DOCSLIB.ORG

Compositions and Methods for Modulating Gene Expression

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

(19) TZZ¥____T (11) EP 3 511 416 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 17.07.2019 Bulletin 2019/29 C12N 15/113 (2010.01) A61P 7/06 (2006.01) A61K 31/7088 (2006.01) A61K 31/712 (2006.01) (2006.01) (21) Application number: 18204559.1 A61K 31/7125 (22) Date of filing: 16.05.2013 (84) Designated Contracting States: • The General Hospital Corporation d/b/a AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Massachusetts General Hospital GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Boston, MA 02114 (US) PL PT RO RS SE SI SK SM TR (72) Inventors: (30) Priority: 16.05.2012 US 201261647949 P • Krieg, Arthur M. 16.05.2012 US 201261648016 P Wellesley, MA 02482 (US) 16.05.2012 US 201261648021 P • Subramanian, Romesh 16.05.2012 US 201261647858 P Framingham, MA 01701 (US) 16.05.2012 US 201261647925 P • McSwiggen, James 16.05.2012 US 201261647886 P Arlington, MA 02474 (US) 16.05.2012 US 201261647901 P • Lee, Jeannie T. 16.05.2012 US 201261648041 P Boston, MA 02114 (US) 16.05.2012 US 201261648051 P 16.05.2012 US 201261648058 P (74) Representative: Hoffmann Eitle 27.10.2012 US 201261719394 P Patent- und Rechtsanwälte PartmbB 14.03.2013 US 201361785832 P Arabellastraße 30 14.03.2013 US 201361785778 P 81925 München (DE) 14.03.2013 US 201361785885 P 14.03.2013 US 201361786232 P Remarks: 14.03.2013 US 201361785956 P •Thecomplete document including Reference Tables 14.03.2013 US 201361785529 P and the Sequence Listing can be downloaded from the EPO website (62) Document number(s) of the earlier application(s) in •This application was filed on 06-11-2018 as a accordance with Art. 76 EPC: divisional application to the application mentioned 13791343.0 / 2 850 189 under INID code 62. •Claims filed after the date of receipt of the divisional (71) Applicants: application (Rule 68(4) EPC). • Translate Bio MA, Inc. Cambridge, MA 02139 (US) (54) COMPOSITIONS AND METHODS FOR MODULATING GENE EXPRESSION (57) Aspects of the invention provide methods for se- sion of a target gene. Further aspects provide single lecting a candidate oligonucleotide for activating expres- stranded oligonucleotides that modulate gene expres- sion of a target gene. Further aspects of the invention sion and compositions and kits comprising the same. provide methods of selecting a set of oligonucleotides Methods for modulating gene expression using the single that is enriched in oligonucleotides that activate expres- stranded oligonucleotides are also provided. EP 3 511 416 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 511 416 A1 Description CROSS-REFERENCE TO RELATED APPLICATIONS 5 [0001] This application claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 61/648,016, entitled, "COMPOSITIONS AND METHODS FOR MODULATING GENE EXPRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/648,021, entitled, "COMPOSITIONS AND METHODS FOR MODULATING GENE EX- PRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/786,232, entitled, "COMPOSITIONS AND METHODS FOR MODULATING GENE EXPRESSION", filed on March 14, 2013, of U.S. Provisional Application No. 10 61/647,858, entitled, "COMPOSITIONS AND METHODS FOR MODULATING SMN GENE FAMILY EXPRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/719,394, entitled, "COMPOSITIONS AND METHODS FOR MODULATING SMN GENE FAMILY EXPRESSION", filed on October 27, 2012, of U.S. Provisional Application No. 61/785,529, entitled, "COMPOSITIONS AND METHODS FOR MODULATING SMN GENE FAMILY EXPRESSION", filed on March 14, 2013, of U.S. Provisional Application No. 61/647,886, entitled, "COMPOSITIONS AND METHODS 15 FOR MODULATING UTRN EXPRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/647,901, entitled, "COMPOSITIONS AND METHODS FOR MODULATING HEMOGLOBIN GENE FAMILY EXPRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/785,956, entitled, "COMPOSITIONS AND METHODS FOR MODULATING HEMOGLOBIN GENE FAMILY EXPRESSION", filed on March 14, 2013, of U.S. Provisional Application No. 61/647,925, entitled, "COMPOSITIONS AND METHODS FOR MODULATING ATP2A2 EXPRESSION", filed on 20 May 16, 2012, of U.S. Provisional Application No. 61/785,832, entitled, "COMPOSITIONS AND METHODS FOR MOD- ULATING ATP2A2 EXPRESSION", filed on March 14, 2013, of U.S. Provisional Application No. 61/647,949, entitled, "COMPOSITIONS AND METHODS FOR MODULATING APOA1 AND ABCA1 EXPRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/785,778, entitled, "COMPOSITIONS AND METHODS FOR MODULATING APOA1 AND ABCA1 EXPRESSION", filed on March 14, 2013, of U.S. Provisional Application No. 61/648,041, entitled, "COM- 25 POSITIONS AND METHODS FOR MODULATING PTEN EXPRESSION", filed on May 16, 2012, of U.S. Provisional Application No. 61/785,885, entitled, "COMPOSITIONS AND METHODS FOR MODULATING PTEN EXPRESSION", filed on March 14, 2013, of U.S. Provisional Application No. 61/648,058, entitled, "COMPOSITIONS AND METHODS FOR MODULATING BDNF EXPRESSION", filed on May 16, 2012, and of U.S. Provisional Application No. 61/648,051, entitled, "COMPOSITIONS AND METHODS FOR MODULATING MECP2 EXPRESSION", filed on May 16, 2012, the 30 contents of each of which are incorporated herein by reference in their entireties. FIELD OF THE INVENTION [0002] The invention relates to oligonucleotide based compositions, as well as methods of using oligonucleotide based 35 compositions for treating disease. BACKGROUND OF THE INVENTION [0003] Transcriptome analyses have suggested that, although only 1-2% of the mammalian genome is protein coding, 40 70-90% is transcriptionally active. Recent discoveries argue that a subset of these non-protein coding transcripts play crucial roles in epigenetic regulation. In spite of their ubiquity, the structure and function of many of such transcripts remains uncharacterized. Recent studies indicate that some long non-coding RNAs function as an epigenetic regula- tor/RNA cofactor in chromatin remodeling through interactions with Polycomb repressor complex 2 (PRC2) and thus function to regulate gene expression. 45 SUMMARY OF THE INVENTION [0004] Aspects of the invention provide methods for selecting oligonucleotides for activating or enhancing expression of target genes. The methods are particularly useful for identifying candidate oligonucleotides for activating or enhancing 50 expression of target genes for which reduced expression or activity results in, or contributes to, disease. Further aspects of the invention provide methods of selecting a set of oligonucleotides that is enriched in oligonucleotides ( e.g., compared with a random selection of oligonucleotides) that activate expression of a target gene. Accordingly, the methods may be used to establish large libraries of clinical candidates that are enriched in oligonucleotides that activate gene expres- sion. Such libraries may be utilized, for example, to identify lead oligonucleotides for therapeutic development. Thus, 55 the methods provided are useful for establishing a broad platform of candidate oligonucleotides for targeting the expres- sion of most known genes, including protein coding genes. Further aspects provide single stranded oligonucleotides that modulate gene expression, and compositions and kits comprising the same. Methods for modulating gene expression using the single stranded oligonucleotides are also provided. 2 EP 3 511 416 A1 [0005] In some aspects, the invention is a method for selecting a candidate oligonucleotide for activating expression of a target gene by selecting a PRC2-associated region within a first nucleotide sequence, wherein the first nucleotide sequence maps to a position in a first chromosome between 50 kilobases upstream of a 5’-end of the target gene and 50 kilobases downstream of a 3’-end of the target gene; determining a second nucleotide sequence that is complementary 5 with at least 8 consecutive nucleotides of the PRC2-associated region; and selecting as the candidate oligonucleotide, a single stranded oligonucleotide comprising the second nucleotide sequence, wherein the oligonucleotide has at least one of following features: a) a sequence comprising 5’-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a seed sequence of a human microRNA, and Z is a nucleotide sequence of 1 to 23 nucleotides in length, wherein X is anchored at the 5’ end of the oligonucleotide; b) a sequence that does not comprise 10 three or more consecutive guanosine nucleotides; c) a sequence that has less than a threshold level of sequence identity with every sequence of nucleotides, of equivalent length to the second nucleotide sequence, that is between 50 kilobases upstream of a 5’-end of an off-target gene and 50 kilobases downstream of a 3’-end of the off-target gene; d) a sequence that is complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising at least two single stranded loops; and/or e) a sequence that has greater than 60% G-C content. 15 [0006] In some embodiments, the single stranded oligonucleotide has only one of features a), b), c), d), and e). In some embodiments, the single stranded oligonucleotide has at least two of features a), b), c), d), and e), each inde- pendently selected. In some embodiments, the single stranded oligonucleotide has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least four of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide 20 has each of features a), b), c), d), and e). In certain embodiments, the oligonucleotide has the sequence 5’X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length. In some embodiments, Y is a sequence selected from Table 3.
Recommended publications
  • Factor XIII and Fibrin Clot Properties in Acute Venous Thromboembolism

    Factor XIII and Fibrin Clot Properties in Acute Venous Thromboembolism

    International Journal of Molecular Sciences Review Factor XIII and Fibrin Clot Properties in Acute Venous Thromboembolism Michał Z ˛abczyk 1,2 , Joanna Natorska 1,2 and Anetta Undas 1,2,* 1 John Paul II Hospital, 31-202 Kraków, Poland; [email protected] (M.Z.); [email protected] (J.N.) 2 Institute of Cardiology, Jagiellonian University Medical College, 31-202 Kraków, Poland * Correspondence: [email protected]; Tel.: +48-12-614-30-04; Fax: +48-12-614-21-20 Abstract: Coagulation factor XIII (FXIII) is converted by thrombin into its active form, FXIIIa, which crosslinks fibrin fibers, rendering clots more stable and resistant to degradation. FXIII affects fibrin clot structure and function leading to a more prothrombotic phenotype with denser networks, characterizing patients at risk of venous thromboembolism (VTE). Mechanisms regulating FXIII activation and its impact on fibrin structure in patients with acute VTE encompassing pulmonary embolism (PE) or deep vein thrombosis (DVT) are poorly elucidated. Reduced circulating FXIII levels in acute PE were reported over 20 years ago. Similar observations indicating decreased FXIII plasma activity and antigen levels have been made in acute PE and DVT with their subsequent increase after several weeks since the index event. Plasma fibrin clot proteome analysis confirms that clot-bound FXIII amounts associated with plasma FXIII activity are decreased in acute VTE. Reduced FXIII activity has been associated with impaired clot permeability and hypofibrinolysis in acute PE. The current review presents available studies on the role of FXIII in the modulation of fibrin clot properties during acute PE or DVT and following these events.
  • Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis

    Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis

    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis.
  • Clinical Utility Gene Card For: 3-M Syndrome – Update 2013

    Clinical Utility Gene Card For: 3-M Syndrome – Update 2013

    European Journal of Human Genetics (2014) 22, doi:10.1038/ejhg.2013.156 & 2014 Macmillan Publishers Limited All rights reserved 1018-4813/14 www.nature.com/ejhg CLINICAL UTILITY GENE CARD UPDATE Clinical utility gene card for: 3-M syndrome – Update 2013 Muriel Holder-Espinasse*,1, Melita Irving1 and Vale´rie Cormier-Daire2 European Journal of Human Genetics (2014) 22, doi:10.1038/ejhg.2013.156; published online 31 July 2013 Update to: European Journal of Human Genetics (2011) 19, doi:10.1038/ejhg.2011.32; published online 2 March 2011 1. DISEASE CHARACTERISTICS nonsense and missense mutations c.4333C4T (p.Arg1445*) and 1.1 Name of the disease (synonyms) c.4391A4C (p.His1464Pro), respectively, render CUL7 deficient 3-M syndrome (gloomy face syndrome, dolichospondylic dysplasia). in recruiting ROC1, leading to impaired ubiquitination. OBSL1: microsatellites analysis of the locus (2q35-36.1) in con- 1.2 OMIM# of the disease sanguineous families. OBSL1: microsatellites analysis of the locus 273750. (2q35-36.1) in consanguineous families. Mutations induce non- sense mediated decay. Knockdown of OBSL1 in HEK293 cells 1.3 Name of the analysed genes or DNA/chromosome segments shows the role of this gene in the maintenance of normal levels of CUL7, OBSL1 and CCDC8.1–5 CUL7. Abnormal IGFBP2 andIGFBP5 mRNA levels in two patients with OBSL1 mutations, suggesting that OBSL1 modulates the 1.4 OMIM# of the gene(s) expression of IGFBP proteins. CCDC8: microsatellites analysis 609577 (CUL7), 610991 (OBSL1) and 614145 (CCDC8). at the locus (19q13.2-q13.32). CCDC8, 1-BP DUP, 612G and CCDC8, 1-BP.
  • Chromosome 1 (Human Genome/Inkae) A

    Chromosome 1 (Human Genome/Inkae) A

    Proc. Nati. Acad. Sci. USA Vol. 89, pp. 4598-4602, May 1992 Medical Sciences Integration of gene maps: Chromosome 1 (human genome/inkae) A. COLLINS*, B. J. KEATSt, N. DRACOPOLIt, D. C. SHIELDS*, AND N. E. MORTON* *CRC Research Group in Genetic Epidemiology, Department of Child Health, University of Southampton, Southampton, S09 4XY, United Kingdom; tDepartment of Biometry and Genetics, Louisiana State University Center, 1901 Perdido Street, New Orleans, LA 70112; and tCenter for Cancer Research, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02139 Contributed by N. E. Morton, February 10, 1992 ABSTRACT A composite map of 177 locI has been con- standard lod tables extracted from the literature. Multiple structed in two steps. The first combined pairwise logarithm- pairwise analysis of these data was performed by the MAP90 of-odds scores on 127 loci Into a comprehensive genetic map. computer program (6), which can estimate an errorfrequency Then this map was projected onto the physical map through e (7) and a mapping parameter p such that map distance w is cytogenetic assignments, and the small amount ofphysical data a function of 0, e and p (8). It also includes a bootstrap to was interpolated for an additional 50 loci each of which had optimize order and a stepwise elimination of weakly sup- been assigned to an interval of less than 10 megabases. The ported loci to identify a conservative set of reliably ordered resulting composite map is on the physical scale with a reso- (framework) markers. The genetic map was combined with lution of 1.5 megabases.
  • Identification and Validation of Methylation-Driven Genes Prognostic Signature for Recurrence of Laryngeal Squamous Cell Carcino

    Identification and Validation of Methylation-Driven Genes Prognostic Signature for Recurrence of Laryngeal Squamous Cell Carcino

    Cui et al. Cancer Cell Int (2020) 20:472 https://doi.org/10.1186/s12935-020-01567-3 Cancer Cell International PRIMARY RESEARCH Open Access Identifcation and validation of methylation-driven genes prognostic signature for recurrence of laryngeal squamous cell carcinoma by integrated bioinformatics analysis Jie Cui3†, Liping Wang2†, Waisheng Zhong4†, Zhen Chen5, Jie Chen4*, Hong Yang3* and Genglong Liu1* Abstract Background: Recurrence remains a major obstacle to long-term survival of laryngeal squamous cell carcinoma (LSCC). We conducted a genome-wide integrated analysis of methylation and the transcriptome to establish methyla- tion-driven genes prognostic signature (MDGPS) to precisely predict recurrence probability and optimize therapeutic strategies for LSCC. Methods: LSCC DNA methylation datasets and RNA sequencing (RNA-seq) dataset were acquired from the Cancer Genome Atlas (TCGA). MethylMix was applied to detect DNA methylation-driven genes (MDGs). By univariate and multivariate Cox regression analyses, fve genes of DNA MDGs was developed a recurrence-free survival (RFS)-related MDGPS. The predictive accuracy and clinical value of the MDGPS were evaluated by receiver operating characteristic (ROC) and decision curve analysis (DCA), and compared with TNM stage system. Additionally, prognostic value of MDGPS was validated by external Gene Expression Omnibus (GEO) database. According to 5 MDGs, the candidate small molecules for LSCC were screen out by the CMap database. To strengthen the bioinformatics analysis results, 30 pairs of clinical samples were evaluated by digoxigenin-labeled chromogenic in situ hybridization (CISH). Results: A total of 88 DNA MDGs were identifed, and fve RFS-related MDGs (LINC01354, CCDC8, PHYHD1, MAGEB2 and ZNF732) were chosen to construct a MDGPS.
  • Factor XIII Deficiency

    Factor XIII Deficiency

    Haemophilia (2008), 14, 1190–1200 DOI: 10.1111/j.1365-2516.2008.01857.x ORIGINAL ARTICLE Factor XIII deficiency L. HSIEH and D. NUGENT Division of Hematology, ChildrenÕs Hospital of Orange County, Orange, CA, USA Summary. Inherited factor XIII (FXIII) deficiency is been more than 60 FXIII mutations identified in the a rare bleeding disorder that can present with current literature. In addition, single nucleotide umbilical bleeding during the neonatal period, polymorphisms have been described, some of which delayed soft tissue bruising, mucosal bleeding and have been shown to affect FXIII activity, contribut- life-threatening intracranial haemorrhage. FXIII defi- ing further to the heterogeneity in patient presenta- ciency has also been associated with poor wound tion and severity of clinical symptoms. Although healing and recurrent miscarriages. FXIII plays an there is a lifelong risk of bleeding, the prognosis is integral role in haemostasis by catalysing the cross- excellent when current prophylactic treatment is linking of fibrin, platelet membrane and matrix available using cryoprecipitate or plasma-derived proteins throughout thrombus formation, thus sta- FXIII concentrate. bilizing the blood clot. The molecular basis of FXIII deficiency is characterized by a high degree of Keywords: bleeding disorders, coagulation, factor heterogeneity, which contributes to the different XIII, factor XIII deficiency, fibrin stabilizing factor, clinical manifestations of the disease. There have protransglutaminase clear that intracellular FXIII, especially in platelet Introduction and vascular bed may play an equally important role Prior to delving into the clinical and biochemical in haemostasis. details which characterize this fascinating clotting In plasma, FXIII circulates as a pro-transglutamin- factor, it is worth taking a moment to consider this ase (FXIII-A2B2) composed of two catalytic A important fact: factor XIII (FXIII) is not just another subunits (FXIII-A2) and two non-catalytic B subunits plasma protein in the clotting cascade.
  • Análise Integrativa De Perfis Transcricionais De Pacientes Com

    Análise Integrativa De Perfis Transcricionais De Pacientes Com

    UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas.
  • NIH Public Access Author Manuscript Mol Cell

    NIH Public Access Author Manuscript Mol Cell

    NIH Public Access Author Manuscript Mol Cell. Author manuscript; available in PMC 2015 June 05. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mol Cell. 2014 June 5; 54(5): 791–804. doi:10.1016/j.molcel.2014.03.047. The 3M complex maintains microtubule and genome integrity Jun Yan1, Feng Yan1, Zhijun Li1, Becky Sinnott4, Kathryn M. Cappell4,7, Yanbao Yu2, Jinyao Mo5, Joseph A. Duncan1,5, Xian Chen2, Valerie Cormier-Daire6, Angelique W. Whitehurst4,8, and Yue Xiong1,2,3,* 1Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA. 2Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA. 3Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA. 4Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA. 5Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA. 6University Paris Descartes, Department of Genetics and INSERM U781, Hospital Necker Enfants-Malades, Paris, France SUMMARY CUL7, OBSL1, and CCDC8 genes are mutated in a mutually exclusive manner in 3M and other growth retardation syndromes. The mechanism underlying the function of the three 3M genes in development is not known. We found that OBSL1 and CCDC8 form a complex with CUL7 and regulate the level and centrosomal localization of CUL7, respectively. CUL7 depletion results in altered microtubule dynamics, prometaphase arrest, tetraploidy and mitotic cell death.
  • Why It Is Difficult to Distinguish the Silver-Russell

    Why It Is Difficult to Distinguish the Silver-Russell

    Why it is dicult to distinguish the Silver-Russell syndrome (SRS) and 3M syndrome in clinical practice Beibei Zhang Department of Endocrinology, Genetics, Metabolism, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China Chunxiu Gong ( [email protected] ) Department of Endocrinology, Genetics, Metabolism, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China Research Keywords: Silver-Russell syndrome, 3M syndrome, NH-CSS, Phenotype Posted Date: April 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-22088/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/10 Abstract Background: To analyze why 3M syndrome can be regarded as a SRS-like syndrome by examining the patients with 3M syndrome and research the connection between 3M syndrome and SRS. Methods: The term “3M syndrome” was retrieved by Web of Science and the 3M patients were screened by NH-CSS to determine whether it was consist with the diagnosis of clinical SRS, and to analyze the relationship between the two diseases by exploring literature. Results: Among patients with 3M syndrome, 60/70 (83%) were in accordance with clinical SRS, and the coincidence rates of CUL7, OBSL1, CCDC8 gene mutations were: 30 (42%), 17 (24%) and 4 (6%) respectively; The phenotypes of 3M syndrome conrmed as clinical SRS were SGA (90%), short stature (100%), forehead protruding (100%), relative macrocephaly (100%), feeding diculties/low BMI (33%), body asymmetry (0); Skeletal abnormalities and pathogenesis were previously considered as the key points of differentiation also were overlaps between two diseases; Symptomatic treatment and GH- treatment were carried out.
  • Identification of DNA Methylation-Driven Genes in Esophageal Squamous Cell Carcinoma: a Study Based on the Cancer Genome Atlas

    Identification of DNA Methylation-Driven Genes in Esophageal Squamous Cell Carcinoma: a Study Based on the Cancer Genome Atlas

    Lu et al. Cancer Cell Int (2019) 19:52 https://doi.org/10.1186/s12935-019-0770-9 Cancer Cell International PRIMARY RESEARCH Open Access Identifcation of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas Tong Lu1, Di Chen2, Yuanyong Wang1, Xiao Sun1, Shicheng Li1, Shuncheng Miao1, Yang Wo1, Yanting Dong1, Xiaoliang Leng1, Wenxing Du1 and Wenjie Jiao1* Abstract Background: Aberrant DNA methylations are signifcantly associated with esophageal squamous cell carcinoma (ESCC). In this study, we aimed to investigate the DNA methylation-driven genes in ESCC by integrative bioinformatics analysis. Methods: Data of DNA methylation and transcriptome profling were downloaded from TCGA database. DNA methylation-driven genes were obtained by methylmix R package. David database and ConsensusPathDB were used to perform gene ontology (GO) analysis and pathway analysis, respectively. Survival R package was used to analyze overall survival analysis of methylation-driven genes. Results: Totally 26 DNA methylation-driven genes were identifed by the methylmix, which were enriched in molecu- lar function of DNA binding and transcription factor activity. Then, ABCD1, SLC5A10, SPIN3, ZNF69, and ZNF608 were recognized as signifcant independent prognostic biomarkers from 26 methylation-driven genes. Additionally, a fur- ther integrative survival analysis, which combined methylation and gene expression data, was identifed that ABCD1, CCDC8, FBXO17 were signifcantly associated with patients’ survival. Also, multiple aberrant methylation sites were found to be correlated with gene expression. Conclusion: In summary, we studied the DNA methylation-driven genes in ESCC by bioinformatics analysis, ofering better understand of molecular mechanisms of ESCC and providing potential biomarkers precision treatment and prognosis detection.
  • Characterization of a Novel Large Deletion Caused by Double-Stranded Breaks in 6-Bp Microhomologous Sequences of Intron 11 and 12 of the F13A1 Gene

    Characterization of a Novel Large Deletion Caused by Double-Stranded Breaks in 6-Bp Microhomologous Sequences of Intron 11 and 12 of the F13A1 Gene

    OPEN Citation: Human Genome Variation (2016) 3, 15059; doi:10.1038/hgv.2015.59 Official journal of the Japan Society of Human Genetics 2054-345X/16 www.nature.com/hgv ARTICLE Characterization of a novel large deletion caused by double-stranded breaks in 6-bp microhomologous sequences of intron 11 and 12 of the F13A1 gene Anne Thomas1,3, Vytautas Ivaškevičius1,3, Christophe Zawadzki2, Jenny Goudemand2, Arijit Biswas1,3 and Johannes Oldenburg1 Coagulation Factor XIII is a heterotetrameric protransglutaminase which stabilizes preformed fibrin clots by covalent crosslinking them. Inherited homozygous or compound heterozygous deficiency of coagulation Factor XIII (FXIII) is a rare severe bleeding disorder affecting 1 in 2 million individuals. Most of the patients with inherited FXIII deficiency described in the literature carry F13A1 gene point mutations (missense, nonsense and splice site defects), whereas large deletions (40.5 kb in size) are underrepresented. In this article we report for the first time the complete characterization of a novel homozygous F13A1 large deletion covering the entire exon 12 in a young patient with a severe FXIII-deficient phenotype from France. Using primer walking on genomic DNA we have identified the deletion breakpoints in the region between g.6.143,016–g.6.148,901 caused by small 6-bp microhomologies at the 5´ and 3´ breakpoints. Parents of the patient were heterozygous carriers. Identification of this large deletion offers the possibility of prenatal diagnosis for the mother in this family who is heterozygous for this deletion. Human Genome Variation (2016) 3, 15059; doi:10.1038/hgv.2015.59; published online 11 February 2016 INTRODUCTION detected in the F13B gene.
  • The GALNT9, BNC1 and CCDC8 Genes Are Frequently Epigenetically Dysregulated in Breast Tumours That Metastasise to the Brain Rajendra P

    The GALNT9, BNC1 and CCDC8 Genes Are Frequently Epigenetically Dysregulated in Breast Tumours That Metastasise to the Brain Rajendra P

    Pangeni et al. Clinical Epigenetics (2015) 7:57 DOI 10.1186/s13148-015-0089-x RESEARCH Open Access The GALNT9, BNC1 and CCDC8 genes are frequently epigenetically dysregulated in breast tumours that metastasise to the brain Rajendra P. Pangeni1, Prasanna Channathodiyil1, David S. Huen2, Lawrence W. Eagles1, Balraj K. Johal2, Dawar Pasha2, Natasa Hadjistephanou2, Oliver Nevell2, Claire L. Davies2, Ayobami I. Adewumi2, Hamida Khanom2, Ikroop S. Samra2, Vanessa C. Buzatto2, Preethi Chandrasekaran2, Thoraia Shinawi3, Timothy P. Dawson4, Katherine M. Ashton4, Charles Davis4, Andrew R. Brodbelt5, Michael D. Jenkinson5, Ivan Bièche6, Farida Latif3, John L. Darling1, Tracy J. Warr1 and Mark R. Morris1,2,3* Abstract Background: Tumour metastasis to the brain is a common and deadly development in certain cancers; 18–30 % of breast tumours metastasise to the brain. The contribution that gene silencing through epigenetic mechanisms plays in these metastatic tumours is not well understood. Results: We have carried out a bioinformatic screen of genome-wide breast tumour methylation data available at The Cancer Genome Atlas (TCGA) and a broad literature review to identify candidate genes that may contribute to breast to brain metastasis (BBM). This analysis identified 82 candidates. We investigated the methylation status of these genes using Combined Bisulfite and Restriction Analysis (CoBRA) and identified 21 genes frequently methylated in BBM. We have identified three genes, GALNT9, CCDC8 and BNC1, that were frequently methylated (55, 73 and 71 %, respectively) and silenced in BBM and infrequently methylated in primary breast tumours. CCDC8 was commonly methylated in brain metastases and their associated primary tumours whereas GALNT9 and BNC1 were methylated and silenced only in brain metastases, but not in the associated primary breast tumours from individual patients.