Nuclear and Mitochondrial Analysis of Patients with Primary Angle-Closure Glaucoma
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Expression Analysis of Asthma Candidate Genes During Human and Murine Lung Development
Expression analysis of asthma candidate genes during human and murine lung development The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Melén, Erik, Alvin T Kho, Sunita Sharma, Roger Gaedigk, J Steven Leeder, Thomas J Mariani, Vincent J Carey, Scott T Weiss, and Kelan G Tantisira. 2011. Expression analysis of asthma candidate genes during human and murine lung development. Respiratory Research 12, no. 1: 86. doi:10.1186/1465-9921-12-86. Published Version doi:10.1186/1465-9921-12-86 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:27002794 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Melén et al. Respiratory Research 2011, 12:86 http://respiratory-research.com/content/12/1/86 RESEARCH Open Access Expression analysis of asthma candidate genes during human and murine lung development Erik Melén1,2,3*, Alvin T Kho4, Sunita Sharma1,5, Roger Gaedigk6, J Steven Leeder6, Thomas J Mariani7, Vincent J Carey1, Scott T Weiss1,5,8 and Kelan G Tantisira1,5,8 Abstract Background: Little is known about the role of most asthma susceptibility genes during human lung development. Genetic determinants for normal lung development are not only important early in life, but also for later lung function. Objective: To investigate the role of expression patterns of well-defined asthma susceptibility genes during human and murine lung development. -
Exome Sequencing Identifies Gene Variants And
Hamvas et al. BMC Genetics (2018) 19:94 https://doi.org/10.1186/s12863-018-0679-7 RESEARCHARTICLE Open Access Exome sequencing identifies gene variants and networks associated with extreme respiratory outcomes following preterm birth Aaron Hamvas1,9*, Rui Feng2, Yingtao Bi3, Fan Wang2, Soumyaroop Bhattacharya4, Jared Mereness4, Madhurima Kaushal5, C Michael Cotten6, Philip L Ballard7, Thomas J Mariani4,8* and PROP Investigators Abstract Background: Previous studies have identified genetic variants associated with bronchopulmonary dysplasia (BPD) in extremely preterm infants. However, findings with genome-wide significance have been rare, and not replicated. We hypothesized that whole exome sequencing (WES) of premature subjects with extremely divergent phenotypic outcomes could facilitate the identification of genetic variants or gene networks contributing disease risk. Results: The Prematurity and Respiratory Outcomes Program (PROP) recruited a cohort of > 765 extremely preterm infants for the identification of markers of respiratory morbidity. We completed WES on 146 PROP subjects (85 affected, 61 unaffected) representing extreme phenotypes of early respiratory morbidity. We tested for association between disease status and individual common variants, screened for rare variants exclusive to either affected or unaffected subjects, and tested the combined association of variants across gene loci. Pathway analysis was performed and disease-related expression patterns were assessed. Marginal association with BPD was observed for numerous common and rare variants. We identified 345 genes with variants unique to BPD-affected preterm subjects, and 292 genes with variants unique to our unaffected preterm subjects. Of these unique variants, 28 (19 in the affected cohort and 9 in unaffected cohort) replicate a prior WES study of BPD-associated variants. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Neurologic Outcomes in Friedreich Ataxia: Study of a Single-Site Cohort E415
Volume 6, Number 3, June 2020 Neurology.org/NG A peer-reviewed clinical and translational neurology open access journal ARTICLE Neurologic outcomes in Friedreich ataxia: Study of a single-site cohort e415 ARTICLE Prevalence of RFC1-mediated spinocerebellar ataxia in a North American ataxia cohort e440 ARTICLE Mutations in the m-AAA proteases AFG3L2 and SPG7 are causing isolated dominant optic atrophy e428 ARTICLE Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy revisited: Genotype-phenotype correlations of all published cases e434 Academy Officers Neurology® is a registered trademark of the American Academy of Neurology (registration valid in the United States). James C. Stevens, MD, FAAN, President Neurology® Genetics (eISSN 2376-7839) is an open access journal published Orly Avitzur, MD, MBA, FAAN, President Elect online for the American Academy of Neurology, 201 Chicago Avenue, Ann H. Tilton, MD, FAAN, Vice President Minneapolis, MN 55415, by Wolters Kluwer Health, Inc. at 14700 Citicorp Drive, Bldg. 3, Hagerstown, MD 21742. Business offices are located at Two Carlayne E. Jackson, MD, FAAN, Secretary Commerce Square, 2001 Market Street, Philadelphia, PA 19103. Production offices are located at 351 West Camden Street, Baltimore, MD 21201-2436. Janis M. Miyasaki, MD, MEd, FRCPC, FAAN, Treasurer © 2020 American Academy of Neurology. Ralph L. Sacco, MD, MS, FAAN, Past President Neurology® Genetics is an official journal of the American Academy of Neurology. Journal website: Neurology.org/ng, AAN website: AAN.com CEO, American Academy of Neurology Copyright and Permission Information: Please go to the journal website (www.neurology.org/ng) and click the Permissions tab for the relevant Mary E. -
RNA Sequencing Reveals a Diverse and Dynamic Repertoire of the Xenopus Tropicalis Transcriptome Over Development
Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Resource RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development Meng How Tan,1,6,7 Kin Fai Au,2,6 Arielle L. Yablonovitch,1,3,6 Andrea E. Wills,1 Jason Chuang,4 Julie C. Baker,1 Wing Hung Wong,2,5 and Jin Billy Li1,7 1Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; 2Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, California 94305, USA; 3Program in Biophysics, School of Humanities and Sciences, Stanford University, Stanford, California 94305, USA; 4Department of Computer Science, School of Engineering, Stanford University, Stanford, California 94305, USA; 5Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California 94305, USA The Xenopus embryo has provided key insights into fate specification, the cell cycle, and other fundamental developmental and cellular processes, yet a comprehensive understanding of its transcriptome is lacking. Here, we used paired end RNA sequencing (RNA-seq) to explore the transcriptome of Xenopus tropicalis in 23 distinct developmental stages. We determined expression levels of all genes annotated in RefSeq and Ensembl and showed for the first time on a genome-wide scale that, despite a general state of transcriptional silence in the earliest stages of development, approximately 150 genes are tran- scribed prior to the midblastula transition. In addition, our splicing analysis uncovered more than 10,000 novel splice junctions at each stage and revealed that many known genes have additional unannotated isoforms. -
"The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. -
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 -
Differential Expression Profile Prioritization of Positional Candidate Glaucoma Genes the GLC1C Locus
LABORATORY SCIENCES Differential Expression Profile Prioritization of Positional Candidate Glaucoma Genes The GLC1C Locus Frank W. Rozsa, PhD; Kathleen M. Scott, BS; Hemant Pawar, PhD; John R. Samples, MD; Mary K. Wirtz, PhD; Julia E. Richards, PhD Objectives: To develop and apply a model for priori- est because of moderate expression and changes in tization of candidate glaucoma genes. expression. Transcription factor ZBTB38 emerges as an interesting candidate gene because of the overall expres- Methods: This Affymetrix GeneChip (Affymetrix, Santa sion level, differential expression, and function. Clara, Calif) study of gene expression in primary cul- ture human trabecular meshwork cells uses a positional Conclusions: Only1geneintheGLC1C interval fits our differential expression profile model for prioritization of model for differential expression under multiple glau- candidate genes within the GLC1C genetic inclusion in- coma risk conditions. The use of multiple prioritization terval. models resulted in filtering 7 candidate genes of higher interest out of the 41 known genes in the region. Results: Sixteen genes were expressed under all condi- tions within the GLC1C interval. TMEM22 was the only Clinical Relevance: This study identified a small sub- gene within the interval with differential expression in set of genes that are most likely to harbor mutations that the same direction under both conditions tested. Two cause glaucoma linked to GLC1C. genes, ATP1B3 and COPB2, are of interest in the con- text of a protein-misfolding model for candidate selec- tion. SLC25A36, PCCB, and FNDC6 are of lesser inter- Arch Ophthalmol. 2007;125:117-127 IGH PREVALENCE AND PO- identification of additional GLC1C fami- tential for severe out- lies7,18-20 who provide optimal samples for come combine to make screening candidate genes for muta- adult-onset primary tions.7,18,20 The existence of 2 distinct open-angle glaucoma GLC1C haplotypes suggests that muta- (POAG) a significant public health prob- tions will not be limited to rare descen- H1 lem. -
A Comprehensive Map of Disease Networks and Molecular Drug Discoveries for Glaucoma Haixin Wang1,2,3, Yanhui Deng1, Ling Wan4 & Lulin Huang1,2,3 ✉
www.nature.com/scientificreports OPEN A comprehensive map of disease networks and molecular drug discoveries for glaucoma Haixin Wang1,2,3, Yanhui Deng1, Ling Wan4 & Lulin Huang1,2,3 ✉ Glaucoma is the leading cause of irreversible blindness worldwide. The molecular etiology of glaucoma is complex and unclear. At present, there are few drugs available for glaucoma treatment. The aim of the present study was to perform a systematic analysis of glaucoma candidate drugs/chemicals based on glaucoma genes, including genetic factors and diferentially expressed (DE) genes. In total, 401 genes from the genetic databases and 1656 genes from the DE gene analysis were included in further analyses. In terms of glaucoma-related genetic factors, 54 pathways were signifcantly enriched (FDR < 0.05), and 96 pathways for DE genes were signifcantly enriched (FDR < 0.05). A search of the PheWAS database for diseases associated with glaucoma-related genes returned 1,289 diseases, and a search for diseases associated with DE glaucoma-related genes returned 1,356 diseases. Cardiovascular diseases, neurodegenerative diseases, cancer, and ophthalmic diseases were highly related to glaucoma genes. A search of the DGIdb, KEGG, and CLUE databases revealed a set of drugs/chemicals targeting glaucoma genes. A subsequent analysis of the electronic medical records (EMRs) of 136,128 patients treated in Sichuan Provincial People’s Hospital for candidate drug usage and the onset of glaucoma revealed nine candidate drugs. Among these drugs, individuals treated with nicardipine had the lowest incidence of glaucoma. Taken together with the information from the drug databases, the 40 most likely candidate drugs for glaucoma treatment were highlighted. -
Genome-Wide Identification and Characterization of Well-Defined Genes Involved in Glaucoma and Pterygium Corneae
Genome-wide identification and characterization of well-defined genes involved in glaucoma and pterygium corneae Den Naturwissenschaftlichen Fakultäten der Friedrich-Alexander-Universität Erlangen-Nürnberg zur Erlangung des Doktorgrades vorgelegt von Gabriela Chavarría Soley aus San José Als Dissertation genehmigt von der Naturwissenschaftlichen Fakultät der Universität Erlangen-Nürnberg Tag der mündlichen Prüfung: 27.03.2008 Vorsitzender der Promotionskommission: Prof. Dr. Eberhard Bänsch Erstberichterstatter: Prof. Dr. Georg Fey Zweitberichterstatter: Prof. Dr. Andreas Winterpacht ii Gedruckt mit Unterstützung des Deuschen Akademischen Austauschdienstes iii iv Index 1 Introduction....................................................................................................................... 1 1.1 Glaucoma, general aspects .................................................................................................. 1 1.1.1 Classification of glaucoma .............................................................................................................. 2 1.2 Genetics of POAG................................................................................................................3 1.2.1 Inheritance and implicated loci ...................................................................................................... 3 1.2.2 Known glaucoma genes .................................................................................................................. 6 1.2.2.1 Myocilin (MYOC) ................................................................................................................ -
Mitochondrial Localization and Ocular Expression of Mutant Opa3 in a Mouse Model of 3-Methylglutaconicaciduria Type III
Biochemistry and Molecular Biology Mitochondrial Localization and Ocular Expression of Mutant Opa3 in a Mouse Model of 3-Methylglutaconicaciduria Type III Kate A. Powell,1 Jennifer R. Davies,1 Elaine Taylor,1 Michael A. Wride,2 and Marcela Votruba1,3 PURPOSE. To investigate the developmental and ocular expres- ereditary optic neuropathies are a group of heteroge- sion of Opa3 in a mouse model of 3-methylglutaconicaciduria Hneous disorders in which degeneration of the retinal type III and the effect of mutation on protein localization and ganglion cells and optic nerve atrophy are the primary mitochondrial morphology. characteristics. Autosomal dominant optic atrophy (ADOA; L122P METHODS. The B6 C3-Opa3 mouse carrying a missense mu- MIM [Mendelian Inheritance in Man] 165500) is the most Ͼ common of these disorders and is frequently associated with tation in exon 2 (c.365T C; p.L122P) of Opa3, which displays 1,2 features of recessive 3-methylglutaconic aciduria type III was mutation of the OPA1 gene. However, optic atrophy has also studied. The expression of Opa3 was determined with RT-PCR, been linked to mutation in an unrelated nuclear gene, OPA3. quantitative PCR, and Western blot, in embryos (embryonic OPA3 is associated with two phenotypically distinct condi- day [E]8 to postnatal day [P]0) and adult tissues, and by ocular tions. ADOA and cataract are characterized by optic atrophy, immunohistochemistry. Mitochondria were stained using a mi- extrapyramidal signs, and blue-dot cerulean cataract (ADOAC, MIM 1653003,4). Two dominant missense mutations that give tochondrion-selective probe in mouse embryonic fibroblasts 4,5 from Opa3Ϫ/Ϫ mutants and imaged by electron microscopy of rise to this disorder have been reported : a heterozygous Ͼ the retinas. -
Association Analyses of 249,796 Individuals Reveal 18 New Loci
ARTICLES Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ~2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10−8), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation. Obesity is a major and increasingly prevalent risk factor for multiple 19 loci associated with BMI at P < 5 × 10−8 (Table 1, Fig. 1a and disorders, including type 2 diabetes and cardiovascular disease1,2. Supplementary Table 1). These 19 loci included all ten loci from Although lifestyle changes have driven its prevalence to epidemic previous GWAS of BMI6–10, two loci previously associated with body proportions, heritability studies provide evidence for a substantial weight10 (at FAIM2 and SEC16B) and one locus previously associated genetic contribution (with heritability estimates (h2) of ~40%–70%) with waist circumference14 (near TFAP2B). The remaining six loci, to obesity risk3,4. BMI is an inexpensive, non-invasive measure of near GPRC5B, MAP2K5-LBXCOR1, TNNI3K, LRRN6C, FLJ35779- obesity that predicts the risk of related complications5.