLOGY: Novel Genetic Causes of Short Stature
J M Wit and others Genetics of short stature 174:4 R145–R173 Review MECHANISMS IN ENDOCRINOLOGY Novel genetic causes of short stature 1 1 2 2 Jan M Wit , Wilma Oostdijk , Monique Losekoot , Hermine A van Duyvenvoorde , Correspondence Claudia A L Ruivenkamp2 and Sarina G Kant2 should be addressed to J M Wit Departments of 1Paediatrics and 2Clinical Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, Email The Netherlands [email protected] Abstract The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFkB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. -
Gene Expression Polymorphisms and Ests Associated with Gravitropic Response of Subterranean Branch Meristems and Growth Habit in Leymus Wildryes
Plant Science 175 (2008) 330–338 Contents lists available at ScienceDirect Plant Science journal homepage: www.elsevier.com/locate/plantsci Gene expression polymorphisms and ESTs associated with gravitropic response of subterranean branch meristems and growth habit in Leymus wildryes Parminder Kaur a, Ivan W. Mott b,*, Steven R. Larson b, B. Shaun Bushman b, Alvaro G. Hernandez c, W. Ryan Kim c, Lei Liu c, Mark A. Mikel d a Plants, Soils, and Climate, Utah State University, Logan, UT 84322-4820, United States b USDA-ARS, Forage and Range Research Laboratory, Utah State University, 690 North 1100 East, Logan, UT 84322-6300, United States c W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States d Department of Crop Sciences and Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States ARTICLE INFO ABSTRACT Article history: Negatively orthogeotropic (NOGT) tiller and diageotropic (DGT) rhizome meristems develop from the Received 15 January 2008 same type of lateral axillary meristems and phytomer structure. Although subterranean NOGT and DGT Received in revised form 7 April 2008 buds appear similar, they display different responses to gravity and perhaps other cues governing branch Accepted 13 May 2008 angle and overall growth habit (GH). Leymus wildryes show remarkable variation in GH and include some Available online 18 May 2008 of the largest native grasses in western North America. Previous studies detected GH QTLs on homoeologous regions of LG3a and LG3b controlling differences between caespitose Leymus cinereus and Keywords: rhizomatous Leymus triticoides allotetraploids. -
Screening of Genetic Variations of SLC15A2, SLC22A1, SLC22A2 and SLC22A6 Genes
Journal of Human Genetics (2011) 56, 666–670 & 2011 The Japan Society of Human Genetics All rights reserved 1434-5161/11 $32.00 www.nature.com/jhg ORIGINAL ARTICLE Screening of genetic variations of SLC15A2, SLC22A1, SLC22A2 and SLC22A6 genes Hyun Sub Cheong1,4, Hae Deun Kim2,4, Han Sung Na2,JiOnKim1, Lyoung Hyo Kim1, Seung Hee Kim2, Joon Seol Bae3, Myeon Woo Chung2 and Hyoung Doo Shin1,3 A growing list of membrane-spanning proteins involved in the transport of a large variety of drugs has been recognized and characterized to include peptide and organic anion/cation transporters. Given such an important role of transporter genes in drug disposition process, the role of single-nucleotide polymorphisms (SNPs) in such transporters as potential determinants of interindividual variability in drug disposition and pharmacological response has been investigated. To define the distribution of transporter gene SNPs across ethnic groups, we screened 450 DNAs in cohorts of 250 Korean, 50 Han Chinese, 50 Japanese, 50 African-American and 50 European-American ancestries for 64 SNPs in four transporter genes encoding proteins of the solute carrier family (SLC15A2, SLC22A1, SLC22A2 and SLC22A6). Of the 64 SNPs, 19 were core pharmacogenetic variants and 45 were HapMap tagging SNPs. Polymorphisms were genotyped using the golden gate genotyping assay. After genetic variability, haplotype structures and ethnic diversity were analyzed, we observed that the distributions of SNPs in a Korean population were similar to other Asian groups (Chinese and Japanese), and significantly different from African-American and European-American cohorts. Findings from this study would be valuable for further researches, including pharmacogenetic studies for drug responses.