Profile of the Genes Expressed in the Human Peripheral Retina, Macula, and Retinal Pigment Epithelium Determined Through Serial Analysis of Gene Expression (SAGE)

Total Page:16

File Type:pdf, Size:1020Kb

Profile of the Genes Expressed in the Human Peripheral Retina, Macula, and Retinal Pigment Epithelium Determined Through Serial Analysis of Gene Expression (SAGE) Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE) Dror Sharon*†, Seth Blackshaw†‡, Constance L. Cepko‡, and Thaddeus P. Dryja*§ *Ocular Molecular Genetics Institute, Massachusetts Eye and Ear Infirmary, and ‡Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02114 Contributed by Thaddeus P. Dryja, October 31, 2001 We used the serial analysis of gene expression (SAGE) technique to a short piece of each transcript (a SAGE tag that is 9–14 bases in catalogue and measure the relative levels of expression of the genes length) is linked in series with 20–50 other such tags in a cloned expressed in the human peripheral retina, macula, and retinal pig- DNA fragment. Sequencing of such a clone provides the sequence ment epithelium (RPE) from one or both of two humans, aged 88 and of 20–50 tags, and a set of a few thousand such clones represents 44 years. The cone photoreceptor contribution to all transcription in a library of SAGE tags. Most individual SAGE tags can be assigned the retina was found to be similar in the macula versus the retinal to specific genes by inspecting available NCBI sequences periphery, whereas the rod contribution was greater in the periphery (SAGEmap). The relative abundance of each tag reliably reflects versus the macula. Genes encoding structural proteins for axons were the level of gene expression based on a comparison with Northern found to be expressed at higher levels in the macula versus the retinal blot analysis (9). The SAGE technique has been used to compare periphery, probably reflecting the large proportion of ganglion cells the profile of mRNA expression in different types of cancer cells in the central retina. In comparison with the younger eye, the (10, 11) and to identify genes that are up- or down-regulated in peripheral retina of the older eye had a substantially higher propor- response to exposure to drugs or other stimuli (12, 13). tion of mRNAs from genes encoding proteins involved in iron me- tabolism or protection against oxidative damage and a substantially Here we describe SAGE libraries constructed from the human lower proportion of mRNAs from genes encoding proteins involved peripheral retina, macula, and RPE. We compared the expression in rod phototransduction. These differences may reflect the differ- profile of the retinal periphery versus the macula of the same eye ence in age between the two donors or merely interindividual and the expression profile of the peripheral retina from two variation. The RPE library had numerous previously unencountered individuals (ages 44 and 88 years). Finally, we evaluated the tags, suggesting that this cell type has a large, idiosyncratic repertoire potential value of the library as a resource for identifying candidate of expressed genes. Comparison of these libraries with 100 reported genes for hereditary retinal diseases. nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a Methods retinal disease and 53 are RPE-specific genes. We expect that these Procurement of Tissue. The patients who donated eyes for this study libraries will serve as a resource for understanding the relative had periocular malignancies that required exenteration of an oth- GENETICS expression levels of genes in the retina and the RPE and for identi- erwise normal eye as part of clinically indicated surgical therapy. fying additional disease genes. Before surgery, the patients were contacted and gave their consent to donate parts of their to-be-enucleated eye for this research. The he human retina is a highly specialized tissue that converts harvesting of the intraocular tissue fragments for this study did not Tphotons into neural signals that are communicated to the brain. interfere with the pathological evaluation of the extraocular ma- This process involves different types of retinal cells, mainly neuronal lignancies. Each exenteration specimen was placed in saline after it cells (e.g., photoreceptors, bipolar cells, and others) and the non- was removed from the patient and promptly transported to the neuronal retinal pigment epithelium (RPE). The set of genes pathology laboratory. Each eye was cut open with a virgin razor expressed by the human neural retina has been elucidated partially, blade, and retinal fragments were excised. The RPE was harvested mainly through reported expressed sequence tag (EST) libraries by gentle scraping with a Pasteur pipette, and fragments of RPE [nonnormalized (1–3) or enriched (4, 5)] that contain over 16,000 were collected by aspiration in sterile 0.9% saline. Tissue fragments EST sequences derived from less than 5,000 genes (6). Our knowl- were collected and frozen within 45 min of the surgical removal of edge of the set of genes expressed by the RPE is more rudimentary, each specimen. The exenteration specimens, including the remain- because only 624 ESTs have been sequenced (refs. 4 and 7, and GenBank Library 6359). Little is known about the variation in gene expression between different regions of the retina (e.g., the retinal Abbreviations: RPE, retinal pigment epithelium; EST, expressed sequence tag; SAGE, serial periphery versus the macula); only a few genes with a preferential analysis of gene expression. expression in the fovea have been identified (1). There is no Data deposition: The tag sequences from the four SAGE libraries reported in this paper have been deposited in the Gene Expression Omnibus database (accession nos. GSM571– counterpart to these different retinal regions in mouse retinas. GSM574). Knowledge of the set of genes expressed in these regions is valuable, †D.S. and S.B. contributed equally to this work. because some common diseases of the retina can affect one region §To whom reprint requests should be addressed at: Massachusetts Eye and Ear Infirmary, preferentially (e.g., age-related macular degeneration). 243 Charles Street, Boston, MA 02114. E-mail: [email protected]. The serial analysis of gene expression (SAGE) procedure, first The publication costs of this article were defrayed in part by page charge payment. This described by Velculescu et al. (8), allows the compilation of article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. thousands of transcripts from a tissue sample. With this technique, §1734 solely to indicate this fact. www.pnas.org͞cgi͞doi͞10.1073͞pnas.012582799 PNAS ͉ January 8, 2002 ͉ vol. 99 ͉ no. 1 ͉ 315–320 Downloaded by guest on September 26, 2021 Table 1. SAGE tags in the human retinal and RPE libraries Peripheral retina Eye 1* Eye 2* Combined Macula, Eye 2* Retina totals RPE, Eye 1* Total no. of tags 59,661 105,312 164,973 102,359 267,332 53,666 Tags for analysis†, (%) 50,193 (84) 90,444 (86) 140,637 (85) 87,555 (86) 228,192 (85) 25,712 (48) Different transcripts 13,344 19,199 23,112 18,660 26,355 10,404 UniGenes‡, (%) 10,942 (82) 15,373 (80) 18,119 (78) 15,023 (81) 20,251 (77) 6,401 (62) *Eye 1 was enucleated from an 88-year-old female, and eye 2 was enucleated from a 44-year-old male. †The number of tags represented at least twice in the current study. The percentage of nonsingleton tags out of the total number of tags is presented in parentheses. ‡Transcripts that correspond to UniGene entries. In parentheses is the percentage of UniGene transcripts out of all different transcripts. ing ocular tissues, were subsequently placed in fixative and pro- After excluding singletons and combining tags derived from cessed as required for diagnostic pathology. the same transcript, the total number of different transcripts The peripheral retinal fragments were derived from regions was 26,355 in the combined retinal libraries and 10,404 in the outside the central vascular arcades. The macular fragment was Ϸ6 RPE library. Approximately 77% of the retinal tags could be mm in diameter and centered at the foveola. The RPE fragments assigned to UniGene entries, but only 62% of the RPE tags could were from the posterior pole and the periphery. be assigned. The high proportion of unassigned RPE tags (38%), together with the high proportion of singleton RPE tags men- SAGE Library Construction and Analysis. We used a modification of tioned in the previous paragraph, suggest that a large proportion the microSAGE protocol (14) to generate the four human SAGE of genes expressed by the RPE are tissue-specific. Many RPE- libraries. The sequences were analyzed by using the SAGE2000 specific tags are from unknown genes. This may be due in part software (courtesy of Victor Velculescu and Ken Kinzler, Johns to the small number of ESTs that have been sequenced from Hopkins University School of Medicine). Tags with ambiguous RPE libraries (4, 7). bases, duplicate ditags, and abnormally short tags (Ͻ14 bases) were eliminated automatically. The identity of the mRNAs correspond- New Tag Assignments. Most of the genes that were known previously ing to the SAGE tags was determined through inspection and to be expressed in the retina or the RPE had corresponding tags in comparison with the SAGEmap (www.ncbi.nlm.nih.gov͞SAGE͞ our SAGE libraries. However, we came across a number of genes SAGEtag.cgi) and UniGene (www.ncbi.nlm.nih.gov͞UniGene͞) known to be expressed in the retina but for which there initially databases. appeared to be no representative tag in our libraries. We considered To identify tags in genomic sequences, we developed a computer the possibility that these genes may produce mRNAs with 3Ј ends program that we have named TAGSEARCH. This program searches different than those reported previously. By using the TAGSEARCH the genomic sequence at the 3Ј end of a specified gene for each software, we tentatively assigned some of the tags in our libraries 14-bp tag, including an NlaIII recognition sequence (CATG), to known genes for which no tags had otherwise been found.
Recommended publications
  • Investigating Cone Photoreceptor Development Using Patient-Derived NRL Null Retinal Organoids
    ARTICLE https://doi.org/10.1038/s42003-020-0808-5 OPEN Investigating cone photoreceptor development using patient-derived NRL null retinal organoids Alyssa Kallman1,11, Elizabeth E. Capowski 2,11, Jie Wang 3, Aniruddha M. Kaushik4, Alex D. Jansen2, Kimberly L. Edwards2, Liben Chen4, Cynthia A. Berlinicke3, M. Joseph Phillips2,5, Eric A. Pierce6, Jiang Qian3, ✉ ✉ Tza-Huei Wang4,7, David M. Gamm2,5,8 & Donald J. Zack 1,3,9,10 1234567890():,; Photoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degeneration are not well understood. Treatment strategies would benefit from improved understanding of gene-expression patterns directing photoreceptor development, as many genes are implicated in both development and degeneration. Neural retina leucine zipper (NRL) is critical for rod photoreceptor genesis and degeneration, with NRL mutations known to cause enhanced S-cone syndrome and retinitis pigmentosa. While murine Nrl loss has been characterized, studies of human NRL can identify important insights for human retinal development and disease. We utilized iPSC organoid models of retinal development to molecularly define developmental alterations in a human model of NRL loss. Consistent with the function of NRL in rod fate specification, human retinal organoids lacking NRL develop S- opsin dominant photoreceptor populations. We report generation of two distinct S-opsin expressing populations in NRL null retinal organoids and identify MEF2C as a candidate regulator of cone development. 1 Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA. 2 Waisman Center, University of Wisconsin-Madison, Madison, USA. 3 Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, USA.
    [Show full text]
  • Transcriptional Control of Tissue-Resident Memory T Cell Generation
    Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells.
    [Show full text]
  • Cellular and Molecular Signatures in the Disease Tissue of Early
    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
    [Show full text]
  • G-Protein ␤␥-Complex Is Crucial for Efficient Signal Amplification in Vision
    The Journal of Neuroscience, June 1, 2011 • 31(22):8067–8077 • 8067 Cellular/Molecular G-Protein ␤␥-Complex Is Crucial for Efficient Signal Amplification in Vision Alexander V. Kolesnikov,1 Loryn Rikimaru,2 Anne K. Hennig,1 Peter D. Lukasiewicz,1 Steven J. Fliesler,4,5,6,7 Victor I. Govardovskii,8 Vladimir J. Kefalov,1 and Oleg G. Kisselev2,3 1Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri 63110, Departments of 2Ophthalmology and 3Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, 4Research Service, Veterans Administration Western New York Healthcare System, and Departments of 5Ophthalmology (Ross Eye Institute) and 6Biochemistry, University at Buffalo/The State University of New York (SUNY), and 7SUNY Eye Institute, Buffalo, New York 14215, and 8Sechenov Institute for Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg 194223, Russia A fundamental question of cell signaling biology is how faint external signals produce robust physiological responses. One universal mechanism relies on signal amplification via intracellular cascades mediated by heterotrimeric G-proteins. This high amplification system allows retinal rod photoreceptors to detect single photons of light. Although much is now known about the role of the ␣-subunit of the rod-specific G-protein transducin in phototransduction, the physiological function of the auxiliary ␤␥-complex in this process remains a mystery. Here, we show that elimination of the transducin ␥-subunit drastically reduces signal amplification in intact mouse rods. The consequence is a striking decline in rod visual sensitivity and severe impairment of nocturnal vision. Our findings demonstrate that transducin ␤␥-complex controls signal amplification of the rod phototransduction cascade and is critical for the ability of rod photoreceptors to function in low light conditions.
    [Show full text]
  • The Evolution of Vertebrate Tetraspanins: Gene Loss, Retention
    Huang et al. BMC Evolutionary Biology 2010, 10:306 http://www.biomedcentral.com/1471-2148/10/306 RESEARCH ARTICLE Open Access The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications Shengfeng Huang, Haozheng Tian, Zelin Chen, Ting Yu, Anlong Xu* Abstract Background: The vertebrate tetraspanin family has many features which make it suitable for preserving the imprint of ancient sequence evolution and amenable for phylogenomic analysis. So we believe that an in-depth analysis of the tetraspanin evolution not only provides more complete understanding of tetraspanin biology, but offers new insights into the influence of the two rounds of whole genome duplication (2R-WGD) at the origin of vertebrates. Results: A detailed phylogeny of vertebrate tetraspanins was constructed by using multiple lines of information, including sequence-based phylogenetics, key structural features, intron configuration and genomic synteny. In particular, a total of 38 modern tetraspanin ortholog lineages in bony vertebrates have been identified and subsequently classified into 17 ancestral lineages existing before 2R-WGD. Based on this phylogeny, we found that the ohnolog retention rate of tetraspanins after 2R-WGD was three times as the average (a rate similar to those of transcription factors and protein kinases). This high rate didn’t increase the tetrapanin family size, but changed the family composition, possibly by displacing vertebrate-specific gene lineages with the lineages conserved across deuterostomes. We also found that the period from 2R-WGD to recent time is controlled by gene losses. Meanwhile, positive selection has been detected on 80% of the branches right after 2R-WGDs, which declines significantly on both magnitude and extensity on the following speciation branches.
    [Show full text]
  • Absence of S100A4 in the Mouse Lens Induces an Aberrant Retina-Specific Differentiation Program and Cataract
    www.nature.com/scientificreports OPEN Absence of S100A4 in the mouse lens induces an aberrant retina‑specifc diferentiation program and cataract Rupalatha Maddala1*, Junyuan Gao2, Richard T. Mathias2, Tylor R. Lewis1, Vadim Y. Arshavsky1,3, Adriana Levine4, Jonathan M. Backer4,5, Anne R. Bresnick4 & Ponugoti V. Rao1,3* S100A4, a member of the S100 family of multifunctional calcium‑binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in diferentiating fber cells of the ocular lens and that S100A4 (−/−) knockout mice develop late‑onset cortical cataracts. Transcriptome profling of lenses from S100A4 (−/−) mice revealed a robust increase in the expression of multiple photoreceptor‑ and Müller glia‑specifc genes, as well as the olfactory sensory neuron‑specifc gene, S100A5. This aberrant transcriptional profle is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of diferentially expressed genes in S100A4 (−/−) lenses identifed Crx and Nrl transcription factors as the most signifcant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high‑density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this fnding, we further documented that S100A4 (−/−) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together,
    [Show full text]
  • G Protein-Coupled Receptors
    G PROTEIN-COUPLED RECEPTORS Overview:- The completion of the Human Genome Project allowed the identification of a large family of proteins with a common motif of seven groups of 20-24 hydrophobic amino acids arranged as α-helices. Approximately 800 of these seven transmembrane (7TM) receptors have been identified of which over 300 are non-olfactory receptors (see Frederikson et al., 2003; Lagerstrom and Schioth, 2008). Subdivision on the basis of sequence homology allows the definition of rhodopsin, secretin, adhesion, glutamate and Frizzled receptor families. NC-IUPHAR recognizes Classes A, B, and C, which equate to the rhodopsin, secretin, and glutamate receptor families. The nomenclature of 7TM receptors is commonly used interchangeably with G protein-coupled receptors (GPCR), although the former nomenclature recognises signalling of 7TM receptors through pathways not involving G proteins. For example, adiponectin and membrane progestin receptors have some sequence homology to 7TM receptors but signal independently of G-proteins and appear to reside in membranes in an inverted fashion compared to conventional GPCR. Additionally, the NPR-C natriuretic peptide receptor has a single transmembrane domain structure, but appears to couple to G proteins to generate cellular responses. The 300+ non-olfactory GPCR are the targets for the majority of drugs in clinical usage (Overington et al., 2006), although only a minority of these receptors are exploited therapeutically. Signalling through GPCR is enacted by the activation of heterotrimeric GTP-binding proteins (G proteins), made up of α, β and γ subunits, where the α and βγ subunits are responsible for signalling. The α subunit (tabulated below) allows definition of one series of signalling cascades and allows grouping of GPCRs to suggest common cellular, tissue and behavioural responses.
    [Show full text]
  • Multi-Functionality of Proteins Involved in GPCR and G Protein Signaling: Making Sense of Structure–Function Continuum with In
    Cellular and Molecular Life Sciences (2019) 76:4461–4492 https://doi.org/10.1007/s00018-019-03276-1 Cellular andMolecular Life Sciences REVIEW Multi‑functionality of proteins involved in GPCR and G protein signaling: making sense of structure–function continuum with intrinsic disorder‑based proteoforms Alexander V. Fonin1 · April L. Darling2 · Irina M. Kuznetsova1 · Konstantin K. Turoverov1,3 · Vladimir N. Uversky2,4 Received: 5 August 2019 / Revised: 5 August 2019 / Accepted: 12 August 2019 / Published online: 19 August 2019 © Springer Nature Switzerland AG 2019 Abstract GPCR–G protein signaling system recognizes a multitude of extracellular ligands and triggers a variety of intracellular signal- ing cascades in response. In humans, this system includes more than 800 various GPCRs and a large set of heterotrimeric G proteins. Complexity of this system goes far beyond a multitude of pair-wise ligand–GPCR and GPCR–G protein interactions. In fact, one GPCR can recognize more than one extracellular signal and interact with more than one G protein. Furthermore, one ligand can activate more than one GPCR, and multiple GPCRs can couple to the same G protein. This defnes an intricate multifunctionality of this important signaling system. Here, we show that the multifunctionality of GPCR–G protein system represents an illustrative example of the protein structure–function continuum, where structures of the involved proteins represent a complex mosaic of diferently folded regions (foldons, non-foldons, unfoldons, semi-foldons, and inducible foldons). The functionality of resulting highly dynamic conformational ensembles is fne-tuned by various post-translational modifcations and alternative splicing, and such ensembles can undergo dramatic changes at interaction with their specifc partners.
    [Show full text]
  • VGLL1 Expression Is Associated with a Triple-Negative Basal-Like Phenotype in Breast Cancer
    MA´ Castilla et al. VGLL1 and basal-like 21:4 587–599 Research breast cancer VGLL1 expression is associated with a triple-negative basal-like phenotype in breast cancer Marı´aA´ ngeles Castilla1,2, Marı´aA´ ngeles Lo´pez-Garcı´a1,2, Marı´a Reina Atienza1, Juan Manuel Rosa-Rosa3, Juan Dı´az-Martı´n1,2, Marı´a Luisa Pecero1, Begon˜a Vieites1,2, Laura Romero-Pe´rez1,2, Javier Benı´tez4, Annarica Calcabrini5 and Jose´ Palacios2,3 1Instituto de Biomedicina de Sevilla–CSIC–Universidad de Sevilla, Hospital Universitario Virgen del Rocı´o, Correspondence Department of Pathology, Avda. Manuel Siurot S/N, 41013 Seville, Spain should be addressed 2Red Tema´ tica de Investigacio´ n Cooperativa en Ca´ ncer (RTICC), ISCIII, Madrid, Spain to J Palacios or M A´ Castilla 3Servicio de Anatomı´a Patolo´ gica, Hospital Universitario Ramo´ n y Cajal and Instituto Ramo´ n y Cajal de Investigacio´ n Emails Sanitaria (IRYCIS), Madrid, Spain jose.palacios@ 4Human Genetics Group, Departamento de Biologı´a del Ca´ ncer, Spanish National Cancer Research Centre salud.madrid.org or (CNIO)–CIBERER, Madrid, Spain macastillamoro@ 5Department of Technology and Health, Istituto Superiore di Sanita` , Rome, Italy gmail.com Abstract Vestigial-like 1 (VGLL1) is a poorly characterized gene encoding a transcriptional co-activator Key Words structurally homologous to TAZ and YAP that modulates the Hippo pathway in Drosophila. " breast cancer In this study, we examined the expression of VGLL1 and its intronic miRNA, miR-934, in breast " Vgll1 cancer. VGLL1 and miR-934 expression miRNA profiling was carried out on frozen samples of " miR-934 " Endocrine-Related Cancer grade 3 invasive ductal carcinomas.
    [Show full text]
  • A System-Level, Molecular Evolutionary Analysis of Mam- Malian Phototransduction (Supplementary Material)
    A system-level, molecular evolutionary analysis of mam- malian phototransduction (supplementary material) Brandon M Invergo1 , Ludovica Montanucci∗1 , Hafid Laayouni1 and Jaume Bertranpetit1 1IBE-Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain Email: Brandon Invergo - [email protected]; Ludovica Montanucci∗- [email protected]; Hafid Laayouni - hafi[email protected]; Jaume Bertranpetit - [email protected]; ∗Corresponding author Table S1 - Classifications of the genes Genes were assigned classifications according to their photoreceptor cell-type specificity, the process in which the encoded protein is primarily active, and the general function of the encoded protein. (Note: here "enzyme" specifically refers to enzymes involved in retinoid recycling.) 1 gene cell type process function ABCA4 shared retinoid cycle enzyme AIPL1 shared phototransduction other ARR3 cone phototransduction signal regulator ASCL1 rod development transcription regulation CNGA1 rod phototransduction ion channel CNGA3 cone phototransduction ion channel CNGB1 rod phototransduction ion channel CNGB3 cone phototransduction ion channel CRX shared development transcription regulation GNAT1 rod phototransduction G protein GNAT2 cone phototransduction G protein GNB1 rod phototransduction G protein GNB3 cone phototransduction G protein GNB5 shared phototransduction G protein GNGT1 rod phototransduction G protein GNGT2 cone phototransduction G protein GPSM2 shared phototransduction other GRK1 shared phototransduction
    [Show full text]
  • Comparative Analyses of Gene Copy Number and Mrna Expression in GBM Tumors And
    Title page Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts J. Graeme Hodgson # *, Ru-Fang Yeh #, Amrita Ray, Nicholas J Wang, Ivan Smirnov, Mamie Yu, Sujatmi Hariono, Joachim Silber, Heidi S. Feiler, Joe W. Gray, Paul T. Spellman, Scott R. Vandenberg, Mitchel S. Berger, C. David James Departments of Neurological Surgery (JGH, IS, MY, SH, JS, SRV, MSB, CDJ), Pathology (SRV), and Epidemiology and Biostatistics (RY) University of California, San Francisco, CA 94143. Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 (AR, NJW, HSF, JWG, PTS) # These authors contributed equally to this work Running title: Genomic analyses of a GBM xenograft tumor panel * Corresponding Author J. Graeme Hodgson Dept. Neurological Surgery UC San Francisco San Francisco, CA 94143-0808 Phone: 415-476-3630 Fax: 415-476-8218 e-mail: [email protected] Abstract Development of model systems that recapitulate the molecular heterogeneity observed amongst GBM tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from The Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7-gain/chromosome-10-loss, a poor prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBMs genomic amplification and overexpression of known GBM oncogenes such as EGFR, MDM2, CDK6 and MYCN, and novel genes including NUP107, SLC35E3, MMP1, MMP13 and DDX1.
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]