325 results on '"Chad A Shaw"'
Search Results
202. Unexpected Chromosomal Abnormalities Identified by CMA Confirmation Studies
- Author
-
Carlos A. Bacino, Amber N. Pursley, Chad A. Shaw, Sau Wai Cheung, Farah A. Ladha, M. Lance Cooper, Stephanie A. Anderson, Roger H. Song, and Ankita Patel
- Subjects
Genetics ,Cancer Research ,Biology ,Molecular Biology - Published
- 2016
203. Abstract B58: CELF1 is a central node in post-transcriptional regulatory programs underlying EMT and metastasis in breast epithelial cells
- Author
-
Arindam Chaudhury, Joseph M. Fachini, Chad A. Shaw, Lukas M. Simon, Sufeng Mao, Tao Wang, Joel R. Neilson, Daniel G. Rosen, Michael Ittmann, Natee Kongchan, and Susan G. Hilsenbeck
- Subjects
Untranslated region ,Regulation of gene expression ,Cancer Research ,Biology ,Bioinformatics ,medicine.disease_cause ,medicine.disease ,CELF1 Protein ,Metastasis ,Oncology ,Translational regulation ,medicine ,Cancer research ,Translational Activation ,Epithelial–mesenchymal transition ,Carcinogenesis - Abstract
The importance of translational regulation in tumorigenesis and metastasis is increasingly appreciated. We have leveraged polyribosomal profiling to prospectively and functionally define translational regulatory programs underlying the epithelial to mesenchymal transition (EMT), one of the early manifestations of metastasis, in breast epithelial cells. Our approach identified scores of mRNAs both enriched and depleted from polyribosomal fractions in mesenchymal cells as compared to their epithelial counterparts. Computational analysis of the 3′ untranslated regions (UTRs) of mRNAs enriched in polysomal fractions derived from the mesenchymal state revealed enrichment of a distinct GU-rich cis-element within these mRNA transcripts. Strikingly, while relative representation of these GU-rich-containing transcripts at the level of bulk mRNA were generally decreased in mesenchymal cells, the protein encoded by each of these mRNAs was dramatically increased. 3′ UTRs from affected transcripts conferred similar regulation upon a fluorescent reporter gene dependent upon the presence of the GU-rich element within the 3′ UTR sequence. Several of the translationally upregulated transcripts were necessary and/or sufficient for the EMT program. We next identified the CELF1 protein as a common regulator of these mRNA transcripts, demonstrating direct binding of the CELF1 protein to affected transcripts dependent upon the presence of the GU-rich element within their 3′ UTRs. CELF1 was itself necessary and sufficient for EMT in several distinct in vitro models as well as for metastatic colonization in vivo. Analysis of publicly available transcriptomic data revealed no increase in the relative expression of CELF1's regulatory targets or CELF1 itself in human breast cancer. We demonstrate that the CELF1 gene product is itself post-translationally regulated during EMT, and that CELF1 protein, but not mRNA, is significantly overexpressed in human breast cancer tissues and correlates with disease progression. Cumulatively, our data present a distinctive model of gene regulation, invisible to traditional transcriptional profiling, in which the CELF1 protein serves as a central node controlling translational activation of the EMT program and ultimately tumor metastasis in human breast cancer. Citation Format: Arindam Chaudhury, Natee Kongchan, Joseph M. Fachini, Lukas M. Simon, Tao Wang, Sufeng Mao, Daniel G. Rosen, Michael M. Ittmann, Susan G. Hilsenbeck, Chad A. Shaw, Joel R. Neilson. CELF1 is a central node in post-transcriptional regulatory programs underlying EMT and metastasis in breast epithelial cells. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Metastasis; 2015 Nov 30-Dec 3; Austin, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(7 Suppl):Abstract nr B58.
- Published
- 2016
204. Erratum: Corrigendum: Mutations in the transcriptional repressor REST predispose to Wilms tumor
- Author
-
Michael Capra, Eamonn Sheridan, Jillian M Birch, Neil J. Sebire, Shawn Yost, Chad A. Shaw, Anna Elliott, Juliet C. Gray, Kristen L. Karlin, Nazneen Rahman, Alexander Renwick, Gill Levitt, Sheila Seal, Elizabeth R Perdeaux, Thomas W. McLean, Sandra Hanks, Emma Ramsay, Shazia Mahamdallie, Judith E. Kingston, Anthony Renwick, Thomas F. Westbrook, Anna Zachariou, Elise Ruark, Juliet Hale, and Charles A. Stiller
- Subjects
0301 basic medicine ,Oncology ,medicine.medical_specialty ,Wilms' tumor ,Biology ,medicine.disease ,03 medical and health sciences ,030104 developmental biology ,Research centre ,Internal medicine ,Genetics ,medicine ,Transcriptional Repressor ,Rest (music) - Abstract
Nat. Genet. 47, 1471–1474 (2015); published online 9 November 2015; corrected after print 8 February 2016 In the version of this article initially published, the authors failed to acknowledge funding from the NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS FoundationTrust and University College London to Neil Sebire.
- Published
- 2016
205. Abstract PR02: The spliceosome is a therapeutic vulnerability in MYC-driven breast cancer
- Author
-
Nicholas J. Neill, Thomas A. Cooper, Chad A. Shaw, Chandraiah Lagisetti, Lukas M. Simon, Thomas R. Webb, Tiffany Y.T. Hsu, Thomas F. Westbrook, Azin Sayad, Benjamin G. Neel, Richard Marcotte, and Kristen L. Karlin
- Subjects
Cancer Research ,Spliceosome ,Hyperactivation ,Oncogene ,Cell ,Intron ,Cancer ,Biology ,medicine.disease ,medicine.anatomical_structure ,Breast cancer ,Oncology ,RNA splicing ,Cancer research ,medicine ,Molecular Biology - Abstract
c-MYC (MYC) hyperactivation is one of the most common drivers of human breast cancer and correlates with poor prognosis. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. Like other classic oncogenes, hyperactivation of MYC leads to collateral stresses onto breast cancer cells, suggesting that tumors harbor unique vulnerabilities arising from oncogenic activation of MYC. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. We demonstrate that core components of the spliceosome and its catalytic activity are required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces global changes in mRNA metabolism and increases the burden on the core spliceosome to process pre-mRNA. In primary human breast cancers, MYC hyperactivation is associated with altered splicing efficiency. In contrast to normal mammary epithelium, partial inhibition of the spliceosome in MYC-hyperactivated breast cancers leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of essential cell processes. Importantly, genetic or pharmacologic inhibition of the spliceosome in vivo impairs survival, tumorigenicity, and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing and that components of the spliceosome are therapeutic entry points for aggressive MYC-driven breast cancers. Citation Format: Tiffany Hsu, Lukas Simon, Nicholas Neill, richard marcotte, Azin Sayad, Kristen Karlin, Chandraiah Lagisetti, Thomas Cooper, Thomas Webb, Benjamin Neel, Chad Shaw, Thomas (“Trey”) Westbrook. The spliceosome is a therapeutic vulnerability in MYC-driven breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr PR02.
- Published
- 2016
206. Abstract A05: The tumor suppressor function of Plk2 in triple-negative breast cancer may be mediated through regulation of Plk1
- Author
-
Sarah J. Kurley, Deanna Acosta, Celina Montemayor, Jeffrey M. Rosen, Chad A. Shaw, Elizabeth Villegas, Rocio Dominguez-Vidana, Thomas F. Westbrook, and Elena B. Kabotyanski
- Subjects
Cancer Research ,Mammary tumor ,Oncogene ,Mammary gland ,Cancer ,Biology ,medicine.disease ,medicine.disease_cause ,PLK1 ,Breast cancer ,medicine.anatomical_structure ,Oncology ,medicine ,Cancer research ,Carcinogenesis ,Molecular Biology ,Triple-negative breast cancer - Abstract
Triple-negative breast cancers (TNBCs) are highly aggressive, associated with poor prognosis and lack targeted therapies. Current breast cancer therapies target the estrogen (ER), progesterone (PR) and human epidermal growth factor (HER2) receptors, which are absent in TNBCs. Developing new treatment strategies for TNBCs requires a better understanding of the signaling networks regulating TNBCs. Polo-like kinase 1 (Plk1) is a putative oncogene in TNBC. Plk1 is frequently overexpressed and promotes mitotic cell division, making it an attractive target for cancer therapy. Several inhibitors of Plk1 exist, one of which has accelerated to phase III clinical trials for acute myeloid leukemia. However, these drugs also inhibit Plk2, another polo-like kinase family member. The impact that the presence of Plk2 has on the effectiveness of Plk1 inhibitors as a cancer therapy is unknown. We reported recently that a loss of Plk2 in the developing mammary gland results in increased proliferation, hyperbranching, misoriented mitotic spindle assembly and defects in polarity (Villegas et al Development 2015). Loss of Plk2 was accompanied by increased expression of Plk1. Genetic rescue experiments, knocking down Plk1 in Plk2 null mouse mammary epithelium, and bimolecular fluorescence complementation assays, using wildtype Plk2 and a kinase dead mutant (KD) of Plk2 as bait, revealed that Plk2 regulates these processes through its direct interaction with Plk1. Our preliminary data suggest that loss of Plk2 results in increased Plk1 protein but not RNA expression. We propose that Plk2 functions as a tumor suppressor by decreasing Plk1 stability in TNBCs. Loss of Plk2, therefore, may sensitize tumors to treatment with Plk1 inhibitors if these tumors display Plk1 oncogene addiction. We hypothesize that Plk2, through targeted degradation of Plk1, inhibits tumorigenesis in TNBC. We observed that loss of Plk2 alone is not sufficient to generate mouse mammary tumors, however more lesions form after multiple pregnancies in Plk2 null glands than wildtype. To examine the tumor suppressor function of Plk2 through its regulation of Plk1 in TNBC, we are generating preclinical mouse mammary tumor models integrating the germline loss of Plk2 with p53 loss or c-Myc overexpression frequently observed in TNBC. Finally, to investigate the clinical relevance of Plk2 in TNBC, we will use available tissue microarrays of TNBC patient derived xenograft (PDX) mouse models to identify those that exhibit loss of Plk2. We will treat the identified PDX models with Plk1 inhibitors to confirm that Plk2 loss promotes Plk1 in human TNBC samples. With these studies, we expect to find that Plk2 is involved in the targeted degradation of Plk1 in TNBC, sensitizing this aggressive breast cancer subtype to treatment with Plk1 inhibitors. The results of these studies should help validate whether Plk2 is a new biomarker for determining which patients will benefit from Plk1 targeted TNBC treatment. Supported by Susan G. Komen Foundation grant SAC110031. Citation Format: Deanna Acosta, Elizabeth Villegas, Elena Kabotyanski, Celina Montemayor, Sarah J. Kurley, Rocio Dominguez-Vidana, Chad A. Shaw, Thomas F. Westbrook, Jeffrey M. Rosen. The tumor suppressor function of Plk2 in triple-negative breast cancer may be mediated through regulation of Plk1. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A05.
- Published
- 2016
207. Rare DNA copy number variants in cardiovascular malformations with extracardiac abnormalities
- Author
-
Lance W. Patterson, Xueqing Wang, Fatima Boricha, Sophia Ali, Seema R. Lalani, Carlos A. Bacino, Brian Dawson, James R. Lupski, Chumei Li, Chad A. Shaw, Patricia Hixson, John L. Jefferies, Runako Whittaker, Aamir Malik, Ankita Patel, Pawel Stankiewicz, Katarzyna E. Kolodziejska, Przemyslaw Szafranski, Zhishuo Ou, Stephanie M. Ware, Sung Hae L. Kang, Arthur L. Beaudet, Qi Tian, John W. Belmont, Lorraine Potocki, Daniel J. Penny, Amina Jinnah, and Sau Wai Cheung
- Subjects
Male ,DNA Copy Number Variations ,Chromosomes, Human, Pair 22 ,Chromosome Disorders ,Biology ,Bioinformatics ,Polymorphism, Single Nucleotide ,Article ,Cohort Studies ,Genetics ,Humans ,In patient ,Genetic Predisposition to Disease ,Copy-number variation ,Eye Abnormalities ,Protein Interaction Maps ,Gene ,Genetics (clinical) ,Sequence Deletion ,Aneuploidy ,DNA Copy Number Variants ,Cardiovascular Diseases ,Cohort ,Cardiovascular malformations ,Female ,Chromosomes, Human, Pair 16 ,Genome-Wide Association Study - Abstract
Clinically significant cardiovascular malformations (CVMs) occur in 5–8 per 1000 live births. Recurrent copy number variations (CNVs) are among the known causes of syndromic CVMs, accounting for an important fraction of cases. We hypothesized that many additional rare CNVs also cause CVMs and can be detected in patients with CVMs plus extracardiac anomalies (ECAs). Through a genome-wide survey of 203 subjects with CVMs and ECAs, we identified 55 CNVs >50 kb in length that were not present in children without known cardiovascular defects (n=872). Sixteen unique CNVs overlapping these variants were found in an independent CVM plus ECA cohort (n=511), which were not observed in 2011 controls. The study identified 12/16 (75%) novel loci including non-recurrent de novo 16q24.3 loss (4/714) and de novo 2q31.3q32.1 loss encompassing PPP1R1C and PDE1A (2/714). The study also narrowed critical intervals in three well-recognized genomic disorders of CVM, such as the cat-eye syndrome region on 22q11.1, 8p23.1 loss encompassing GATA4 and SOX7 and 17p13.3-p13.2 loss. An analysis of protein-interaction databases shows that the rare inherited and de novo CNVs detected in the combined cohort are enriched for genes encoding proteins that are direct or indirect partners of proteins known to be required for normal cardiac development. Our findings implicate rare variants such as 16q24.3 loss and 2q31.3-q32.1 loss, and delineate regions within previously reported structural variants known to cause CVMs.
- Published
- 2012
208. Incidental copy-number variants identified by routine genome testing in a clinical population
- Author
-
Arthur L. Beaudet, Pawel Stankiewicz, Ian M. Campbell, James R. Lupski, Amy L. McGuire, Sharon E. Plon, Sau Wai Cheung, Ankita Patel, Zachry T. Soens, Chad A. Shaw, and Philip M. Boone
- Subjects
Male ,DNA Copy Number Variations ,Population ,Inheritance Patterns ,Disease ,Biology ,Bioinformatics ,Genome ,Article ,Cancer syndrome ,Gene Order ,medicine ,Humans ,Genetic Predisposition to Disease ,Copy-number variation ,Age of Onset ,education ,Gene ,Genetics (clinical) ,Genetics ,education.field_of_study ,Comparative Genomic Hybridization ,Base Sequence ,Chromosome Mapping ,Reproducibility of Results ,medicine.disease ,Female ,Age of onset ,Comparative genomic hybridization - Abstract
Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained. Array comparative genomic hybridization, a method for genome-wide detection of DNA copy-number variants, was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. Multigene copy-number variants affecting dominant, adult-onset cancer syndrome genes were also assessed. In our cohort, 83 single-gene copy-number variants affected 40 unique genes associated with dominant, adult-onset disorders and unrelated to the patients’ referring diagnoses (i.e., incidental) were found. Fourteen of these copy-number variants are likely disease-predisposing, 25 are likely benign, and 44 are of unknown clinical consequence. When incidental copy-number variants spanning up to 20 genes were considered, 27 copy-number variants affected 17 unique genes associated with dominant, adult-onset cancer predisposition. Copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing. Some of these mutations may be medically actionable, enabling disease surveillance or prevention; however, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient. Genet Med 2013:15(1):45–54
- Published
- 2012
209. P4‐114: Integrated copy number and gene expression analysis detects a CREB1 association with Alzheimer's disease
- Author
-
Irene Sheffer, Norbert Sule, Rachelle S. Doody, James R. Lupski, Noman Zaidi, Kirk C. Wilhelmsen, Yanchun Li, Chad A. Shaw, Kinga Szigeti, and Suzanne Zein-Eldin Powell
- Subjects
Genetics ,Epidemiology ,Health Policy ,Association (object-oriented programming) ,Disease ,Biology ,Psychiatry and Mental health ,Cellular and Molecular Neuroscience ,Developmental Neuroscience ,Gene expression ,biology.protein ,Neurology (clinical) ,Geriatrics and Gerontology ,CREB1 - Published
- 2012
210. A common X-linked inborn error of carnitine biosynthesis may be a risk factor for nondysmorphic autism
- Author
-
Stephen Sanders, Rui Luo, Patrícia B. S. Celestino-Soper, Frédéric M. Vaz, Ronald J.A. Wanders, Anath C. Lionel, Robin P. Goin-Kochel, Edwin H. Cook, Richard J. Schroer, Arthur L. Beaudet, Roger E. Stevenson, Peter Szatmari, Richard E. Person, Marwan Shinawi, Stephen W. Scherer, Suzanne M. Leal, Kwanghyuk Lee, Ni Huang, Sara Violante, Guiqing Cai, Catalina Betancur, Bekim Sadikovic, Wendy Roberts, Kun Gao, Diane Treadwell-Deering, Daniel H. Geschwind, Chad A. Shaw, Joseph D. Buxbaum, Timothy J. Moss, Bridget A. Fernandez, Elsa Delaby, Emily L. Crawford, Charlene Lo, James S. Sutcliffe, Matthew E. Hurles, Jennifer R. German, Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Baylor University-Baylor University, Laboratory Genetic Metabolic Disease, University of Amsterdam [Amsterdam] (UvA)-Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), Metabolism and Genetics Group, Universidade de Lisboa (ULISBOA)-Research Institute for Medicines and Pharmaceutical Sciences, Department of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt University [Nashville]-Centers for Human Genetics Research and Molecular Neuroscience, Department of Human Genetics, UCLA, University of California [Los Angeles] (UCLA), University of California-University of California-Semel Institute, Program in Genetics and Genomic Biology, Hospital for Sick Children-University of Toronto McLaughlin Centre, Physiopathologie des Maladies du Système Nerveux Central, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Human Genetics Center, The University of Texas Health Science Center at Houston (UTHealth), Department of Neurology, Johns Hopkins University (JHU), Texas Children's Hospital [Houston, USA], Department of psychiatry, Department of Psychiatry and Behavioural Neurosciences, McMaster University [Hamilton, Ontario]-Offord Centre for Child Studies, Autism Research Unit, The Hospital for sick children [Toronto] (SickKids)-University of Toronto, Disciplines of Genetics and Medicine, Memorial University of Newfoundland [St. John's], The Greenwood Genetic Center, Departments of Psychiatry and Genetics, Yale University School of Medicine, Department of Psychiatry, Institute for Juvenile Research-University of Illinois [Chicago] (UIC), University of Illinois System-University of Illinois System, Department of pediatrics, The AGRE is a program of Autism Speaks and is supported, in part, by Grant 1U24MH081810 from the National Institute of Mental Health (to Clara M. Lajonchere). Part of this work was supported by Grant SFARI 124827 from the Simons Foundation (to the investigators of the SSC Genetic Consortium) and Grant HD-37283 (to A.L.B) and Grant P30HD-0240640 from the National Institutes of Health. Part of this work was financially supported by the Fundação para a Ciência e Tecnologia, Lisbon, Portugal, by Grant SFRH/BD/38074/2007 (to. S.V.). Part of this work was supported by National Institutes of Health Grants R01 MH061009 and R01 NS049261 (to J.S.S.). Funding for part of this work was provided by the Wellcome Trust under Award 076113 and by Grant 077014/Z/05/Z. Funding for the Paris Autism Research International Sibpair study was provided, in part, by the Institut National de la Santé et de la Recherche Médicale, Fondation de France, Fondation Orange, Fondation pour la Recherche Médicale, Assistance Publique- Hôpitaux de Paris, and the Swedish Science Council., Génétique de l'autisme = Genetics of Autism (NPS-01), Neuroscience Paris Seine (NPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA), Universidade de Lisboa = University of Lisbon (ULISBOA)-Research Institute for Medicines and Pharmaceutical Sciences, University of California (UC)-University of California (UC)-Semel Institute, Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada] (MUN), Yale School of Medicine [New Haven, Connecticut] (YSM), AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory Genetic Metabolic Diseases, Betancur, Catalina, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Neurosciences Paris Seine (NPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Mazalérat, Charlotte
- Subjects
Male ,Proband ,Penetrance ,MESH: Cognition ,[SDV.GEN] Life Sciences [q-bio]/Genetics ,Mixed Function Oxygenases ,Cognition ,0302 clinical medicine ,Genes, X-Linked ,Risk Factors ,MESH: Penetrance ,MESH: Risk Factors ,Heritability of autism ,X chromosome ,Genetics ,0303 health sciences ,Multidisciplinary ,MESH: Carnitine ,Exons ,Biological Sciences ,MESH: Mixed Function Oxygenases ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,medicine.drug ,MESH: Metabolism, Inborn Errors ,TMLHE ,MESH: Autistic Disorder ,Biology ,MESH: Chromosomes, Human, X ,03 medical and health sciences ,Carnitine ,medicine ,Humans ,[SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,Autistic Disorder ,030304 developmental biology ,Chromosomes, Human, X ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,MESH: Humans ,Siblings ,medicine.disease ,MESH: Male ,MESH: Siblings ,MESH: Genes, X-Linked ,MESH: Gene Deletion ,Carnitine biosynthesis ,Autism ,MESH: Exons ,Gene Deletion ,Metabolism, Inborn Errors ,030217 neurology & neurosurgery - Abstract
We recently reported a deletion of exon 2 of the trimethyllysine hydroxylase epsilon ( TMLHE ) gene in a proband with autism. TMLHE maps to the X chromosome and encodes the first enzyme in carnitine biosynthesis, 6- N -trimethyllysine dioxygenase. Deletion of exon 2 of TMLHE causes enzyme deficiency, resulting in increased substrate concentration (6- N -trimethyllysine) and decreased product levels (3-hydroxy-6- N -trimethyllysine and γ-butyrobetaine) in plasma and urine. TMLHE deficiency is common in control males (24 in 8,787 or 1 in 366) and was not significantly increased in frequency in probands from simplex autism families (9 in 2,904 or 1 in 323). However, it was 2.82-fold more frequent in probands from male-male multiplex autism families compared with controls (7 in 909 or 1 in 130; P = 0.023). Additionally, six of seven autistic male siblings of probands in male-male multiplex families had the deletion, suggesting that TMLHE deficiency is a risk factor for autism (metaanalysis Z-score = 2.90 and P = 0.0037), although with low penetrance (2–4%). These data suggest that dysregulation of carnitine metabolism may be important in nondysmorphic autism; that abnormalities of carnitine intake, loss, transport, or synthesis may be important in a larger fraction of nondysmorphic autism cases; and that the carnitine pathway may provide a novel target for therapy or prevention of autism.
- Published
- 2012
211. Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome
- Author
-
Margaret A. Goodell, Aleksandar Milosavljevic, Tomasz Gambin, Anna Gambin, Sau Wai Cheung, Ankita Patel, Mira Jeong, Sung-Hae L. Kang, Jian Jian Li, Cristian Coarfa, Chad A. Shaw, R. Alan Harris, Lisa D. White, James R. Lupski, and A. Craig Chinault
- Subjects
Male ,Cancer Research ,lcsh:QH426-470 ,DNA Copy Number Variations ,Population ,Biology ,Genome ,Germline ,Genomic Instability ,Epigenesis, Genetic ,Structural variation ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Segmental Duplications, Genomic ,Mutation Rate ,Genetics ,Animals ,Humans ,Disease ,Copy-number variation ,education ,Homologous Recombination ,Molecular Biology ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Comparative Genomic Hybridization ,Genome, Human ,Computational Biology ,Genomics ,DNA Methylation ,Spermatozoa ,lcsh:Genetics ,Germ Cells ,DNA methylation ,Human genome ,030217 neurology & neurosurgery ,Comparative genomic hybridization ,Research Article - Abstract
The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ∼1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR–mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease., Author Summary The human genome contains many loci with high incidence of structural mutations, including insertions and deletions of chromosomal segments. This excessive mutability has accelerated evolution and contributed to human disease but has yet to be explained. Segments of DNA repeated in low-copy numbers (LCRs) have been previously implicated in promoting structural mutability in specific disease-associated loci. Lack of methylation (hypomethylation) of genomic DNA has been previously associated with high structural mutability in gibbons and in human cancer cells, but the association with structural mutability in the human germline has not been explored prior to this study. Our analyses confirm the role of LCRs in promoting structural mutability on the genome scale but also reveal a surprisingly strong association of genomic instability with hypomethylation. Specifically, evolutionary analyses reveal that methylation deserts, the ∼1% fraction of the human genome with the lowest methylation in human sperm, harbor a tenfold higher number of structural mutations than genome-wide average. Moreover, the structural mutations in individuals diagnosed with schizophrenia, bipolar disorder, developmental delay, and autism are significantly more concentrated within hypomethylated regions. Our findings suggest a new connection between methylation of genomic DNA, selective structural mutability, evolution, and human disease.
- Published
- 2012
212. Human Genome-Wide Association and Mouse Knockout Approaches Identify Platelet Supervillin as an Inhibitor of Thrombus Formation under Shear Stress
- Author
-
Stephen N. Jones, Ying Jin, Tara C. Smith, Chad A. Shaw, Xianguo Kong, Molly S. Bray, Elizabeth J. Luna, Wolfgang Bergmeier, Firdos Ahmad, Paul F. Bray, Altaf A. Kondkar, Zhiyou Fang, Daniel Covarrubias, Srikanth Nagalla, Moritz Stolla, Suzanne M. Leal, Ian B. Gibson, Leonard C. Edelstein, and Nacima Hadjout-Rabi
- Subjects
Adult ,Blood Platelets ,Male ,Genotype ,Genome-wide association study ,Biology ,Polymorphism, Single Nucleotide ,Article ,White People ,Mice ,Platelet Adhesiveness ,Physiology (medical) ,Platelet adhesiveness ,Shear stress ,medicine ,Animals ,Humans ,Platelet ,cardiovascular diseases ,Thrombus ,education ,Cell Size ,Mice, Knockout ,education.field_of_study ,Microfilament Proteins ,Membrane Proteins ,Thrombosis ,Middle Aged ,medicine.disease ,Cell biology ,Black or African American ,Mice, Inbred C57BL ,Membrane protein ,Immunology ,Models, Animal ,Supervillin ,Female ,Stress, Mechanical ,Cardiology and Cardiovascular Medicine ,Genome-Wide Association Study - Abstract
Background— High shear force critically regulates platelet adhesion and thrombus formation during ischemic vascular events. To identify genetic factors that influence platelet thrombus formation under high shear stress, we performed a genome-wide association study and confirmatory experiments in human and animal platelets. Methods and Results— Closure times in the shear-dependent platelet function analyzer (PFA)–100 were measured on healthy, nondiabetic European Americans (n=125) and blacks (n=116). A genome-wide association ( P −8 ) was identified with 2 single-nucleotide polymorphisms within the SVIL gene (chromosome 10p11.23) in African Americans but not European Americans. Microarray analyses of human platelet RNA demonstrated the presence of SVIL isoform 1 (supervillin) but not muscle-specific isoforms 2 and 3 (archvillin, SmAV). SVIL mRNA levels were associated with SVIL genotypes ( P ≤0.02) and were inversely correlated with PFA-100 closure times ( P P Conclusions— We show for the first time that (1) platelets contain supervillin; (2) platelet thrombus formation in the PFA-100 is associated with human SVIL variants and low SVIL expression; and (3) murine platelets lacking supervillin exhibit enhanced platelet thrombus formation at high shear stress. These data are consistent with an inhibitory role for supervillin in platelet adhesion and arterial thrombosis.
- Published
- 2012
213. Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing
- Author
-
Hans-Georg O. Bock, Carlos A. Bacino, James R. Lupski, Christine M. Eng, Arthur L. Beaudet, Chad A. Shaw, Weimin Bi, Pawel Stankiewicz, Chun-hui Tsai, Frank J. Probst, Amber N. Pursley, Seema R. Lalani, Sau Wai Cheung, Joanna Wiszniewska, Patricia Hixson, Ankita Patel, Tomasz Gambin, Sung-Hae L. Kang, Maria Descartes, and Fernando Scaglia
- Subjects
Heterozygote ,DNA Copy Number Variations ,Genotyping Techniques ,uniparental disomy ,medically actionable variants ,Copy number analysis ,SNP ,Biology ,Molecular Inversion Probe ,Polymorphism, Single Nucleotide ,Article ,absence of heterozygosity ,Genetics ,Humans ,array CGH ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,Comparative Genomic Hybridization ,Genome, Human ,Genomics ,Tag SNP ,SNP genotyping ,Virtual karyotype ,SNP array ,Comparative genomic hybridization - Abstract
In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner.
- Published
- 2012
214. Detection of ≥1Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays
- Author
-
Weimin, Bi, Amy, Breman, Chad A, Shaw, Pawel, Stankiewicz, Tomasz, Gambin, Xinyan, Lu, Sau Wai, Cheung, Laird G, Jackson, James R, Lupski, Ignatia B, Van den Veyver, and Arthur L, Beaudet
- Subjects
Williams Syndrome ,Comparative Genomic Hybridization ,Gene Dosage ,Chromosome Disorders ,Aneuploidy ,Cell Line ,Charcot-Marie-Tooth Disease ,Humans ,Lymphocytes ,Down Syndrome ,Single-Cell Analysis ,Oligonucleotide Probes ,Preimplantation Diagnosis ,Oligonucleotide Array Sequence Analysis - Abstract
High resolution detection of genomic copy number abnormalities in a single cell is relevant to preimplantation genetic diagnosis and potentially to noninvasive prenatal diagnosis. Our objective is to develop a reliable array comparative genomic hybridization (CGH) platform to detect genomic imbalances as small as ~1Mb ina single cell.We empirically optimized the conditions for oligonucleotide-based array CGH using single cells from multiple lymphoblastoid cell lines with known copy number abnormalities. To improve resolution, we designed custom arrays with high density probes covering clinically relevant genomic regions.The detection of megabase-sized copy number variations (CNVs) in a single cell was influenced by the number of probes clustered in the interrogated region. Using our custom array, we reproducibly detected multiple chromosome abnormalities including trisomy 21, a 1.2Mb Williams syndrome deletion, and a 1.3Mb CMT1A duplication. Replicate analyses yielded consistent results.Aneuploidy and genomic imbalances with CNVs as small as 1.2Mb in a single cell are detectable by array CGH using arrays with high-density coverage in the targeted regions. This approach has the potential to be applied for preimplantation genetic diagnosis to detect aneuploidy and common microdeletion/duplication syndromes and for noninvasive prenatal diagnosis if single fetal cells can be isolated.
- Published
- 2012
215. Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression
- Author
-
Olena Morozova, Yan Huang, Marco A. Marra, Leah I. Elizondo, Thomas Lücke, Kira Y. Dionis, Arend Bökenkamp, Peter Stenzel, Jonathan Zonana, Kyoung Sang Cho, Clara Myung, Hok Khim Fam, Darren Bridgewater, Cornelius F. Boerkoel, Kunho Choi, Kimberly Beirnes, Chad A. Shaw, Maarten van Lohuizen, David B. Lewis, Danny Leung, Kory Keller, Joanna M. Lubieniecka, Alireza Baradaran-Heravi, Bas Tolhuis, Marie Morimoto, Christy Mayfield, Mrinmoy Sanyal, Pediatric surgery, and ICaR - Ischemia and repair
- Subjects
Subfamily ,Embryo, Nonmammalian ,Nephrotic Syndrome ,Arteriosclerosis ,Primary Immunodeficiency Diseases ,Gene Expression ,Penetrance ,Environment ,Osteochondrodysplasias ,Mice ,Gene expression ,Genetics ,Animals ,Humans ,Allele ,Molecular Biology ,Genetics (clinical) ,Alleles ,Transcriptionally active chromatin ,biology ,Schimke immuno-osseous dysplasia ,DNA Helicases ,Immunologic Deficiency Syndromes ,Helicase ,General Medicine ,Articles ,Chromatin ,Disease Models, Animal ,Mutation ,biology.protein ,Drosophila ,Pulmonary Embolism - Abstract
Biallelic mutations of the DNA annealing helicase SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1) cause Schimke immuno-osseous dysplasia (SIOD, MIM 242900), an incompletely penetrant autosomal recessive disorder. Using human, Drosophila and mouse models, we show that the proteins encoded by SMARCAL1 orthologs localize to transcriptionally active chromatin and modulate gene expression. We also show that, as found in SIOD patients, deficiency of the SMARCAL1 orthologs alone is insufficient to cause disease in fruit flies and mice, although such deficiency causes modest diffuse alterations in gene expression. Rather, disease manifests when SMARCAL1 deficiency interacts with genetic and environmental factors that further alter gene expression. We conclude that the SMARCAL1 annealing helicase buffers fluctuations in gene expression and that alterations in gene expression contribute to the penetrance of SIOD.
- Published
- 2012
216. Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats
- Author
-
Jill A. Rosenfeld, Marwan Shinawi, Scott Saunders, Livija Medne, Shashikant Kulkarni, Avinash V. Dharmadhikari, Carsten G. Bönnemann, Suneeta Madan-Khetarpal, Pawel Stankiewicz, Samarth Bhatt, Stephanie E. Vallee, Fernando Scaglia, Marshall L. Summar, Zhilian Xia, Carlos A. Bacino, Ann Martin, Brendan Lee, Alexander Asamoah, Jacques S. Beckmann, Wendy E. Smith, Sau Wai Cheung, Sumit Parikh, Rizwan Hamid, Tracy L. McGregor, Amber N. Pursley, Jean P. Pfotenhauer, Kathryn Platky, Lisa G. Shaffer, Chad A. Shaw, Ankita Patel, Polly Irwin, Paul S. Simons, Dorothy K. Grange, Sung-Hae L. Kang, Gary Bellus, Victoria P. Dalzell, John B. Moeschler, Jennifer Kussmann, Srirangan Sampath, Danielle Martinet, Alex R. Paciorkowski, Michael J. Noetzel, Carolyn Lovell, Susan Sparks, Blake C. Ballif, Kathryn Golden-Grant, Florence Fellmann, David B. Flannery, Jacqueline M. Hoover, Tamim H. Shaikh, M. Lance Cooper, Valerie Banks, and Jerome L. Gorski
- Subjects
Male ,Ataxia ,DNA Copy Number Variations ,Developmental Disabilities ,Vesicular Acetylcholine Transport Proteins ,Non-allelic homologous recombination ,Penetrance ,Biology ,Article ,Abnormalities, Multiple/genetics ,Child ,Child, Preschool ,Chromosome Aberrations ,Chromosome Mapping ,Chromosomes, Human, Pair 10 ,Developmental Disabilities/complications ,Developmental Disabilities/genetics ,Female ,Genetic Variation ,Homologous Recombination ,Humans ,In Situ Hybridization, Fluorescence ,Infant ,Intellectual Disability/complications ,Intellectual Disability/genetics ,Nerve Growth Factors/genetics ,Oligonucleotide Array Sequence Analysis ,Segmental Duplications, Genomic/genetics ,Sequence Deletion ,Vesicular Acetylcholine Transport Proteins/genetics ,Segmental Duplications, Genomic ,Intellectual Disability ,Genetics ,medicine ,Abnormalities, Multiple ,Nerve Growth Factors ,Expressivity (genetics) ,Gene ,Genetics (clinical) ,Segmental duplication ,Low copy repeats ,Hypotonia ,medicine.symptom - Abstract
We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers.
- Published
- 2012
217. Identification of the Genetic Mechanism Responsible for Racially-Dimorphic Expression of the Thrombin-Receptor Regulator, Pctp
- Author
-
Xiango Kong, Michael Holinstat, Paul F. Bray, Lukas M. Simon, Leonard C. Edelstein, Chad A. Shaw, and Katrina Leung
- Subjects
Genetics ,Immunology ,Single-nucleotide polymorphism ,MiRNA binding ,Genome-wide association study ,Cell Biology ,Hematology ,Biology ,Biochemistry ,DNA binding site ,Expression quantitative trait loci ,Hypersensitive site ,Gene ,Allele frequency - Abstract
Genome wide association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with various healthy and pathological phenotypes. The majority of these SNPs do not fall into protein-coding regions of the genome, leading to the hypothesis that variants in genomic regulatory regions are critical regulators of physiology. Efforts by the ENCODE project and others to annotate the genome have enabled researchers to better identify and test SNPs for their functional effect on gene expression. We now report the identification of a SNP responsible for the racially differential expression of phosphatidylcholine transfer p (PCTP), a protein we have previously identified as a regulator of the human platelet thrombin receptor, protease activated receptor 4 (PAR4). In the Platelet RNA and eXpression 1 (PRAX1) study, we learned that platelets from black subjects were more active in response to signaling through the PAR4 receptor and contained approximately four times more PCTP mRNA and 50% more PC-TP protein as compared to platelets from white subjects. PCTP levels are significantly associated platelet PAR4 reactivity even after accounting for a racially dimorphic PAR4 polymorphism (Ala120Thr) that alters the receptor's function. We obtained from the 154 PRAX1 subjects genome wide platelet mRNA expression profiles and 4.3 million genotypes. Using this expression and genotype data, we were able to perform an expression Quantitative Trait Locus (eQTL) analysis to identify single nucleotide polymorphisms associated with the expression level of genes located within 50kb of the variant. This analysis revealed 16 highly linked SNPs associated with PCTP levels at genome-wide significance (P eQTL SNPs can influence gene expression through a variety of mechanisms: (1) Altering the core promoter; (2) Altering the binding site of transcriptional regulators such as a transcription factors (TFs); (3) Altering RNA stability signals such as miRNA binding sites. Because none of the PCTP eQTL SNPs fall within the annotated core promoter, we reasoned the causative SNPs would fall within predicted transcription factor binding sites or miRNA target sites. To prioritize the 16 candidate SNPs for functional testing, we annotated each one according to the following criteria: (1) The SNP fell within a predicted binding site for a platelet-expressed TF or miRNA; (2) ChIP-Seq data from megakaryocytes, CD34+ hematopoietic stem cells or K562 erythroleukemia cells indicated TF binding in the region of the SNP; (3) The SNP falls in a regulatory region as indicated by epigenetic marks or DNAse hypersensitivity; (4) The allele frequency of the SNP is racially dimorphic, corresponding with PCTP expression. Using these criteria, we investigated rs2912553, a racially dimorphic SNP located in the first intron of PCTP. rs2912553 falls within a DNAse hypersensitive genomic locus that contains Lys4 monomethylated histone H3, a marker of enhancers. Cloning different sized fragments of this region 5' to a luciferase expression cassette replicated the observed PCTP expression pattern, with the vectors containing the allele most common in black subjects generating 2-8 fold higher luciferase expression than vectors containing the common allele in whites. In agreement with these results electromobility shift assays indicate that protein complexes have a threefold higher affinity for the common allele in blacks as compared to the common allele in whites (P=0.02), and that these complexes can be interrupted with an anti-GATA1 antibody. Concordantly, siRNA knockdown of GATA1 expression reduced luciferase activity in both alleles. Together, these data indicate that the racially dimorphic SNP, rs2912553, causes differential recruitment of a GATA-1 containing transcriptional complex that is responsible for higher PCTP expression in blacks. This suggests the hypothesis that these genetic variances contribute to the dissimilar thrombotic risk between blacks and whites. Future studies should address the utility of rs2912553 as a biomarker for diseases or drug effects that differ by race. Disclosures No relevant conflicts of interest to declare.
- Published
- 2015
218. A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis
- Author
-
Tingting Sun, Mamie Z. Li, Earlene M. Schmitt, Zachary C. Hartman, Peng Yu, Nicole L. Solimini, Bing Yu, Rachel Schiff, Stephen J. Elledge, Rocio Dominguez-Vidana, Tiffany Y.T. Hsu, Ido Golding, Ji Luo, Jessica D. Kessler, Anthony C. Liang, Chad A. Shaw, Michael R. Schlabach, Kristen L. Meerbrey, Kristopher T. Kahle, Thomas F. Westbrook, C. Kent Osborne, Susan G. Hilsenbeck, Ronald J. Bernardi, Samuel O. Skinner, Mitchell Rao, Chad J. Creighton, and Qikai Xu
- Subjects
Transcription, Genetic ,Transplantation, Heterologous ,SUMO protein ,Genes, myc ,Mice, Nude ,Mitosis ,Breast Neoplasms ,Synthetic lethality ,Spindle Apparatus ,Ubiquitin-Activating Enzymes ,Biology ,medicine.disease_cause ,Proto-Oncogene Proteins c-myc ,Mice ,RNA interference ,Cell Line, Tumor ,medicine ,Animals ,Humans ,RNA, Small Interfering ,Mitotic catastrophe ,Transcription factor ,Regulation of gene expression ,Multidisciplinary ,Gene Expression Profiling ,Cell Cycle ,Mammary Neoplasms, Experimental ,Sumoylation ,Cell cycle ,Gene Expression Regulation, Neoplastic ,Cell Transformation, Neoplastic ,Cancer research ,Female ,RNA Interference ,Carcinogenesis ,Neoplasm Transplantation - Abstract
Taking the Myc Despite nearly 30 years of research into the mechanisms by which Myc oncogene dysregulation contributes to tumorigenesis, there are still no effective therapies that inhibit Myc activity. Kessler et al. (p. 348 , published online 8 December; see the Perspective by Evan ) searched for gene products that support Myc-driven tumorigenesis. One pharmacologically tractable target that emerged from the screen was the SUMO-activating enzyme complex SAE1/2, which catalyzes a posttranslational modification (SUMOylation) that alters protein behavior and function. SUMOylation was found to control the Myc transcriptional response, and its inhibition caused mitotic defects and apoptosis in Myc-dependent breast cancer cells.
- Published
- 2011
219. High frequency of known copy number abnormalities and maternal duplication 15q11-q13 in patients with combined schizophrenia and epilepsy
- Author
-
Chad A. Shaw, Arthur L. Beaudet, Larissa R. Stewart, Sung-Hae L. Kang, and April L Hall
- Subjects
Male ,lcsh:Internal medicine ,medicine.medical_specialty ,Bipolar Disorder ,lcsh:QH426-470 ,DNA Copy Number Variations ,Chromosomes, Human, Pair 22 ,Chromosome Disorders ,Trisomy ,Biology ,Bioinformatics ,behavioral disciplines and activities ,03 medical and health sciences ,Epilepsy ,0302 clinical medicine ,Internal medicine ,Chromosome Duplication ,mental disorders ,Intellectual disability ,Genetics ,medicine ,Humans ,Genetics(clinical) ,Bipolar disorder ,Copy-number variation ,lcsh:RC31-1245 ,Genetics (clinical) ,030304 developmental biology ,Chromosomes, Human, Pair 15 ,Comparative Genomic Hybridization ,0303 health sciences ,Case-control study ,medicine.disease ,3. Good health ,lcsh:Genetics ,Chromosomes, Human, Pair 1 ,Schizophrenia ,Case-Control Studies ,Autism ,Female ,Chromosome Deletion ,030217 neurology & neurosurgery ,Research Article - Abstract
Background Many copy number variants (CNVs) are documented to be associated with neuropsychiatric disorders, including intellectual disability, autism, epilepsy, schizophrenia, and bipolar disorder. Chromosomal deletions of 1q21.1, 3q29, 15q13.3, 22q11.2, and NRXN1 and duplications of 15q11-q13 (maternal), 16p11, and 16p13.3 have the strongest association with schizophrenia. We hypothesized that cases with both schizophrenia and epilepsy would have a higher frequency of disease-associated CNVs and would represent an enriched sample for detection of other mutations associated with schizophrenia. Methods We used array comparative genomic hybridization (CGH) to analyze 235 individuals with both schizophrenia and epilepsy, 80 with bipolar disorder and epilepsy, and 191 controls. Results We detected 10 schizophrenia plus epilepsy cases in 235 (4.3%) with the above mentioned CNVs compared to 0 in 191 controls (p = 0.003). Other likely pathological findings in schizophrenia plus epilepsy cases included 1 deletion 16p13 and 1 duplication 7q11.23 for a total of 12/235 (5.1%) while a possibly pathogenic duplication of 22q11.2 was found in one control for a total of 1 in 191 (0.5%) controls (p = 0.008). The rate of abnormality in the schizophrenia plus epilepsy of 10/235 for the more definite CNVs compares to a rate of 75/7336 for these same CNVs in a series of unselected schizophrenia cases (p = 0.0004). Conclusion We found a statistically significant increase in the frequency of CNVs known or likely to be associated with schizophrenia in individuals with both schizophrenia and epilepsy compared to controls. We found an overall 5.1% detection rate of likely pathological findings which is the highest frequency of such findings in a series of schizophrenia patients to date. This evidence suggests that the frequency of disease-associated CNVs in patients with both schizophrenia and epilepsy is significantly higher than for unselected schizophrenia.
- Published
- 2011
220. Protein interactome reveals converging molecular pathways among autism disorders
- Author
-
Zaina Al-Mohtaseb, David E. Hill, Brian Dawson, Chad A. Shaw, Yasunari Sakai, Diana V. Dugas, and Huda Y. Zoghbi
- Subjects
Nerve Tissue Proteins ,Biology ,Interactome ,behavioral disciplines and activities ,Article ,Cell Line ,Mice ,Interaction network ,Two-Hybrid System Techniques ,Gene duplication ,mental disorders ,Protein Interaction Mapping ,medicine ,FLNA ,Animals ,Humans ,Immunoprecipitation ,Copy-number variation ,Genetics ,Infant, Newborn ,Brain ,General Medicine ,medicine.disease ,Phenotype ,medicine.anatomical_structure ,Child Development Disorders, Pervasive ,Autism ,TSC1 - Abstract
To uncover shared pathogenic mechanisms among the highly heterogeneous autism spectrum disorders (ASDs), we developed a protein interaction network that identified hundreds of new interactions among proteins encoded by ASD-associated genes. We discovered unexpectedly high connectivity between SHANK and TSC1, previously implicated in syndromic autism, suggesting that common molecular pathways underlie autistic phenotypes in distinct syndromes. ASD patients were more likely to harbor copy number variations that encompass network genes than were control subjects. We also identified, in patients with idiopathic ASD, three de novo lesions (deletions in 16q23.3 and 15q22 and one duplication in Xq28) that involve three network genes (NECAB2, PKM2, and FLNA). The protein interaction network thus provides a framework for identifying causes of idiopathic autism and for understanding molecular pathways that underpin both syndromic and idiopathic ASDs.
- Published
- 2011
221. Platelet microRNA-mRNA coexpression profiles correlate with platelet reactivity
- Author
-
Lin Ma, Jing-fei Dong, Ying Jin, Jose A. Lopez, Srikanth Nagalla, Paul F. Bray, Suzanne M. Leal, G. Stanley McKnight, Chad A. Shaw, Altaf A. Kondkar, Xianguo Kong, Leonard C. Edelstein, Junmei Chen, Linghai Yang, and Molly S. Bray
- Subjects
Blood Platelets ,Three prime untranslated region ,Gene Expression Profiling ,Immunology ,Gene Expression ,Cell Biology ,Hematology ,Biology ,Platelets and Thrombopoiesis ,Platelet Activation ,Biochemistry ,Molecular biology ,Gene expression profiling ,MicroRNAs ,RNA interference ,microRNA ,Gene expression ,Gene silencing ,Cluster Analysis ,Humans ,Platelet ,Platelet activation ,RNA, Messenger ,Genome-Wide Association Study ,Oligonucleotide Array Sequence Analysis - Abstract
MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3′-untranslated regions of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5, and miR-107:CLOCK) were selected from this list, and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets.
- Published
- 2011
222. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism
- Author
-
John D. Murdoch, Sindhuja Kammela, Stephen Sanders, Rui Luo, Kyle A. Meyer, Donna M. Martin, Arthur L. Beaudet, Timothy W. Yu, Lambertus Klei, Kathryn Roeder, Lea K. Davis, Daniel Moreno-De-Luca, Nicole R. Davis Wright, David H. Ledbetter, Michael P. Moreau, A. Gulhan Ercan-Sencicek, Andrew Brooks, Richard P. Lifton, Christopher E. Mason, Youeun Song, Christopher A. Walsh, Bernie Devlin, Matthew W. State, Michael Sheldon, Dorothy E. Grice, Christa Lese Martin, Kaya Bilguvar, Abha R. Gupta, Susanne Thomson, Michael DiCola, Brian L. Yaspan, Rita M. Cantor, Vanessa Hus, Shrikant Mane, Su H. Chu, Sabata C. Lund, Vikram Fielding-Singh, Ilana R. Yurkiewicz, Edwin H. Cook, Murat Gunel, Martin Curland, Brian J. O'Roak, Nicholas M. DiLullo, Rahul M. Dhodapkar, Eric Fombonne, Patrícia B. S. Celestino-Soper, Gerald Goh, Stephanie Frahm, Jay A. Tischfield, Emily L. Crawford, Daniel O. Fishman, James S. Sutcliffe, Michael T. Murtha, Eric M. Morrow, Gordon T. Ober, William J. Moffat, Anna D. McGrew, Rouben Garagaloyan, Melanie J. Raubeson, Catherine Lord, Murim Choi, Rebecca S. Pottenger, Thomas V. Fernandez, Daniel H. Geschwind, Chad A. Shaw, Jennifer K. Lowe, and Qi Wang
- Subjects
Proband ,Male ,Williams Syndrome ,congenital, hereditary, and neonatal diseases and abnormalities ,Adolescent ,DNA Copy Number Variations ,Genotype ,Neuroscience(all) ,Cell Adhesion Molecules, Neuronal ,Epigenetics of autism ,Nerve Tissue Proteins ,Biology ,Article ,Ubiquitin-Specific Peptidase 7 ,Gene Duplication ,mental disorders ,medicine ,Humans ,Heritability of autism ,Child ,Gene ,Neural Cell Adhesion Molecules ,Oligonucleotide Array Sequence Analysis ,Genetics ,Family Health ,Chromosomes, Human, X ,General Neuroscience ,Gene Expression Profiling ,Siblings ,Calcium-Binding Proteins ,Proteins ,medicine.disease ,Cadherins ,Phenotype ,Autism spectrum disorder ,Child Development Disorders, Pervasive ,Child, Preschool ,Autism ,Human genome ,Female ,Williams syndrome ,Ubiquitin Thiolesterase ,Chromosomes, Human, Pair 16 ,Chromosomes, Human, Pair 7 ,Genome-Wide Association Study - Abstract
Given prior evidence for the contribution of rare copy number variations (CNVs) to autism spectrum disorders (ASD), we studied these events in 4,457 individuals from 1,174 simplex families, composed of parents, a proband and, in most kindreds, an unaffected sibling. We find significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome, featuring a highly social personality. We identify rare recurrent de novo CNVs at five additional regions including two novel ASD loci, 16p13.2 (including the genes USP7 and C16orf72) and Cadherin13, and implement a rigorous new approach to evaluating the statistical significance of these observations. Overall, we find large de novo CNVs carry substantial risk (OR=3.55; CI =2.16-7.46, p=6.9 × 10−6); estimate the presence of 130-234 distinct ASD-related CNV intervals across the genome; and, based on data from multiple studies, present compelling evidence for the association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin1.
- Published
- 2011
223. Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes
- Author
-
Zhilian Xia, M. Lance Cooper, A. Craig Chinault, Zhishuo Ou, Chad A. Shaw, Sau Wai Cheung, Brian Dawson, Paul M. Fernhoff, Sally Rosengren, Ankita Patel, Przemyslaw Szafranski, Lina Shao, Elizabeth Roeder, Mitchell Rao, Karlene Coleman, Amy M. Breman, Victoria B. Enciso, Sung Hae L. Kang, Marcel J. Deray, Sarah T. South, Joanna Wiszniewska, Pawel Stankiewicz, and James R. Lupski
- Subjects
Male ,Sequence analysis ,Molecular Sequence Data ,Non-allelic homologous recombination ,Chromosomal translocation ,Chromosome Disorders ,Biology ,Receptors, Odorant ,Polymerase Chain Reaction ,DNA sequencing ,Translocation, Genetic ,Segmental Duplications, Genomic ,Genetics ,Humans ,Family ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,Recombination, Genetic ,Comparative Genomic Hybridization ,Chromosomes, Human, Pair 11 ,Research ,Breakpoint ,Chromosome Mapping ,Chromosome Breakage ,Sequence Analysis, DNA ,Phenotype ,Multigene Family ,Human genome ,Female ,Chromosome breakage ,Chromosomes, Human, Pair 4 ,Comparative genomic hybridization - Abstract
Four unrelated families with the same unbalanced translocation der(4)t(4;11)(p16.2;p15.4) were analyzed. Both of the breakpoint regions in 4p16.2 and 11p15.4 were narrowed to large ∼359-kb and ∼215-kb low-copy repeat (LCR) clusters, respectively, by aCGH and SNP array analyses. DNA sequencing enabled mapping the breakpoints of one translocation to 24 bp within interchromosomal paralogous LCRs of ∼130 kb in length and 94.7% DNA sequence identity located in olfactory receptor gene clusters, indicating nonallelic homologous recombination (NAHR) as the mechanism for translocation formation. To investigate the potential involvement of interchromosomal LCRs in recurrent chromosomal translocation formation, we performed computational genome-wide analyses and identified 1143 interchromosomal LCR substrate pairs, >5 kb in size and sharing >94% sequence identity that can potentially mediate chromosomal translocations. Additional evidence for interchromosomal NAHR mediated translocation formation was provided by sequencing the breakpoints of another recurrent translocation, der(8)t(8;12)(p23.1;p13.31). The NAHR sites were mapped within 55 bp in ∼7.8-kb paralogous subunits of 95.3% sequence identity located in the ∼579-kb (chr 8) and ∼287-kb (chr 12) LCR clusters. We demonstrate that NAHR mediates recurrent constitutional translocations t(4;11) and t(8;12) and potentially many other interchromosomal translocations throughout the human genome. Furthermore, we provide a computationally determined genome-wide “recurrent translocation map.”
- Published
- 2011
224. Olfactory copy number association with age at onset of Alzheimer disease
- Author
-
Rachelle S. Doody, Kinga Szigeti, John W. Belmont, Joanna Wiszniewska, Scott A. Chasse, W. Jin, S. N.Y. Zaidi, Kirk C. Wilhelmsen, Brian Dawson, Chad A. Shaw, Yi Li, and J. R. Lupski
- Subjects
DNA Copy Number Variations ,Apolipoprotein E4 ,Gene Dosage ,Biology ,Receptors, Odorant ,Disease cluster ,Gene dosage ,Cohort Studies ,Alzheimer Disease ,Genetic variation ,medicine ,Humans ,Multiplex ,Copy-number variation ,Age of Onset ,Proportional Hazards Models ,Chromosomes, Human, Pair 14 ,Genetics ,Comparative Genomic Hybridization ,Olfactory receptor ,Chromosome Mapping ,Articles ,Heritability ,medicine.disease ,medicine.anatomical_structure ,Neurology (clinical) ,Alzheimer's disease - Abstract
Objectives: Copy number variants (CNVs) have been recognized as a source of genetic variation that contributes to disease phenotypes. Alzheimer disease (AD) has high heritability for occurrence and age at onset (AAO). We performed a cases-only genome-wide CNV association study for age at onset of AD. Methods: The discovery case series (n = 40 subjects with AD) was evaluated using array comparative genome hybridization (aCGH). A replication case series (n = 507 subjects with AD) was evaluated using Affymetrix array (n = 243) and multiplex ligation-dependent probe amplification (n = 264). Hazard models related onset age to CNV. Results: The discovery sample identified a chromosomal segment on 14q11.2 (19.3–19.5 Mb, NCBI build 36, UCSC hg18 March 2006) as a region of interest (genome-wide adjusted p = 0.032) for association with AAO of AD. This region encompasses a cluster of olfactory receptors. The replication sample confirmed the association (p = 0.035). The association was found for each APOE4 gene dosage (0, 1, and 2). Conclusion: High copy number in the olfactory receptor region on 14q11.2 is associated with younger age at onset of AD.
- Published
- 2011
- Full Text
- View/download PDF
225. Identification of de novo copy number variants associated with human disorders of sexual development
- Author
-
Shuo Han, Svetlana A. Yatsenko, Sung-Hae L. Kang, Dolores J. Lamb, Sean T. Corbett, Mounia Tannour-Louet, Jean-Francois Louet, Lindsay Meyers, Sau Wai Cheung, and Chad A. Shaw
- Subjects
Candidate gene ,Gonad ,Genetic counseling ,Gene Dosage ,lcsh:Medicine ,Biology ,Bioinformatics ,03 medical and health sciences ,0302 clinical medicine ,Gene duplication ,medicine ,Humans ,Sex organ ,Copy-number variation ,lcsh:Science ,In Situ Hybridization, Fluorescence ,030304 developmental biology ,Oligonucleotide Array Sequence Analysis ,Genetics ,0303 health sciences ,030219 obstetrics & reproductive medicine ,Multidisciplinary ,Sexual Development ,lcsh:R ,Chromosome Mapping ,3. Good health ,medicine.anatomical_structure ,Testis determining factor ,Case-Control Studies ,Karyotyping ,lcsh:Q ,Comparative genomic hybridization - Abstract
Disorders of sexual development (DSD), ranging in severity from genital abnormalities to complete sex reversal, are among the most common human birth defects with incidence rates reaching almost 3%. Although causative alterations in key genes controlling gonad development have been identified, the majority of DSD cases remain unexplained. To improve the diagnosis, we screened 116 children born with idiopathic DSD using a clinically validated array-based comparative genomic hybridization platform. 8951 controls without urogenital defects were used to compare with our cohort of affected patients. Clinically relevant imbalances were found in 21.5% of the analyzed patients. Most anomalies (74.2%) evaded detection by the routinely ordered karyotype and were scattered across the genome in gene-enriched subtelomeric loci. Among these defects, confirmed de novo duplication and deletion events were noted on 1p36.33, 9p24.3 and 19q12-q13.11 for ambiguous genitalia, 10p14 and Xq28 for cryptorchidism and 12p13 and 16p11.2 for hypospadias. These variants were significantly associated with genitourinary defects (P = 6.08×10(-12)). The causality of defects observed in 5p15.3, 9p24.3, 22q12.1 and Xq28 was supported by the presence of overlapping chromosomal rearrangements in several unrelated patients. In addition to known gonad determining genes including SRY and DMRT1, novel candidate genes such as FGFR2, KANK1, ADCY2 and ZEB2 were encompassed. The identification of risk germline rearrangements for urogenital birth defects may impact diagnosis and genetic counseling and contribute to the elucidation of the molecular mechanisms underlying the pathogenesis of human sexual development.
- Published
- 2010
226. Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics
- Author
-
Lina Shao, Patricia Hixson, Ankita Patel, Chad A. Shaw, Chung Che Chang, Svetlana A. Yatsenko, Jian Li, Sau Wai Cheung, Sung Hae L. Kang, Jesalyn J. Taylor, and Aleksandar Milosavljevic
- Subjects
Genetics ,Chromosome Aberrations ,medicine.diagnostic_test ,Isochromosome ,Aneuploidy ,Nucleic Acid Hybridization ,Biology ,medicine.disease ,Molecular biology ,Pathology and Forensic Medicine ,Hematologic Neoplasms ,Tetrasomy ,medicine ,Molecular Medicine ,Humans ,Hematological neoplasm ,Trisomy ,Virtual karyotype ,In Situ Hybridization, Fluorescence ,Fluorescence in situ hybridization ,Comparative genomic hybridization ,Oligonucleotide Array Sequence Analysis ,Regular Articles - Abstract
Application of array comparative genomic hybridization (aCGH) has allowed an unprecedented high-resolution analysis of cancer genomes. We developed a custom genome-wide oligonucleotide microarray interrogating 493 genes involved in hematological disorders. We analyzed 55 patients with hematological neoplasms by using this microarray. In 33 patients with apparent normal conventional cytogenetic analysis, aneuploidy or isochromosomes were detected in 12% (4 of 33) of the patients by aCGH. The chromosomal changes included trisomy of chromosomes 10, 14, and 15, tetrasomy 11, and isochromosome 17q. In 17 patients with chronic lymphocytic leukemia who were initially investigated by using a panel of standard fluorescence in situ hybridization probes, additional copy number changes that were not interrogated by the fluorescence in situ hybridization (FISH) panel were detected in 47% (8 of 17) of the patients by aCGH. Important copy number changes included gain on 2p16 involving REL and BCL11A genes, rearrangements of chromosomes 8 and 15, and trisomy of chromosomes 19 and 22. In five patients with known abnormal karyotypes, aCGH identified the origin of two marker chromosomes and detected microdeletions at five breakpoints involved in three apparent balanced translocations. Our results suggest that a subset of potentially significant genomic alterations is missed by the currently available cytogenetic techniques. This pilot study clearly demonstrates high sensitivity of oligonucleotide aCGH for potential use in diagnosis and follow-up in patients with hematological neoplasms.
- Published
- 2010
227. Detection of clinically relevant exonic copy-number changes by array CGH
- Author
-
Sau Wai Cheung, Arthur L. Beaudet, Yaping Yang, Frank J. Probst, Tomasz Gambin, James B. Gibson, Philip M. Boone, Magdalena Bartnik, Amber N. Pursley, Zhilian Xia, Patricia A. Eng, Weimin Bi, Joanna Wiszniewska, Barbara Wisniowiecka-Kowalnik, Lorraine Potocki, Seema R. Lalani, Tyler Reimschisel, Katarzyna Derwińska, Carlos A. Bacino, Ankita Patel, Pawel Stankiewicz, James R. Lupski, Daniela del Gaudio, Fernando Scaglia, Christian P. Schaaf, Jennifer A. Bowers, Anne C.H. Tsai, Maciej Sykulski, Chad A. Shaw, La Donna Immken, Patricia Hixson, Beata Nowakowska, Sung Hae L. Kang, and Gayle Simpson-Patel
- Subjects
Male ,Candidate gene ,Adolescent ,DNA Copy Number Variations ,Sequence analysis ,Molecular Sequence Data ,Biology ,Genome ,Article ,Exon ,Chromosome Breakpoints ,Young Adult ,Genetics ,Humans ,Copy-number variation ,Child ,Gene ,Genetics (clinical) ,Genetic Association Studies ,Sequence Deletion ,Comparative Genomic Hybridization ,Base Sequence ,Infant, Newborn ,Infant ,Exons ,Sequence Analysis, DNA ,Phenotype ,Child, Preschool ,Female ,Comparative genomic hybridization - Abstract
Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications--those including genomic intervals of a size smaller than a gene--have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.
- Published
- 2010
228. Insertional Translocation Detected Using FISH Confirmation of Array-Comparative Genomic Hybridization (aCGH) Results
- Author
-
Pawel Stankiewicz, Chad A. Shaw, Sung-Hae L. Kang, Ankita Patel, Carlos A. Bacino, Zhishuo Ou, M. Lance Cooper, James R. Lupski, Trilochan Sahoo, Sau Wai Cheung, A. Craig Chinault, Amber N. Pursley, and Patricia A. Eng
- Subjects
Male ,Monosomy ,Adolescent ,Chromosomal translocation ,Chromosomal rearrangement ,In situ hybridization ,Biology ,Article ,Translocation, Genetic ,Genetics ,medicine ,Humans ,Child ,Gene ,Genetics (clinical) ,In Situ Hybridization, Fluorescence ,Comparative Genomic Hybridization ,medicine.diagnostic_test ,Infant, Newborn ,Infant ,Reproducibility of Results ,medicine.disease ,Mutagenesis, Insertional ,Child, Preschool ,Chromosomes, Human, Pair 6 ,Female ,Chromosomes, Human, Pair 3 ,Chromosome Deletion ,Trisomy ,Fluorescence in situ hybridization ,Comparative genomic hybridization - Abstract
Insertional translocations (ITs) are rare events that require at least three breaks in the chromosomes involved and thus qualify as complex chromosomal rearrangements (CCR). In the current study, we identified 40 ITs from approximately 18,000 clinical cases (1:500) using array-comparative genomic hybridization (aCGH) in conjunction with fluorescence in situ hybridization (FISH) confirmation of the aCGH findings, and parental follow-up studies. Both submicroscopic and microscopically visible IT events were detected. They were divided into three major categories: (1) simple intrachromosomal and interchromosomal IT resulting in pure segmental trisomy, (2) complex IT involving more than one abnormality, (3) deletion inherited from a parent with a balanced IT resulting in pure segmental monosomy. Of the cases in which follow-up parental studies were available, over half showed inheritance from an apparently unaffected parent carrying the same unbalanced rearrangement detected in the propositi, thus decreasing the likelihood that these IT events are clinically relevant. Nevertheless, we identified six cases in which small submicroscopic events were detected involving known disease-associated genes/genomic segments and are likely to be pathogenic. We recommend that copy number gains detected by clinical aCGH analysis should be confirmed using FISH analysis whenever possible in order to determine the physical location of the duplicated segment. We hypothesize that the increased use of aCGH in the clinic will demonstrate that IT occurs more frequently than previously considered but can identify genomic rearrangements with unclear clinical significance.
- Published
- 2010
229. P4‐127: Olfactory receptor cluster copy number is associated with age at onset of Alzheimer's disease
- Author
-
Kinga Szigeti, James R. Lupski, John W. Belmont, Yanchun Li, Chad A. Shaw, and Rachelle S. Doody
- Subjects
Genetics ,Olfactory receptor ,Epidemiology ,Health Policy ,Disease ,Biology ,Disease cluster ,Psychiatry and Mental health ,Cellular and Molecular Neuroscience ,medicine.anatomical_structure ,Developmental Neuroscience ,medicine ,Neurology (clinical) ,Geriatrics and Gerontology - Published
- 2009
230. Gene expression in Barrett's esophagus: laser capture versus whole tissue
- Author
-
Gretchen J. Darlington, Toni-Ann Mistretta, Zhannat Z. Nurgalieva, Chad A. Shaw, Hashem B. El-Serag, Milton J. Finegold, Rhonda F. Souza, and Susan G. Hilsenbeck
- Subjects
Pathology ,medicine.medical_specialty ,Biopsy ,Biology ,Article ,Barrett Esophagus ,medicine ,Humans ,Esophagus ,Microdissection ,Laser capture microdissection ,Analysis of Variance ,medicine.diagnostic_test ,Esophageal disease ,Gene Expression Profiling ,Lasers ,Gastroenterology ,equipment and supplies ,medicine.disease ,Fold change ,Epithelium ,Gene Expression Regulation, Neoplastic ,surgical procedures, operative ,medicine.anatomical_structure ,Barrett's esophagus ,sense organs ,Esophagoscopy ,Biomarkers - Abstract
Diagnosis of Barrett's esophagus (BE) is typically done through morphologic analysis of esophageal tissue biopsy. Such samples contain several cell types. Laser capture microdissection (LCM) allows the isolation of specific cells from heterogeneous cell populations. The purpose of this study was to determine the degree of overlap of the two sample types and to define a set of genes that might serve as biochemical markers for BE.Biopsies were obtained from regions of the glandular tissue of BE and normal esophagus from 9 subjects with BE. Samples from 5 subjects were examined as whole tissue (BE [whole]; E [whole]), and in 4 subjects the glandular epithelium of BE was isolated using LCM (BE [LCM]) and compared with the averaged values (E [LCM]) for both basal cell (B [LCM]) and squamous cell (S [LCM]) epithelium.Gene expression revealed 1797 probe sets between BE [whole] and E [whole] (fold change2.0; p0.001). Most of these genes (74%) were also differentially expressed between BE [LCM] and E [LCM], showing that there was high concordance between the two sampling methods. LCM provided a great deal of additional information (2113 genes) about the alterations in gene expression that may represent the BE phenotype.There are differences in gene expression profiles depending on whether specimens are whole tissue biopsies or LCM dissected. Whole tissue biopsies should prove satisfactory for diagnostic purposes. Because the data from LCM samples delineated many more Barrett's-specific genes, this procedure might provide more information regarding pathogenesis than would whole tissue material.
- Published
- 2009
231. Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus
- Author
-
Shay Ben-Shachar, Maria H. Chahrour, Christina Thaller, Chad A. Shaw, and Huda Y. Zoghbi
- Subjects
congenital, hereditary, and neonatal diseases and abnormalities ,Methyl-CpG-Binding Protein 2 ,Pair-rule gene ,Gene Dosage ,Hypothalamus ,Rett syndrome ,Mice, Transgenic ,Biology ,Gene dosage ,MECP2 ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Cerebellum ,Gene duplication ,Gene expression ,mental disorders ,Genetics ,medicine ,Rett Syndrome ,Animals ,Humans ,Molecular Biology ,Gene ,Genetics (clinical) ,030304 developmental biology ,Regulation of gene expression ,Mice, Knockout ,0303 health sciences ,General Medicine ,Articles ,medicine.disease ,nervous system diseases ,Mice, Inbred C57BL ,Disease Models, Animal ,Gene Expression Regulation ,030217 neurology & neurosurgery - Abstract
A group of post-natal neurodevelopmental disorders collectively referred to as MeCP2 disorders are caused by aberrations in the gene encoding methyl-CpG-binding protein 2 (MECP2). Loss of MeCP2 function causes Rett syndrome (RTT), whereas increased copy number of the gene causes MECP2 duplication or triplication syndromes. MeCP2 acts as a transcriptional repressor, however the gene expression changes observed in the hypothalamus of MeCP2 disorder mouse models suggest that MeCP2 can also upregulate gene expression, given that the majority of genes are downregulated upon loss of MeCP2 and upregulated in its presence. To determine if this dual role of MeCP2 extends beyond the hypothalamus, we studied gene expression patterns in the cerebellum of Mecp2-null and MECP2-Tg mice, modeling RTT and MECP2 duplication syndrome, respectively. We found that abnormal MeCP2 dosage causes alterations in the expression of hundreds of genes in the cerebellum. The majority of genes were upregulated in MECP2-Tg mice and downregulated in Mecp2-null mice, consistent with a role for MeCP2 as a modulator that can both increase and decrease gene expression. Interestingly, many of the genes altered in the cerebellum, particularly those increased by the presence of MeCP2 and decreased in its absence, were similarly altered in the hypothalamus. Our data suggest that either gain or loss of MeCP2 results in gene expression changes in multiple brain regions and that some of these changes are global. Further delineation of the expression pattern of MeCP2 target genes throughout the brain might identify subsets of genes that are more amenable to manipulation, and can thus be used to modulate some of the disease phenotypes.
- Published
- 2009
232. Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA
- Author
-
Zhishuo Ou, Chad A. Shaw, Svetlana A. Yatsenko, A. Craig Chinault, Weimin Bi, Sau Wai Cheung, Ankita Patel, James R. Lupski, Arthur L. Beaudet, and Amber N. Pursley
- Subjects
Male ,Aneuploidy ,Biology ,Y chromosome ,Sensitivity and Specificity ,Pathology and Forensic Medicine ,chemistry.chemical_compound ,medicine ,Humans ,X chromosome ,Oligonucleotide Array Sequence Analysis ,Genetics ,Chromosome Aberrations ,Bacterial artificial chromosome ,Comparative Genomic Hybridization ,Sex Characteristics ,Sex Chromosomes ,Oligonucleotide ,Chromosome ,DNA ,Reference Standards ,medicine.disease ,chemistry ,Cytogenetic Analysis ,Molecular Medicine ,Female ,Comparative genomic hybridization ,Regular Articles - Abstract
In array-comparative genomic hybridization (array-CGH) experiments, the measurement of DNA copy number of sex chromosomal regions depends on the sex of the patient and the reference DNAs used. We evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately one-half of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. Sex-matched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs. Using sex-mismatched reference DNAs in array-CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, thus masking potential pathogenic genomic imbalances. Therefore, to optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, we suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs.
- Published
- 2009
233. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching
- Author
-
Amber Pursley, Magdalena Nawara, Y. Jane Tavyev, Pengfei Liu, James R. Lupski, Claudia M.B. Carvalho, Angela Maria Vianna-Morgante, Sau Wai Cheung, Trilochan Sahoo, Huda Y. Zoghbi, Feng Zhang, Ankita Patel, Pawel Stankiewicz, Chad A. Shaw, Sandra Peacock, Melissa B. Ramocki, Carlos A. Bacino, and Ewa Obersztyn
- Subjects
Male ,DNA Repair ,Transcription, Genetic ,Inverted Repeat Sequences ,Methyl-CpG-Binding Protein 2 ,Population ,Biology ,Genome ,Structural variation ,Cohort Studies ,Gene Duplication ,Gene duplication ,Genetics ,Humans ,education ,Molecular Biology ,Gene ,Genetics (clinical) ,Gene Rearrangement ,education.field_of_study ,Breakpoint ,DNA Breaks ,Genetic Diseases, X-Linked ,General Medicine ,Gene rearrangement ,Articles ,Templates, Genetic ,Female - Abstract
Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from approximately 250 kb to approximately 2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2.
- Published
- 2009
234. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases†
- Author
-
James R. Lupski, Arthur L. Beaudet, Amber N. Pursley, Ankita Patel, Weimin Bi, Patricia A. Ward, Sarah E. Neill, Sung Hae L. Kang, Christine M. Eng, Sandra Darilek, Ignatia B. Van den Veyver, Sau Wai Cheung, Marcia J. Simovich, Chad A. Shaw, Lisa D. White, and Anthony Johnson
- Subjects
Adult ,Pathology ,medicine.medical_specialty ,Genetic counseling ,Gene Dosage ,Chorionic villus sampling ,Prenatal diagnosis ,Genetic Counseling ,Biology ,Article ,Pregnancy ,Prenatal Diagnosis ,medicine ,Humans ,Clinical significance ,Copy-number variation ,Advanced maternal age ,Genetics (clinical) ,Comparative Genomic Hybridization ,medicine.diagnostic_test ,Obstetrics ,Obstetrics and Gynecology ,Microarray Analysis ,Chorionic Villi Sampling ,Karyotyping ,Amniocentesis ,Female ,Comparative genomic hybridization - Abstract
Objective To evaluate the use of array comparative genomic hybridization (aCGH) for prenatal diagnosis, including assessment of variants of uncertain significance, and the ability to detect abnormalities not detected by karyotype, and vice versa. Methods Women undergoing amniocentesis or chorionic villus sampling (CVS) for karyotype were offered aCGH analysis using a targeted microarray. Parental samples were obtained concurrently to exclude maternal cell contamination and determine if copy number variants (CNVs) were de novo, or inherited prior to issuing a report. Results We analyzed 300 samples, most were amniotic fluid (82%) and CVS (17%). The most common indications were advanced maternal age (N = 123) and abnormal ultrasound findings (N = 84). We detected 58 CNVs (19.3%). Of these, 40 (13.3%) were interpreted as likely benign, 15 (5.0%) were of defined pathological significance, while 3 (1.0%) were of uncertain clinical significance. For seven (∼2.3% or 1/43), aCGH contributed important new information. For two of these (1% or ∼1/150), the abnormality would not have been detected without aCGH analysis. Conclusion Although aCGH-detected benign inherited variants in 13.3% of cases, these did not present major counseling difficulties, and the procedure is an improved diagnostic tool for prenatal detection of chromosomal abnormalities. Copyright © 2008 John Wiley & Sons, Ltd.
- Published
- 2009
235. Dominant versus recessive traits conveyed by allelic mutations - to what extent is nonsense-mediated decay involved?
- Author
-
Mehrdad Khajavi, Han G. Brunner, Shay Ben-Shachar, J.H.L.M. van Bokhoven, Marjorie Withers, Chad A. Shaw, and J. R. Lupski
- Subjects
Genetics and epigenetic pathways of disease [NCMLS 6] ,Inheritance Patterns ,Limb Deformities, Congenital ,Genes, Recessive ,Receptors, Cell Surface ,Biology ,Receptor Tyrosine Kinase-like Orphan Receptors ,medicine.disease_cause ,Genomic disorders and inherited multi-system disorders [IGMD 3] ,Genetics ,medicine ,Humans ,Missense mutation ,Abnormalities, Multiple ,Allele ,Alleles ,Cells, Cultured ,Genetics (clinical) ,Genes, Dominant ,Bone Diseases, Developmental ,Mutation ,Brachydactyly ,Autosomal dominant trait ,ROR2 ,Syndrome ,medicine.disease ,Robinow syndrome ,Phenotype - Abstract
Contains fulltext : 80905.pdf (Publisher’s version ) (Closed access) Mutations in ROR2, encoding a receptor tyrosine kinase, can cause autosomal recessive Robinow syndrome (RRS), a severe skeletal dysplasia with limb shortening, brachydactyly, and a dysmorphic facial appearance. Other mutations in ROR2 result in the autosomal dominant disease, brachydactyly type B (BDB1). No functional mechanisms have been delineated to effectively explain the association between mutations and different modes of inheritance causing different phenotypes. BDB1-causing mutations in ROR2 result from heterozygous premature termination codons (PTCs) in downstream exons and the conveyed phenotype segregates as an autosomal dominant trait, whereas heterozygous missense mutations and PTCs in upstream exons result in carrier status for RRS. Given that the distribution of PTC mutations revealed a correlation between the phenotype and the mode of inheritance conveyed, we investigated the potential role for the nonsense-mediated decay (NMD) pathway in the abrogation of possible aberrant effects of selected mutant alleles. Our experiments show that triggering or escaping NMD may cause different phenotypes with a distinct mode of inheritance. We generalize these findings to other disease-associated genes by examining PTC mutation distribution correlation with conveyed phenotype and inheritance patterns. Indeed, NMD may explain distinct phenotypes and different inheritance patterns conveyed by allelic truncating mutations enabling better genotype-phenotype correlations in several other disorders.
- Published
- 2009
236. Genomic imbalances in neonates with birth defects: high detection rates by using chromosomal microarray analysis
- Author
-
James R. Lupski, Seema R. Lalani, Mai T. Phung, Xin Yan Lu, Carlos A. Bacino, Kim Pham, Pawel Stankiewicz, Chad A. Shaw, Arthur L. Beaudet, Trilochan Sahoo, Sau Wai Cheung, Sarah E. Neil, Sung Hae Lee Kang, A. Craig Chinault, and Ankita Patel
- Subjects
Male ,medicine.medical_specialty ,Aneuploidy ,Bioinformatics ,Sensitivity and Specificity ,Genomic Instability ,Article ,Congenital Abnormalities ,Cohort Studies ,medicine ,Humans ,Abnormalities, Multiple ,Copy-number variation ,In Situ Hybridization, Fluorescence ,Oligonucleotide Array Sequence Analysis ,Chromosome Aberrations ,Comparative Genomic Hybridization ,business.industry ,Microarray analysis techniques ,Mosaicism ,Cytogenetics ,Infant, Newborn ,Chromosome ,Karyotype ,medicine.disease ,Subtelomere ,Pediatrics, Perinatology and Child Health ,Female ,business ,Comparative genomic hybridization - Abstract
OBJECTIVES. Our aim was to determine the frequency of genomic imbalances in neonates with birth defects by using targeted array-based comparative genomic hybridization, also known as chromosomal microarray analysis. METHODS. Between March 2006 and September 2007, 638 neonates with various birth defects were referred for chromosomal microarray analysis. Three consecutive chromosomal microarray analysis versions were used: bacterial artificial chromosome–based versions V5 and V6 and bacterial artificial chromosome emulated oligonucleotide–based version V6 Oligo. Each version had targeted but increasingly extensive genomic coverage and interrogated >150 disease loci with enhanced coverage in genomic rearrangement–prone pericentromeric and subtelomeric regions. RESULTS. Overall, 109 (17.1%) patients were identified with clinically significant abnormalities with detection rates of 13.7%, 16.6%, and 19.9% on V5, V6, and V6 Oligo, respectively. The majority of these abnormalities would not be defined by using karyotype analysis. The clinically significant detection rates by use of chromosomal microarray analysis for various clinical indications were 66.7% for “possible chromosomal abnormality” ± “others” (other clinical indications), 33.3% for ambiguous genitalia ± others, 27.1% for dysmorphic features + multiple congenital anomalies ± others, 24.6% for dysmorphic features ± others, 21.8% for congenital heart disease ± others, 17.9% for multiple congenital anomalies ± others, and 9.5% for the patients referred for others that were different from the groups defined. In all, 16 (2.5%) patients had chromosomal aneuploidies, and 81 (12.7%) patients had segmental aneusomies including common microdeletion or microduplication syndromes and other genomic disorders. Chromosomal mosaicism was found in 12 (1.9%) neonates. CONCLUSIONS. Chromosomal microarray analysis is a valuable clinical diagnostic tool that allows precise and rapid identification of genomic imbalances and mosaic abnormalities as the cause of birth defects in neonates. Chromosomal microarray analysis allows for timely molecular diagnoses and detects many more clinically relevant genomic abnormalities than conventional cytogenetic studies, enabling more informed decision-making and management and appropriate assessment of recurrence risk.
- Published
- 2008
237. Brachy-syndactyly caused by loss of Sfrp2 function
- Author
-
Pia Hermanns, Bernhard Zabel, Terry Bertin, Brendan Lee, Yuqing Chen, Elda Munivez, Roy Morello, Silke Schlaubitz, Chad A. Shaw, and Sujatha Kakuru
- Subjects
Frizzled ,Physiology ,Mesenchyme ,Cellular differentiation ,Clinical Biochemistry ,Gene Expression ,Apoptosis ,Biology ,Polymerase Chain Reaction ,Article ,Bone and Bones ,Mice ,Chondrocytes ,WNT4 ,medicine ,In Situ Nick-End Labeling ,Animals ,In Situ Hybridization ,Genetics ,Brachydactyly ,Wnt signaling pathway ,LRP6 ,Gene Expression Regulation, Developmental ,Membrane Proteins ,LRP5 ,Cell Differentiation ,Extremities ,Cell Biology ,medicine.disease ,Blotting, Northern ,Cell biology ,medicine.anatomical_structure ,Cartilage ,Syndactyly ,Chondrogenesis - Abstract
Wnt signaling pathways are regulated both at the intracellular and extracellular levels. During embryogenesis, the in vivo effects of the secreted frizzled related protein (Sfrp) family of Wnt inhibitors are poorly understood. Here, we show that inactivation of Sfrp2 results in subtle limb defects in mice with mesomelic shortening and consistent shortening of all autopodal elements that is clinically manifested as brachydactyly. In addition, there is soft tissue syndactyly of the hindlimb. The brachydactyly is caused by decreased chondrocyte proliferation and delayed differentiation in distal limb chondrogenic elements. These data suggest that Sfrp2 can regulate both chondrogenesis and regression of interdigital mesenchyme in distal limb. Sfrp2 can also repress canonical Wnt signaling by Wnt1, Wnt9a, and Wnt4 in vitro. Sfrp2-/- and TOPGAL/Sfrp2-/- mice have a mild increase in beta-catenin and beta-galactosidase staining, respectively, in some phalangeal elements. This however does not exclude a potential concurrent effect on non-canonical Wnt signaling in the growth plate. In combination with what is known about BMP and Wnt signaling in human brachydactylies, our data establish a critical role for Sfrp2 in proper distal limb formation and suggest SFPR2 could be a novel candidate gene for human brachy-syndactyly defects.
- Published
- 2008
238. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
- Author
-
Michael T. McManus, Arash O. Naghavi, Ankur K. Nagaraja, Donna M. Muzny, Gemunu H. Gunaratne, Francis C. Lynn, David B. Corry, Martin M. Matzuk, Mahjabeen F. Khan, Richard A. Gibbs, Michael S. German, Huifeng Zhu, Jeffrey G. Reid, Jonathan Miller, Michelle K. Weiss, Jayantha B. Tennakoon, Chad A. Shaw, Rafal B. Drabek, and Preethi H. Gunaratne
- Subjects
Letter ,RNA Stability ,Molecular Sequence Data ,Biology ,Genome ,Mice ,microRNA ,Genetics ,Animals ,Nucleotide ,RNA, Messenger ,Genetics (clinical) ,Cells, Cultured ,chemistry.chemical_classification ,Messenger RNA ,Massive parallel sequencing ,Base Sequence ,RNA ,RNA Nucleotidyltransferases ,Embryo, Mammalian ,RNA silencing ,MicroRNAs ,chemistry ,RNA editing ,Nucleic Acid Conformation ,Female ,RNA Editing ,Deoxyuracil Nucleotides ,RNA, Guide, Kinetoplastida - Abstract
Massively parallel sequencing of millions of Inha−/−). An excess of U-insertions (14.8%) over U-deletions (1.5%) and the presence of cleaved intermediates suggest that a mammalian TUTase (terminal uridylyl transferase) mediated dUTP-dependent U-insertion/U-deletion cycle may be a possible mechanism. We speculate that mRNA target site-directed editing of mmu-let-7a duplex-bulges stabilizes “loose” miRNA:mRNA target associations and functions to expand the target repertoire and/or enhance mRNA decay over translational repression. Our results also demonstrate that the systematic study of sequence variation within specific RNA classes in a given cell type from millions of sequences generated by next-generation sequencing (NGS) technologies (“intranomics”) can be used broadly to infer functional constraints on specific parts of completely uncharacterized RNAs.
- Published
- 2008
239. Identification of Chromosome Abnormalities in Subtelomeric Regions by Microarray Analysis: A Study of 5,380 Cases
- Author
-
Pawel Stankiewicz, Trilochan Sahoo, Lina Shao, Svetlana A. Yatsenko, Carlos A. Bacino, Sau Wai Cheung, James R. Lupski, Arthur L. Beaudet, Ankita Patel, A. Craig Chinault, Sarah E. Neill, Yinfeng Li, Xin Yan Lu, Chad A. Shaw, Seema R. Lalani, and Amber N. Pursley
- Subjects
Adult ,Microarray ,Adolescent ,Developmental Disabilities ,Gene Dosage ,Chromosomal translocation ,Chromosome Disorders ,Biology ,Article ,Gene Duplication ,Intellectual Disability ,Gene duplication ,Genetics ,medicine ,Humans ,Abnormalities, Multiple ,Autistic Disorder ,Child ,Genetics (clinical) ,In Situ Hybridization, Fluorescence ,Aged ,Oligonucleotide Array Sequence Analysis ,Sequence Deletion ,Chromosome Aberrations ,medicine.diagnostic_test ,Genome, Human ,Infant, Newborn ,Chromosome ,Infant ,Karyotype ,Middle Aged ,Telomere ,Subtelomere ,Molecular biology ,Chromosome Banding ,Child, Preschool ,Karyotyping ,Fluorescence in situ hybridization ,Comparative genomic hybridization - Abstract
Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances.
- Published
- 2008
240. Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells
- Author
-
Chad A. Shaw, Xiaolian Gao, Richard A. Gibbs, Rafal B. Drabek, David A. Wheeler, Xiaochuan Zhou, Arash O. Naghavi, Chad J. Creighton, Preethi H. Gunaratne, David M. Hoang, Glen B. Legge, Mahjabeen F. Khan, Jeffrey G. Reid, Jonathan Miller, Austin J. Cooney, Jad El-daye, Michelle K. Weiss, David Steffen, Peter L. Tran, and Peili Gu
- Subjects
Time Factors ,Cellular differentiation ,Gene regulatory network ,lcsh:Medicine ,Tretinoin ,Biology ,Models, Biological ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,Animals ,Humans ,False Positive Reactions ,RNA, Messenger ,Genetics and Genomics/Genomics ,lcsh:Science ,Conserved Sequence ,Embryonic Stem Cells ,030304 developmental biology ,Genetics ,Regulation of gene expression ,0303 health sciences ,Messenger RNA ,Multidisciplinary ,Models, Genetic ,lcsh:R ,food and beverages ,Computational Biology ,Genetics and Genomics ,Genetics and Genomics/Gene Expression ,Cell Differentiation ,Genetics and Genomics/Bioinformatics ,Blotting, Northern ,Embryonic stem cell ,Cell biology ,MicroRNAs ,lcsh:Q ,Genetics and Genomics/Gene Discovery ,Stem cell ,DNA microarray ,030217 neurology & neurosurgery ,Algorithms ,Research Article - Abstract
Background MicroRNAs (miRNAs: a class of short non-coding RNAs) are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence). Methodology/Principal Findings In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES) cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer −/−) ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues) during retinoic acid (RA)-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF −/−) cells, which display loss of repression of pluripotence genes upon differentiation. Conclusion/Significance Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF −/−) mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.
- Published
- 2008
241. Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses
- Author
-
Condie E. Carmack, A. Craig Chinault, Sung-Hae L. Kang, Zhishuo Ou, Chad A. Shaw, Lisa D. White, Sau Wai Cheung, Ankita Patel, and Arthur L. Beaudet
- Subjects
Genetics ,Whole genome sequencing ,Bacterial artificial chromosome ,Chromosomes, Artificial, Bacterial ,Oligonucleotide ,Copy number analysis ,Gene Dosage ,Nucleic Acid Hybridization ,Biology ,Gene dosage ,Article ,genomic DNA ,Nucleic acid thermodynamics ,Humans ,Genetics (clinical) ,In Situ Hybridization, Fluorescence ,Comparative genomic hybridization ,Oligonucleotide Array Sequence Analysis - Abstract
Purpose: The goal of this work was to test the ability of oligonucleotide-based arrays to reproduce the results of focused bacterial artificial chromosome (BAC)-based arrays used clinically in comparative genomic hybridization experiments to detect constitutional copy number changes in genomic DNA. Methods: Custom oligonucleotide (oligo) arrays were designed using the Agilent Technologies platform to give high-resolution coverage of regions within the genome sequence coordinates of BAC/P1 artificial chromosome (PAC) clones that had already been validated for use in previous versions of clone arrays used in clinical practice. Standard array-comparative genomic hybridization experiments, including a simultaneous blind analysis of a set of clinical samples, were conducted on both array platforms to identify copy number differences between patient samples and normal reference controls. Results: Initial experiments successfully demonstrated the capacity of oligo arrays to emulate BAC data without the need for dye-reversal comparisons. Empirical data and computational analyses of oligo response and distribution from a pilot array were used to design an optimized array of 44,000 oligos (44K). This custom 44K oligo array consists of probes localized to the genomic positions of >1400 fluorescence in situ hybridization-verified BAC/PAC clones covering more than 140 regions implicated in genetic diseases, as well as all clinically relevant subtelomeric and pericentromeric regions. Conclusions: Our data demonstrate that oligo-based arrays offer a valid alternative for focused BAC arrays. Furthermore, they have significant advantages, including better design flexibility, avoidance of repetitive sequences, manufacturing processes amenable to good manufacturing practice standards in the future, increased robustness because of an enhanced dynamic range (signal to background), and increased resolution that allows for detection of smaller regions of change.
- Published
- 2008
242. Low-level mosaicism of trisomy 14: phenotypic and molecular characterization
- Author
-
Carlos A. Bacino, Marwan Shinawi, Vernon R. Sutton, Sau Wai Cheung, Chad A. Shaw, Lina Shao, Ankita Patel, John W. Belmont, and Linda Jo Bone Jeng
- Subjects
Male ,Pathology ,medicine.medical_specialty ,Developmental Disabilities ,Aneuploidy ,Skin Pigmentation ,Trisomy ,Biology ,Clinical history ,Genetics ,medicine ,Humans ,Child ,Genetics (clinical) ,In Situ Hybridization, Fluorescence ,Oligonucleotide Array Sequence Analysis ,Chromosomes, Human, Pair 14 ,Mosaicism ,Infant, Newborn ,Chromosome ,Infant ,medicine.disease ,Phenotype ,Failure to Thrive ,Developmental disorder ,Trisomy 14 Mosaicism ,Child, Preschool ,Cytogenetic Analysis ,Female ,Comparative genomic hybridization - Abstract
Trisomy 14 mosaicism is a rare cytogenetic abnormality with a defined and recognizable clinical phenotype. We present a detailed clinical history and physical findings of five patients with low-level mosaicism of trisomy 14 detected by array-based comparative genomic hybridization (array-CGH) analysis or by routine chromosome analysis. These patients exhibited growth and developmental delays with variable severity, congenital anomalies, pigmentary skin lesions, and dysmorphic features. The phenotype of our patients was compared with previously described cases. This report suggests that trisomy 14 mosaicism may be more common than has been previously appreciated and also illustrates the important application of array-CGH to detect low-level mosaic chromosome abnormalities. We predict that a wider application of the array-CGH technology will significantly increase the detection rate of low-level mosaicism and will subsequently improve our ability to provide a diagnosis for patients with dysmorphic features, congenital anomalies, and developmental delay.
- Published
- 2008
243. Hematopoietic Fingerprints: an expression database of stem cells and their progeny
- Author
-
Megan P. Tierney, Nathan C. Boles, David C. Weksberg, Olga Sirin, Akil Merchant, Margaret A. Goodell, Stuart M. Chambers, Teresa V. Bowman, Mehveen G. Merchant, Kuan Yin K. Lin, Alice J. Chen, Chad A. Shaw, C. Joseph Fisk, and Steven B. Bradfute
- Subjects
Cell type ,Genotype ,Transcription, Genetic ,Cellular differentiation ,Biology ,computer.software_genre ,Article ,Cell Line ,Proto-Oncogene Protein c-ets-2 ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Databases, Genetic ,Genetics ,medicine ,Animals ,Cell Lineage ,030304 developmental biology ,Cell Proliferation ,0303 health sciences ,Database ,Monocyte ,Gene Expression Profiling ,Wnt signaling pathway ,Computational Biology ,Cell Differentiation ,Cell Biology ,Chromatin Assembly and Disassembly ,Hematopoietic Stem Cells ,Molecular biology ,STEMCELL ,Gene expression profiling ,DNA-Binding Proteins ,Mice, Inbred C57BL ,Wnt Proteins ,Haematopoiesis ,medicine.anatomical_structure ,Phenotype ,Gene Expression Regulation ,030220 oncology & carcinogenesis ,Molecular Medicine ,Female ,Stem cell ,computer ,Stem cell lineage database - Abstract
Hematopoietic stem cells (HSCs) continuously regenerate the hematologic system, yet few genes regulating this process have been defined. To identify candidate factors involved in differentiation and self-renewal, we have generated an expression database of hematopoietic stem cells and their differentiated progeny, including erythrocytes, granulocytes, monocytes, NK cells, activated and naive T cells, and B cells. Bioinformatic analysis revealed HSCs were more transcriptionally active than their progeny and shared a common activation mechanism with T cells. Each cell type also displayed unique biases in the regulation of particular genetic pathways, with Wnt signaling particularly enhanced in HSCs. We identified approximately 100-400 genes uniquely expressed in each cell type, termed lineage "fingerprints." In overexpression studies, two of these genes, Zfp 105 from the NK cell lineage, and Ets2 from the monocyte lineage, were able to significantly influence differentiation toward their respective lineages, demonstrating the utility of the fingerprints for identifying genes that regulate differentiation.
- Published
- 2007
244. Microarray-based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics
- Author
-
Carlos A. Bacino, Sau Wai Cheung, David T. Miller, Robert P. Erickson, Andrea L. Gropman, Pawel Stankiewicz, Jiangzhen Li, Margretta R. Seashore, James R. Lupski, A. Craig Chinault, Ankita Patel, Trilochan Sahoo, Arthur L. Beaudet, Amber Pursley, Chad A. Shaw, Daryl A. Scott, Anne Summers, and V. Reid Sutton
- Subjects
medicine.medical_specialty ,Microarray ,Somatic cell ,Trisomy ,Fertilization in Vitro ,Biology ,Sensitivity and Specificity ,Pallister–Killian syndrome ,Gene duplication ,Genetics ,medicine ,Humans ,Clinical significance ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,Chromosome Aberrations ,medicine.diagnostic_test ,Mosaicism ,Cytogenetics ,Chromosome Mapping ,Nucleic Acid Hybridization ,medicine.disease ,Female ,Comparative genomic hybridization ,Fluorescence in situ hybridization - Abstract
Somatic chromosomal mosaicism is a well-established cause for birth defects, mental retardation, and, in some instances, specific genetic syndromes. We have developed a clinically validated, targeted BAC clone array as a platform for comparative genomic hybridization (aCGH) to enable detection of a wide range of pathologic copy number changes in DNA. It is designed to provide high sensitivity to detect well-characterized submicroscopic micro-deletion and duplication disorders while at the same time minimizing detection of variation of uncertain clinical significance. In the course of studying 2,585 samples submitted to our clinical laboratory, chromosomal mosaicism was detected in 12 patient samples; 10 of these cases were reported to have had a normal blood chromosome analysis. This enhanced ability of aCGH to detect mosaicism missed by routine chromosome analysis may be due to some combination of testing multiple cell lineages and/or failure of cytogenetically abnormal T lymphocytes to respond to mitogens. This suggests that aCGH may detect somatic chromosomal mosaicism that would be missed by conventional cytogenetics.
- Published
- 2007
245. Identification of novel deletions of 15q11q13 in Angelman syndrome by array-CGH: molecular characterization and genotype-phenotype correlations
- Author
-
Virginia Kimonis, Jennifer R. German, Sarika U. Peters, Susan E. Waisbren, Chad A. Shaw, Lynne M. Bird, Irinia Anselm, Trilochan Sahoo, Arthur L. Beaudet, and Carlos A. Bacino
- Subjects
Male ,Genotype ,Biology ,Angelman syndrome ,Happy puppet syndrome ,Genetics ,medicine ,Humans ,Genetics (clinical) ,Genomic organization ,Oligonucleotide Array Sequence Analysis ,Chromosomes, Human, Pair 15 ,Psychological Tests ,Breakpoint ,Chromosome ,Infant ,Chromosome Breakage ,medicine.disease ,Phenotype ,Child, Preschool ,Female ,Chromosome breakage ,Angelman Syndrome ,Chromosome Deletion ,Comparative genomic hybridization - Abstract
Angelman syndrome (AS) is a neurodevelopmental disorder characterized by mental retardation, absent speech, ataxia, and a happy disposition. Deletions of the 15q11q13 region are found in approximately 70% of AS patients. The deletions are sub-classified into class I and class II based on their sizes of approximately 6.8 and approximately 6.0, respectively, with two different proximal breakpoints and a common distal breakpoint. Utilizing a chromosome 15-specific comparative genomic hybridization genomic microarray (array-CGH), we have identified, determined the deletion sizes, and mapped the breakpoints in a cohort of 44 cases, to relate those breakpoints to the genomic architecture and derive more precise genotype-phenotype correlations. Interestingly four patients of the 44 studied (9.1%) had novel and unusually large deletions, and are reported here. This is the first report of very large deletions of 15q11q13 resulting in AS; the largest deletion being >10.6 Mb. These novel deletions involve three different distal breakpoints, two of which have been earlier shown to be involved in the generation of isodicentric 15q chromosomes (idic15). Additionally, precise determination of the deletion breakpoints reveals the presence of directly oriented low-copy repeats (LCRs) flanking the recurrent and novel breakpoints. The LCRs are adequate in size, orientation, and homology to enable abnormal recombination events leading to deletions and duplications. This genomic organization provides evidence for a common mechanism for the generation of both common and rare deletion types. Larger deletions result in a loss of several genes outside the common Angelman syndrome-Prader-Willi syndrome (AS-PWS) critical interval, and a more severe phenotype.
- Published
- 2007
246. Chromosomal microarray analysis (CMA) detects a large X chromosome deletion including FMR1, FMR2, and IDS in a female patient with mental retardation
- Author
-
Jiangzhen Li, Yanghong Gu, M. Lance Cooper, Sau Wai Cheung, A. Craig Chinault, Robert F. Stratton, Patricia A. Eng, Zhishuo Ou, Elizabeth Roeder, Frank J. Probst, Victoria B. Enciso, Chad A. Shaw, V. Reid Sutton, and David L. Nelson
- Subjects
Biology ,Fragile X Mental Retardation Protein ,X Chromosome Inactivation ,Intellectual Disability ,Genetics ,medicine ,Humans ,Copy-number variation ,Child ,Genetics (clinical) ,X chromosome ,Chromosomal Deletion ,In Situ Hybridization, Fluorescence ,Glycoproteins ,Oligonucleotide Array Sequence Analysis ,Chromosomes, Human, X ,Iduronate-2-sulfatase ,Nuclear Proteins ,Hunter syndrome ,medicine.disease ,FMR1 ,Fragile X syndrome ,Phenotype ,Trans-Activators ,Female ,Chromosome Deletion ,Comparative genomic hybridization - Abstract
Chromosomal microarray analysis (CMA) by array-based comparative genomic hybridization (CGH) is a new clinical test for the detection of well-characterized genomic disorders caused by chromosomal deletions and duplications that result in gene copy number variation (CNV). This powerful assay detects an abnormality in approximately 7-9% of patients with various clinical phenotypes, including mental retardation. We report here on the results found in a 6-year-old girl with mildly dysmorphic facies, obesity, and marked developmental delay. CMA was requested and showed a heterozygous loss in copy number with clones derived from the genomic region cytogenetically defined as Xq27.3-Xq28. This loss was not cytogenetically visible but was seen on FISH analysis with clones from the region. Further studies confirmed a loss of one copy each of the FMR1, FMR2, and IDS genes (which are mutated in Fragile X syndrome, FRAXE syndrome, and Hunter syndrome, respectively). Skewed X-inactivation has been previously reported in girls with deletions in this region and can lead to a combined Fragile X/Hunter syndrome phenotype in affected females. X-inactivation and iduronate 2-sulfatase (IDS) enzyme activity were therefore examined. X-inactivation was found to be random in the child's peripheral leukocytes, and IDS enzyme activity was approximately half of the normal value. This case demonstrates the utility of CMA both for detecting a submicroscopic chromosomal deletion and for suggesting further testing that could possibly lead to therapeutic options for patients with developmental delay.
- Published
- 2007
247. Lithium therapy improves neurological function and hippocampal dendritic arborization in a spinocerebellar ataxia type 1 mouse model
- Author
-
Chad A. Shaw, Richard Atkinson, Kei Watase, Ronald Richman, Effat S. Emamian, Harry T. Orr, Huda Y. Zoghbi, Hidehiro Mizusawa, Yaling Sun, and Jennifer R. Gatchel
- Subjects
Male ,Spinocerebellar Ataxia Type 1 ,lcsh:Medicine ,Hippocampal formation ,Hippocampus ,chemistry.chemical_compound ,Glycogen Synthase Kinase 3 ,Mice ,0302 clinical medicine ,Antimanic Agents ,Phosphorylation ,Ataxin-1 ,Genetics ,0303 health sciences ,Nuclear Proteins ,General Medicine ,Polyglutamine tract ,3. Good health ,Motor coordination ,Neurology ,Ataxins ,Female ,Research Article ,medicine.medical_specialty ,Ataxin 1 ,Nerve Tissue Proteins ,Neuropathology ,Biology ,Motor Activity ,Neuroprotection ,Neurological Disorders ,03 medical and health sciences ,Mice, Neurologic Mutants ,Lithium Carbonate ,Memory ,Internal medicine ,medicine ,Animals ,Spinocerebellar Ataxias ,Protein Methyltransferases ,RNA, Messenger ,Motor Neuron Disease ,Maze Learning ,030304 developmental biology ,Glycogen Synthase Kinase 3 beta ,Lithium carbonate ,lcsh:R ,Genetics and Genomics ,Dendrites ,Mice, Inbred C57BL ,Endocrinology ,chemistry ,biology.protein ,Proto-Oncogene Proteins c-akt ,030217 neurology & neurosurgery ,Neuroscience - Abstract
Background Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited neurodegenerative disorder characterized by progressive motor and cognitive dysfunction. Caused by an expanded polyglutamine tract in ataxin 1 (ATXN1), SCA1 pathogenesis involves a multifactorial process that likely begins with misfolding of ATXN1, which has functional consequences on its interactions, leading to transcriptional dysregulation. Because lithium has been shown to exert neuroprotective effects in a variety of conditions, possibly by affecting gene expression, we tested the efficacy of lithium treatment in a knock-in mouse model of SCA1 (Sca1154Q/2Q mice) that replicates many features of the human disease. Methods and Findings Sca1154Q/2Q mice and their wild-type littermates were fed either regular chow or chow that contained 0.2% lithium carbonate. Dietary lithium carbonate supplementation resulted in improvement of motor coordination, learning, and memory in Sca1154Q/2Q mice. Importantly, motor improvement was seen when treatment was initiated both presymptomatically and after symptom onset. Neuropathologically, lithium treatment attenuated the reduction of dendritic branching in mutant hippocampal pyramidal neurons. We also report that lithium treatment restored the levels of isoprenylcysteine carboxyl methyltransferase (Icmt; alternatively, Pccmt), down-regulation of which is an early marker of mutant ATXN1 toxicity. Conclusions The effect of lithium on a marker altered early in the course of SCA1 pathogenesis, coupled with its positive effect on multiple behavioral measures and hippocampal neuropathology in an authentic disease model, make it an excellent candidate treatment for human SCA1 patients., Huda Zoghbi and colleagues show that lithium treatment initiated before or after disease onset improves multiple symptoms of neurodegeneration in a mouse model of spinocerebellar ataxia., Editors' Summary Background. Spinocerebellar ataxia type 1 (SCA1) is an inherited, incurable neurodegenerative disease in which the neurons (cells that transmit information between the brain and body) in the cerebellum (the brain region that coordinates movement) gradually die. Symptoms of the disease, which usually begins in early adult life, include poor coordination of movement (ataxia), slurred speech, and cognitive (learning and memory) problems. As more neurons die, these symptoms get worse until breathing difficulties eventually cause death. SCA1 is a “triplet repeat disease.” Information for making proteins is stored in DNA as groups of three nucleotides (codons), each specifying a different amino acid (the building blocks of proteins). In triplet repeat diseases, patients inherit a mutant gene containing abnormally long stretches of repeated codons. In SCA1, the repeated codon is CAG, which specifies glutamine. Consequently, SCA1 is a “polyglutamine disease,” a group of neurodegenerative disorders in which an abnormal protein (a different one for each disease) containing a long stretch of glutamine forms nuclear inclusions (insoluble lumps of protein) in neurons that, possibly by trapping essential proteins, cause neuronal death. In SCA1, the abnormal protein is ataxin 1, which is made in many neurons including the cerebellar neurons (Purkinje cells) that coordinate movement. Why Was This Study Done? Early in SCA1, the production of several messenger RNAs (the templates for protein production) decreases, possibly because transcription factors (proteins that control gene expression) interact with the mutant protein. Could the progression of SCA1 be slowed, therefore, by using an agent that affects gene expression? In this study, the researchers have investigated whether lithium can slow disease progression in an animal model of SCA1. They chose lithium for their study because this drug (best known for stabilizing mood in people with bipolar [manic] depression) affects gene expression, is neuroprotective, and has beneficial effects in animal models of Huntington disease, another polyglutamine disease. What Did the Researchers Do and Find? The researchers bred mice carrying one mutant gene for ataxin 1 containing a very long CAG repeat and one normal gene (Sca1154Q/2Q mice; genes come in pairs). These mice develop symptoms similar to those seen in people with SCA1. After weaning, the mice and their normal littermates were fed normal food or food supplemented with lithium for several weeks before assessing their ability to coordinate their movements and testing their cognitive skills. Dietary lithium (given before or after symptoms appeared) improved both coordination and learning and memory in the Sca1154Q/2Q mice but had little effect in the normal mice. Lithium did not change the overall appearance of the cerebellum in the Sca1154Q/2Q mice nor reduce the occurrence of nuclear inclusions, but it did partly reverse hippocampal neuron degeneration in these animals. The researchers discovered this effect by examining the shape of the hippocampal neurons in detail. These neurons normally have extensive dendrites—branch-like projections that make contact with other cells—but these gradually disappear in Sca1154Q/2Q mice; lithium partly reversed this loss. Finally, lithium also restored the level of Icmt/Pccmt mRNA in the cerebellum to near normal in the Sca1154Q/2Q mice—this mRNA is one of the first to be reduced by ataxin 1 toxicity. What Do These Findings Mean? These findings show that treatment with lithium slows neurodegeneration in a mouse model of SCA1, even when it is given only after the first symptoms of the disease have appeared. Unfortunately, lithium did not improve the life span of the Sca1154Q/2Q mice (although this could be because the mutant SCA1 protein has some deleterious effects outside the brain). Thus, lithium is unlikely to cure SCA1, but it could provide some help to people with this devastating disease, even if (as is usual), their condition is not diagnosed until the disease is quite advanced. However, because drugs that work in animal models of diseases do not necessarily work in people, patients with SCA1 (or other polyglutamine diseases, which might also benefit from lithium supplementation) should not be treated with lithium until human trials of this approach have been completed. Additional Information. Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040182. The US National Ataxia Foundation provides information for patients International Network of Ataxia Friends has information for patients and carergivers on ataxias, including SCA1 GeneTests provides information for health care providers and researchers about SCA1 Online Mendelian Inheritance in Man (OMIM) has detailed scientific information on SCA1 Huntington's Outreach Project for Education offers information for lay people from Stanford University on trinucleotide repeat disorders including SCA1
- Published
- 2007
248. Retroviral vector insertion sites associated with dominant hematopoietic clones mark 'stemness' pathways
- Author
-
Margaret A. Goodell, Kerstin Cornils, Gottfried von Keudell, Gerard Wagemaker, Kalpana Nattamai, Dick de Ridder, Stuart M. Chambers, Chad A. Shaw, Ute Modlich, Hartmut Geiger, Boris Fehse, Zhixiong Li, Martijn H. Brugman, Christopher Baum, Olga S. Kustikova, Karin Pike-Overzet, Frank J. T. Staal, Hematology, and Immunology
- Subjects
Databases, Factual ,Transcription, Genetic ,Cellular differentiation ,Genetic Vectors ,Immunology ,Polymerase Chain Reaction ,Biochemistry ,Viral vector ,Transcriptome ,Mice ,Retrovirus ,Cell Line, Tumor ,Animals ,Humans ,Progenitor cell ,Gene ,Bone Marrow Transplantation ,Probability ,Genetics ,biology ,Stem Cells ,Cell Differentiation ,Cell Biology ,Hematology ,biology.organism_classification ,Phenotype ,Hematopoiesis ,Mice, Inbred C57BL ,Retroviridae ,Mutation ,Stem cell - Abstract
Evidence from model organisms and clinical trials reveals that the random insertion of retrovirus-based vectors in the genome of long-term repopulating hematopoietic cells may increase self-renewal or initiate malignant transformation. Clonal dominance of nonmalignant cells is a particularly interesting phenotype as it may be caused by the dysregulation of genes that affect self-renewal and competitive fitness. We have accumulated 280 retrovirus vector insertion sites (RVISs) from murine long-term studies resulting in benign or malignant clonal dominance. RVISs (22.5%) are located in or near (up to 100 kb [kilobase]) to known proto-oncogenes, 49.6% in signaling genes, and 27.9% in other or unknown genes. The resulting insertional dominance database (IDDb) shows substantial overlaps with the transcriptome of hematopoietic stem/progenitor cells and the retrovirus-tagged cancer gene database (RTCGD). RVISs preferentially marked genes with high expression in hematopoietic stem/progenitor cells, and Gene Ontology revealed an overrepresentation of genes associated with cell-cycle control, apoptosis signaling, and transcriptional regulation, including major “stemness” pathways. The IDDb forms a powerful resource for the identification of genes that stimulate or transform hematopoietic stem/progenitor cells and is an important reference for vector biosafety studies in human gene therapy.
- Published
- 2007
249. Abstract 721: Mevalonate pathway mediates acquired anti-HER2 treatment resistance in HER2+ breast cancer
- Author
-
Laura M. Heiser, Lukas M. Simon, Nicholas J. Wang, Joe W. Gray, Gary C. Chamness, Lanfang Qin, Agostina Nardone, C. Kent Osborne, Rachel Schiff, Chad A. Shaw, and Huizhong Hu
- Subjects
Cancer Research ,Cell growth ,Pharmacology ,chemistry.chemical_compound ,Oncology ,chemistry ,Downregulation and upregulation ,Apoptosis ,Biosynthetic process ,Cancer research ,Mevalonate pathway ,Growth inhibition ,Transcription factor ,PI3K/AKT/mTOR pathway - Abstract
Background: Compelling evidence suggests that a more complete blockade of the HER receptor layer and its signaling, by combining anti-HER2 drugs such as Trastuzumab (T) and Lapatinib (L), is highly effective. However, resistance remains a challenge. To understand resistance mechanisms, we established a broad panel of L, T, and L+T resistant cell line models. Initial mRNA expression profiling identified upregulation or restoration of the mevalonate (MVA) pathway in some models where HER signaling is completely and sustainably blocked, suggesting a possible role of the MVA pathway in resistance. This pathway is a biosynthetic process for cholesterol and isoprenoid intermediates, particularly farnesyl and geranylgeranyl pyrophosphates (FPP and GGPP). Coordinating gene expression of this pathway is regulated by the master transcription factor, SREBP. Statins, cholesterol-lowering drugs, block this pathway via inhibiting the rate-limiting enzyme, HMG-CoA reductase. While a role of the MVA pathway in tumor initiation and progression was reported, its role in anti-HER2 resistance has remained elusive. Methods: SKBR3, AU565, and UACC812 parental HER2+ cells and their T, L, and L+T resistant derivatives (TR, LR, and LTR) were used. SREBP activity was determined by a reporter luciferase assay. Cell growth was assayed by methylene blue staining. Apoptosis was determined by Annexin V staining and the protein level of cleaved PARP. Molecular signaling analysis was performed by western blotting (WB) and reverse phase protein array (RPPA). Results: Reporter assays showed the inhibition of the SREBP activity upon LT treatment and its restoration at resistance. Blocking the MVA pathway with statins led to a marked growth inhibition or apoptosis in LR/LTR models, in which the HER signaling remains sustainably inhibited, while cognate parental cells and TR cells, in which HER is (re)activated, were slightly inhibited. Prevention of statin-induced growth inhibition or apoptosis by exogenous MVA indicated the specific role of this pathway in resistance. Cholesterol or its precursor squalene could not rescue growth inhibition. In contrast, both FPP and GGPP reversed the growth inhibition or apoptosis in SKBR3 and AU565 LR/LTR models, while in the UACC812LTR model only GGPP rescued. WB showed that mTOR and estrogen receptor (ER) are downstream effectors mediating the MVA pathway to anti-HER2 resistance. Proteomic analysis revealed additional novel MVA effectors which are currently under biochemical and functional validation. Conclusion: The MVA pathway plays a key role as an escape pathway by activating alternative signaling, including mTOR and ER pathways, in acquired resistance to potent HER2 inhibition in a cholesterol-independent but FPP/GGPP-dependent manner. Targeting the MVA pathway or its downstream effectors might provide a novel therapeutic strategy to overcome anti-HER2 resistance. Citation Format: Huizhong Hu, Lukas Simon, Lanfang Qin, Agostina Nardone, Chad Shaw, Gary Chamness, Laura Heiser, Nicholas Wang, Joe W. Gray, C. Kent Osborne, Rachel Schiff. Mevalonate pathway mediates acquired anti-HER2 treatment resistance in HER2+ breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 721. doi:10.1158/1538-7445.AM2015-721
- Published
- 2015
250. Abstract 738: Combined inhibition of non-canonical HER2 signaling as a strategy to overcome resistance to HER2-targeted therapies
- Author
-
Rocio Dominguez-Vidana, Siddhartha Tyagi, Christopher S. Bland, Tamika Mitchell, Martin Shea, Earlene M. Schmitt, Rachel Schiff, Kathleen A. Scorsone, Mitchell Rao, Thomas F. Westbrook, Susan G. Hilsenbeck, Ronald J. Bernardi, Sarmistha Nanda, C. Kent Osborne, and Chad A. Shaw
- Subjects
Cancer Research ,Oncology ,Resistance (ecology) ,Non canonical ,Chemistry ,Computational biology - Abstract
Despite the availability of drugs directly targeting HER2, resistance to therapy remains a major clinical problem in HER2-positive breast cancer. Leveraging a series of RNAi genetic screens, we identify a novel signaling network governing response to HER2 inhibition in vitro and in vivo. We define WEE1 as a core component of this network. Genetic or pharmacologic inhibition of WEE1 or its upstream regulators kills HER2-positive breast cancer cells in combination with HER-family inhibitors. Mechanistically, we demonstrate a non-canonical role of HER2 in governing mitotic progression. Combined inhibition of WEE1 and HER2 abolishes this critical regulation, leading to mitotic catastrophe and apoptosis. Thus, we demonstrate an unexpected convergence of non-canonical HER2 signaling and WEE1 that can be exploited to overcome drug resistance. Our findings provide a strong mechanistic and pre-clinical rationale for combined HER2 and WEE1 inhibition as a treatment strategy for HER2-positive breast cancer. Citation Format: Ronald J. Bernardi, Rocio Dominguez-Vidana, Christopher S. Bland, Kathleen A. Scorsone, Siddhartha Tyagi, Earlene M. Schmitt, Martin J. Shea, Tamika Mitchell, Mitchell Rao, Sarmistha Nanda, Susan G. Hilsenbeck, Chad Shaw, C. Kent Osborne, Rachel Schiff, Thomas F. Westbrook. Combined inhibition of non-canonical HER2 signaling as a strategy to overcome resistance to HER2-targeted therapies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 738. doi:10.1158/1538-7445.AM2015-738
- Published
- 2015
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.