DOCSLIB.ORG

Mutational Inactivation of Mtorc1 Repressor Gene DEPDC5 in Human Gastrointestinal Stromal Tumors

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mutational Inactivation of Mtorc1 Repressor Gene DEPDC5 in Human Gastrointestinal Stromal Tumors Mutational inactivation of mTORC1 repressor gene DEPDC5 in human gastrointestinal stromal tumors Yuzhi Panga,1, Feifei Xiea,1, Hui Caob,1, Chunmeng Wangc,d,1, Meijun Zhue, Xiaoxiao Liua, Xiaojing Lua, Tao Huangf, Yanying Sheng,KeLia, Xiaona Jiaa, Zhang Lia, Xufen Zhenga, Simin Wanga,YiHeh, Linhui Wangi, Jonathan A. Fletchere,2, and Yuexiang Wanga,2 aKey Laboratory of Tissue Microenvironment and Tumor, Shanghai Institutes for Biological Sciences–Changzheng Hospital Joint Center for Translational Medicine, Changzheng Hospital, Institutes for Translational Medicine, Chinese Academy of Sciences–Second Military Medical University, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031 Shanghai, China; bDepartment of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China; cDepartment of Bone and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, 200032 Shanghai, China; dDepartment of Oncology, Shanghai Medical College, Fudan University, 200032 Shanghai, China; eDepartment of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115; fShanghai Information Center for Life Sciences, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China; gDepartment of Pathology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China; hDepartment of Urology, No.1 Hospital of Jiaxing, 314000 Jiaxing, China; and iDepartment of Urology, Changzheng Hospital, Second Military Medical University, 200003 Shanghai, China Edited by Kenneth W. Kinzler, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, and approved October 1, 2019 (received for review August 26, 2019) Gastrointestinal stromal tumors (GISTs) are the most common demonstrate that chromosome 22q-targeting DEPDC5, silenced human sarcoma and are initiated by activating mutations in the by somatic mutations, is a GIST specific tumor suppressor and a KIT or PDGFRA receptor tyrosine kinases. Chromosome 22q dele- TKI treatment response modifier. tions are well-recognized frequent abnormalities in GISTs, occur- ring in ∼50% of GISTs. These deletions are thought to contribute Results and Discussion to the pathogenesis of this disease via currently unidentified tu- Whole Exome Sequencing Identifies Recurrent Inactivating DEPDC5 mor suppressor mechanisms. Using whole exome sequencing, we Aberrations in GISTs. To identify the causative tumor suppressor DEPDC5 report recurrent genomic inactivated gene mutations in genes at chromosome 22q in GISTs, we performed whole exome GISTs (16.4%, 9 of 55 patients). The demonstration of clonal sequencing in 40 GIST patients (Dataset S1). These studies con- DEPDC5 inactivation mutations in longitudinal specimens and in firmed reported GIST genes, such as KIT (3), PDGFRA (4), RB1 multiple metastases from individual patients suggests that these CDKN2A DMD MAX SETD2 mutations have tumorigenic roles in GIST progression. DEPDC5 in- (15), (15), (16), (17), and (18) activation promotes GIST tumor growth in vitro and in nude mice. (Datasets S2 and S3). Notably, these studies revealed somatic ho- DEPDC5 reduces cell proliferation through the mTORC1-signaling mozygous inactivating genomic DEPDC5 (encoding Dishevelled, Egl- pathway and subsequently induces cell-cycle arrest. Furthermore, 10 and Pleckstrin [DEP] domain-containing protein 5) aberrations, DEPDC5 modulates the sensitivity of GIST to KIT inhibitors, and the combination therapy with mTOR inhibitor and KIT inhibitor may Significance work better in GIST patients with DEPDC5 inactivation. These find- ings of recurrent genomic alterations, together with functional Activating mutations of KIT or PDGFRA are initiating events in data, validate the DEPDC5 as a bona fide tumor suppressor con- most gastrointestinal stromal tumors (GISTs) and indeed are tributing to GIST progression and a biologically relevant target of present in micro-GISTs, which are asymptomatic subcentimeter the frequent chromosome 22q deletions. lesions found in one-third of the general population. The bio- logical underpinnings of GIST progression are poorly un- sarcoma | GIST | KIT tyrosine kinase inhibitors | DEPDC5 derstood. Chromosome 22q deletions are well-recognized abnormalities in GISTs. However, the crucial gene has been arcomas are diverse mesenchymal malignancies that account unknown. We report recurrent genomic inactivated DEPDC5 Sfor ∼20% of pediatric and 1% of adult cancers (1). Gastro- mutations in GISTs. The DEPDC5 inactivated mutations are intestinal stromal tumors (GISTs) are the most common human prognostic in that they are associated with aggressive GISTs in sarcoma (2), which are mostly initiated by activating mutations of which they promote GIST progression and reduce sensitivity to the receptor tyrosine kinase KIT (75–80%) or PDGFRA (5–10%) KIT inhibitors. (3, 4). Although sharing the same KIT/PDGFRA mutations, micro- GISTs have a limited growth potential and hence are restrained at Author contributions: J.A.F. and Y.W. designed research; Y.P., F.X., H.C., C.W., M.Z., X. Liu, the subcentimeter level. The fact that micro-GISTs are common in X. Lu, Y.S., K.L., X.J., Z.L., X.Z., S.W., and Y.W. performed research; Y.P., F.X., H.C., C.W., and J.A.F. provided samples and clinical data; Y.P., F.X., C.W., M.Z., X. Liu, X. Lu, T.H., Y.S., general individuals (found in one-third of the general population) K.L., X.J., Z.L., X.Z., S.W., Y.H., L.W., J.A.F., and Y.W. analyzed data; and Y.P. and Y.W. without clinical symptoms (5–7) indicates that additional genetic wrote the paper. alterations contribute to the progression of clinical GISTs. Chro- The authors declare no competing interest. mosome 22q deletions are frequent chromosomal abnormalities in This article is a PNAS Direct Submission. ∼ – human GISTs, occurring in 50% of GISTs (2, 8 11), and are Published under the PNAS license. thought to contribute to the pathogenesis of this disease by yet- – Data deposition: Whole exome sequencing and RNA sequencing data reported in this unidentified tumor suppressor mechanisms (2, 8 11). study have been deposited in the National Omics Data Encyclopedia (accession no. Most GISTs with activating mutations in KIT often respond to OEP000478). treatment with KIT tyrosine kinase inhibitors (TKIs), such as first- 1Y.P., F.X., H.C., and C.W. contributed equally to this work. line imatinib, second-line sunitinib and third-line regorafenib, but 2To whom correspondence may be addressed. Email: [email protected] or the magnitude of tumor regression is variable (12–14). This het- [email protected]. erogeneity in TKI response could result from genetic modifiers This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. that regulate the degree to which tumor cells are dependent upon 1073/pnas.1914542116/-/DCSupplemental. the driver kinase and the response to TKI treatment. Here we First published October 21, 2019. 22746–22753 | PNAS | November 5, 2019 | vol. 116 | no. 45 www.pnas.org/cgi/doi/10.1073/pnas.1914542116 Downloaded by guest on September 24, 2021 including nonsense mutation, frameshift mutation, and dele- have somatic homozygous DEPDC5-inactivating aberrations tions in 7 of 40 (17.5%) GIST patients (Figs. 1 A and B and Dataset in 9 GIST patients (16.4%). Of 55 patients, 31 (∼56%) har- S1). Homozygous DEPDC5 mutations were confirmed by Sanger bored chromosome 22 loss (Dataset S4). All of the 9 patients sequencing (SI Appendix,Fig.S1A), single-nucleotide polymorphism harboring genomic DEPDC5 aberrations contain chromosome 22 (SNP) arrays (SI Appendix,Fig.S1B), quantitative PCR (SI Appendix, loss (Dataset S4). Therefore, DEPDC5 aberrations are significantly Fig. S1C), and fluorescence in situ hybridization (SI Appendix,Fig. more frequent in GISTs with chromosome 22 loss compared to S1D). Somatic inactivating genomic DEPDC5 aberrations were vali- chromosome 22 normal copy number (29 vs. 0%, P = 0.01177, 2- dated in 2 of 15 (13.3%) additional GIST patients (cases 41 to 55, tailed Fisher’stest)(Dataset S4). All of the 9 patients with genomic Dataset S4). This total set of 55 GIST patients was shown to DEPDC5 aberrations have both copies of DEPCD5 inactivated MEDICAL SCIENCES Fig. 1. Genomic DEPDC5 aberrations in 40 GIST patients. (A) Whole exome sequencing identifies genomic DEPDC5 aberrations in 7 of 40 (17.5%) GIST patients. Inactivating DEPDC5 mutations were intragenic homozygous deletions (blue lines indicate deleted exons) and hemizygous nucleotide alterations. Mutations are described according to international guidelines for sequence variant nomenclature provided by the Human Genome Variation Society (http:// varnomen.hgvs.org). Annotations in blue represent the nucleotide coding sequence mutations (indicated by “c.”) whereas annotations in green represent the resultant protein sequence mutations (indicated by “p.”). (B) Integrative genome viewer images of part of chromosome 22q from matched tumor and nonneoplastic cell DNAs from the same patients, demonstrating the tumor-restricted nature of DEPDC5 mutations. Pang et al. PNAS | November 5, 2019 | vol. 116 | no. 45 | 22747 Downloaded by guest on September 24, 2021 Fig. 2. Genomic DEPDC5 aberrations are a clonal genetic event in GIST progression. (A) Multiple tumors from the same patients share the
Load more

Recommended publications
  • Acute Knockdown of Depdc5 Leads to Synaptic Defects in Mtor-Related Epileptogenesis
    Acute knockdown of Depdc5 leads to synaptic defects in mTOR-related epileptogenesis Antonio de Fusco, Maria Sabina Cerullo, Antonella Marte, Caterina Michetti, Alessandra Romei, Enrico Castroflorio, Stéphanie Baulac, Fabio Benfenati To cite this version: Antonio de Fusco, Maria Sabina Cerullo, Antonella Marte, Caterina Michetti, Alessandra Romei, et al.. Acute knockdown of Depdc5 leads to synaptic defects in mTOR-related epileptogenesis. Neurobiology of Disease, Elsevier, In press, 10.1016/j.nbd.2020.104822. hal-02498215 HAL Id: hal-02498215 https://hal.sorbonne-universite.fr/hal-02498215 Submitted on 4 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Journal Pre-proof Acute knockdown of Depdc5 leads to synaptic defects in mTOR- related epileptogenesis Antonio De Fusco, Maria Sabina Cerullo, Antonella Marte, Caterina Michetti, Alessandra Romei, Enrico Castroflorio, Stephanie Baulac, Fabio Benfenati PII: S0969-9961(20)30097-8 DOI: https://doi.org/10.1016/j.nbd.2020.104822 Reference: YNBDI 104822 To appear in: Neurobiology of Disease Received date: 13 November 2019 Revised date: 2 February 2020 Accepted date: 26 February 2020 Please cite this article as: A. De Fusco, M.S. Cerullo, A. Marte, et al., Acute knockdown of Depdc5 leads to synaptic defects in mTOR-related epileptogenesis, Neurobiology of Disease(2020), https://doi.org/10.1016/j.nbd.2020.104822 This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record.
    [Show full text]
  • In Silico Prediction of High-Resolution Hi-C Interaction Matrices
    ARTICLE https://doi.org/10.1038/s41467-019-13423-8 OPEN In silico prediction of high-resolution Hi-C interaction matrices Shilu Zhang1, Deborah Chasman 1, Sara Knaack1 & Sushmita Roy1,2* The three-dimensional (3D) organization of the genome plays an important role in gene regulation bringing distal sequence elements in 3D proximity to genes hundreds of kilobases away. Hi-C is a powerful genome-wide technique to study 3D genome organization. Owing to 1234567890():,; experimental costs, high resolution Hi-C datasets are limited to a few cell lines. Computa- tional prediction of Hi-C counts can offer a scalable and inexpensive approach to examine 3D genome organization across multiple cellular contexts. Here we present HiC-Reg, an approach to predict contact counts from one-dimensional regulatory signals. HiC-Reg pre- dictions identify topologically associating domains and significant interactions that are enri- ched for CCCTC-binding factor (CTCF) bidirectional motifs and interactions identified from complementary sources. CTCF and chromatin marks, especially repressive and elongation marks, are most important for HiC-Reg’s predictive performance. Taken together, HiC-Reg provides a powerful framework to generate high-resolution profiles of contact counts that can be used to study individual locus level interactions and higher-order organizational units of the genome. 1 Wisconsin Institute for Discovery, 330 North Orchard Street, Madison, WI 53715, USA. 2 Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, USA. *email: [email protected] NATURE COMMUNICATIONS | (2019) 10:5449 | https://doi.org/10.1038/s41467-019-13423-8 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-13423-8 he three-dimensional (3D) organization of the genome has Results Temerged as an important component of the gene regulation HiC-Reg for predicting contact count using Random Forests.
    [Show full text]
  • NPRL3 Gene NPR3 Like, GATOR1 Complex Subunit
    NPRL3 gene NPR3 like, GATOR1 complex subunit Normal Function The NPRL3 gene provides instructions for making a protein that is one piece of a group of proteins (complex) called GATOR1. This complex is found in cells throughout the body, where it regulates a signaling pathway called the mTOR pathway. The mTOR pathway is involved in cell growth and division (proliferation), the survival of cells, and the creation (synthesis) of new proteins. The role of the GATOR1 complex is to block this pathway by inhibiting (stopping) the activity of a complex called mTOR complex 1 ( mTORC1) that is integral to the mTOR pathway. In the brain, the mTOR pathway regulates many processes, including the growth and development of nerve cells and their ability to change and adapt over time (plasticity). Health Conditions Related to Genetic Changes Familial focal epilepsy with variable foci At least ten NPRL3 gene mutations have been found to cause familial focal epilepsy with variable foci (FFEVF), which is an uncommon form of recurrent seizures (epilepsy) that runs in families. Most of these mutations lead to the production of an abnormally short, nonfunctional protein. As a result, formation of normal GATOR1 complex is reduced, leading to overactivity of mTORC1 and excessive signaling of the mTOR pathway. It is not clear how an abnormally active mTOR pathway leads to the seizures of FFEVF. Research suggests that increased mTOR pathway signaling in the brain leads to changes in the connections between nerve cells (synapses) and increased activation (excitation)
    [Show full text]
  • DEPDC5 Takes a Second Hit in Familial Focal Epilepsy
    DEPDC5 takes a second hit in familial focal epilepsy Matthew P. Anderson J Clin Invest. 2018;128(6):2194-2196. https://doi.org/10.1172/JCI121052. Commentary Loss-of-function mutations in a single allele of the gene encoding DEP domain–containing 5 protein (DEPDC5) are commonly linked to familial focal epilepsy with variable foci; however, a subset of patients presents with focal cortical dysplasia that is proposed to result from a second-hit somatic mutation. In this issue of the JCI, Ribierre and colleagues provide several lines of evidence to support second-hit DEPDC5 mutations in this disorder. Moreover, the authors use in vivo, in utero electroporation combined with CRISPR-Cas9 technology to generate a murine model of the disease that recapitulates human manifestations, including cortical dysplasia–like changes, focal seizures, and sudden unexpected death. This study provides important insights into familial focal epilepsy and provides a preclinical model for evaluating potential therapies. Find the latest version: https://jci.me/121052/pdf COMMENTARY The Journal of Clinical Investigation DEPDC5 takes a second hit in familial focal epilepsy Matthew P. Anderson Departments of Neurology and Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA. Boston Children’s Hospital Intellectual and Developmental Disabilities Research Center, Boston, Massachusetts, USA. Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA. These detailed genetic and biochemical correlations in the human tissues then led Loss-of-function mutations in a single allele of the gene encoding DEP them to design tests of causality in a mouse domain–containing 5 protein (DEPDC5) are commonly linked to familial model, in which they reconstituted many focal epilepsy with variable foci; however, a subset of patients presents with features of the human disorder.
    [Show full text]
  • Repetitive Elements in Humans
    International Journal of Molecular Sciences Review Repetitive Elements in Humans Thomas Liehr Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany; [email protected] Abstract: Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well. Keywords: variable numbers of tandem repeats (VNTRs); microsatellites; minisatellites; small-scale repetitive elements (SSREs); chromosomal heteromorphisms (CHs); higher-order repeat (HOR); retroviral DNA 1. Introduction Citation: Liehr, T. Repetitive In humans, like in other higher species, the genome of one individual never looks 100% Elements in Humans. Int. J. Mol. Sci. alike to another one [1], even among those of the same gender or between monozygotic 2021, 22, 2072.
    [Show full text]
  • The Genetics of Bipolar Disorder
    Molecular Psychiatry (2008) 13, 742–771 & 2008 Nature Publishing Group All rights reserved 1359-4184/08 $30.00 www.nature.com/mp FEATURE REVIEW The genetics of bipolar disorder: genome ‘hot regions,’ genes, new potential candidates and future directions A Serretti and L Mandelli Institute of Psychiatry, University of Bologna, Bologna, Italy Bipolar disorder (BP) is a complex disorder caused by a number of liability genes interacting with the environment. In recent years, a large number of linkage and association studies have been conducted producing an extremely large number of findings often not replicated or partially replicated. Further, results from linkage and association studies are not always easily comparable. Unfortunately, at present a comprehensive coverage of available evidence is still lacking. In the present paper, we summarized results obtained from both linkage and association studies in BP. Further, we indicated new potential interesting genes, located in genome ‘hot regions’ for BP and being expressed in the brain. We reviewed published studies on the subject till December 2007. We precisely localized regions where positive linkage has been found, by the NCBI Map viewer (http://www.ncbi.nlm.nih.gov/mapview/); further, we identified genes located in interesting areas and expressed in the brain, by the Entrez gene, Unigene databases (http://www.ncbi.nlm.nih.gov/entrez/) and Human Protein Reference Database (http://www.hprd.org); these genes could be of interest in future investigations. The review of association studies gave interesting results, as a number of genes seem to be definitively involved in BP, such as SLC6A4, TPH2, DRD4, SLC6A3, DAOA, DTNBP1, NRG1, DISC1 and BDNF.
    [Show full text]
  • Stranded Breaks in Drosophila Youheng Wei1,2†, Lucia Bettedi1†, Chun-Yuan Ting1, Kuikwon Kim1, Yingbiao Zhang1, Jiadong Cai2, Mary a Lilly1*
    RESEARCH ARTICLE The GATOR complex regulates an essential response to meiotic double- stranded breaks in Drosophila Youheng Wei1,2†, Lucia Bettedi1†, Chun-Yuan Ting1, Kuikwon Kim1, Yingbiao Zhang1, Jiadong Cai2, Mary A Lilly1* 1Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States; 2College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China Abstract The TORC1 regulator GATOR1/SEACIT controls meiotic entry and early meiotic events in yeast. However, how metabolic pathways influence meiotic progression in metazoans remains poorly understood. Here we examine the role of the TORC1 regulators GATOR1 and GATOR2 in the response to meiotic double-stranded breaks (DSB) during Drosophila oogenesis. We find that in mutants of the GATOR2 component mio, meiotic DSBs trigger the constitutive downregulation of TORC1 activity and a permanent arrest in oocyte growth. Conversely, in GATOR1 mutants, high TORC1 activity results in the delayed repair of meiotic DSBs and the hyperactivation of p53. Unexpectedly, we found that GATOR1 inhibits retrotransposon expression in the presence of meiotic DSBs in a pathway that functions in parallel to p53. Thus, our studies have revealed a link between oocyte metabolism, the repair of meiotic DSBs and retrotransposon expression. DOI: https://doi.org/10.7554/eLife.42149.001 *For correspondence: [email protected] Introduction †These authors contributed We are interested in understanding how metabolism impacts meiotic progression during oogenesis. equally to this work Target of Rapamycin Complex 1 (TORC1) is a multi-protein complex that functions as a master regu- lator of metabolism (Loewith and Hall, 2011; Laplante and Sabatini, 2012a; Jewell and Guan, Competing interests: The 2013).
    [Show full text]
  • Genomic Diagnostics Within a Medically Underserved Population: Efficacy and Implications
    © American College of Medical Genetics and Genomics ORIGINAL RESEARCH ARTICLE Genomic diagnostics within a medically underserved population: efficacy and implications Kevin A. Strauss, MD1, Claudia Gonzaga-Jauregui, PhD2, Karlla W. Brigatti, MS1, Katie B. Williams, MD, PhD1, Alejandra K. King, PhD2, Cristopher Van Hout, PhD2, Donna L. Robinson, CRNP1, Millie Young, RNC1, Kavita Praveen, PhD2, Adam D. Heaps, MS1, Mindy Kuebler, MS1, Aris Baras, MD2, Jeffrey G. Reid, PhD2, John D. Overton, PhD2, Frederick E. Dewey, MD2, Robert N. Jinks, PhD3, Ian Finnegan, BA3, Scott J. Mellis, MD, PhD2, Alan R. Shuldiner, MD2 and Erik G. Puffenberger, PhD1 Purpose: We integrated whole-exome sequencing (WES) and Compared to trio analysis, “family” WES (average seven exomes chromosomal microarray analysis (CMA) into a clinical workflow per proband) reduced filtered candidate variants from 22 ± 6to to serve an endogamous, uninsured, agrarian community. 5 ± 3 per proband. Nineteen (51%) alleles were de novo and 17 Methods: Seventy-nine probands (newborn to 49.8 years) who (46%) inherited; the latter added to a population-based diagnostic presented between 1998 and 2015 remained undiagnosed after panel. We found actionable secondary variants in 21 (4.2%) of 502 biochemical and molecular investigations. We generated WES data subjects, all of whom opted to be informed. for probands and family members and vetted variants through Conclusion: CMA and family-based WES streamline and rephenotyping, segregation analyses, and population studies. economize diagnosis of rare genetic disorders, accelerate novel Results: The most common presentation was neurological disease gene discovery, and create new opportunities for community-based (64%). Seven (9%) probands were diagnosed by CMA.
    [Show full text]
  • Nprl3 Gene Intron That Enhances Its Transcription in Peripheral Blood
    Scuola Internazionale Superiore di Studi Avanzati PhD Course in Functional and Structural Genomics Discovery of a human VNTR allelic variant in Nprl3 gene intron that enhances its transcription in peripheral blood Thesis submitted for the degree of “Philosophiæ Doctor” Candidate Supervisor Maria Bertuzzi Prof. Stefano Gustincich Academic Year 2014-2015 Table of contents Table of contents Abstract ....................................................................................................................................1 Introduction ..............................................................................................................................3 Gene expression regulation ..................................................................................................3 Gene expression profiling ................................................................................................5 NanoCAGE ......................................................................................................................6 TSS complexity ................................................................................................................7 Expression Quantitative Trait Loci (eQTL) .....................................................................8 Repetitive elements in the mammalian genome.................................................................10 Minisatellites and human diseases .................................................................................11 Parkinson’s disease.............................................................................................................14
    [Show full text]
  • Epileptic Spasms Are a Feature of DEPDC5 Mtoropathy
    Epileptic spasms are a feature of DEPDC5 mTORopathy Gemma L. Carvill, PhD ABSTRACT Douglas E. Crompton, Objective: To assess the presence of DEPDC5 mutations in a cohort of patients with epileptic PhD, MBBS spasms. Brigid M. Regan, BSc Methods: We performed DEPDC5 resequencing in 130 patients with spasms, segregation anal- (Hons) ysis of variants of interest, and detailed clinical assessment of patients with possibly and likely Jacinta M. McMahon, pathogenic variants. BSc (Hons) DEPDC5 Julia Saykally Results: We identified 3 patients with variants in in the cohort of 130 patients with DEPDC5 Matthew Zemel, BS spasms. We also describe 3 additional patients with alterations and epileptic spasms: 2 Amy L. Schneider, MGen from a previously described family and a third ascertained by clinical testing. Overall, we describe DEPDC5 Couns 6 patients from 5 families with spasms and variants; 2 arose de novo and 3 were Leanne Dibbens, PhD familial. Two individuals had focal cortical dysplasia. Clinical outcome was highly variable. Katherine B. Howell, Conclusions: While recent molecular findings in epileptic spasms emphasize the contribution of de MBBS (Hons), novo mutations, we highlight the relevance of inherited mutations in the setting of a family history BMedSc of focal epilepsies. We also illustrate the utility of clinical diagnostic testing and detailed pheno- Simone Mandelstam, typic evaluation in characterizing the constellation of phenotypes associated with DEPDC5 alter- MBChB ations. We expand this phenotypic spectrum to include epileptic spasms, aligning DEPDC5 Richard J. Leventer, epilepsies more with the recognized features of other mTORopathies. Neurol Genet 2015;1:e17; MBBS, PhD doi: 10.1212/NXG.0000000000000016 A.
    [Show full text]
  • NPRL3 (L-20): Sc-242062
    SAN TA C RUZ BI OTEC HNOL OG Y, INC . NPRL3 (L-20): sc-242062 BACKGROUND PRODUCT NPRL3 (nitrogen permease regulator 3-like protein), also known as CGTHBA Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide (conserved gene telomeric to α globin cluster), MARE, NPR3 or RMD11, is a and 0.1% gelatin. 569 amino acid protein that belongs to the NPR3 family. NPRL3 is widely ex- Blocking peptide available for competition studies, sc-242062 P, (100 µg pressed and forms a heterodimer with NPRL2. The gene that encodes NPRL3 peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). consists of approximately 54,587 bases and maps to human chromosome 16p13.3. Encoding over 900 genes and consisting of approximately 90 mil lion APPLICATIONS base pairs, chromosome 16 makes up nearly 3% of the human genome and is associated with a variety of genetic disorders. The GAN gene is located on NPRL3 (L-20) is recommended for detection of NPRL3 of mouse, rat and chromosome 16 and, when mutated, may lead to giant axonal neuropathy, a human origin by Western Blotting (starting dilution 1:200, dilution range nervous system disorder characterized by increasing malfunction with growth. 1:100-1:1000), immunofluorescence (starting dilution 1:50, dilution range Alterations in the CREB gene and NOD2 gene, both of which are located on 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution range chromosome 16, results in Rubinstein-Taybi syndrome and Crohn’s disease, 1:30-1:3000).
    [Show full text]
  • Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
    Epigenetic mechanisms are involved in the oncogenic properties of ZNF518B in colorectal cancer Francisco Gimeno-Valiente, Ángela L. Riffo-Campos, Luis Torres, Noelia Tarazona, Valentina Gambardella, Andrés Cervantes, Gerardo López-Rodas, Luis Franco and Josefa Castillo SUPPLEMENTARY METHODS 1. Selection of genomic sequences for ChIP analysis To select the sequences for ChIP analysis in the five putative target genes, namely, PADI3, ZDHHC2, RGS4, EFNA5 and KAT2B, the genomic region corresponding to the gene was downloaded from Ensembl. Then, zoom was applied to see in detail the promoter, enhancers and regulatory sequences. The details for HCT116 cells were then recovered and the target sequences for factor binding examined. Obviously, there are not data for ZNF518B, but special attention was paid to the target sequences of other zinc-finger containing factors. Finally, the regions that may putatively bind ZNF518B were selected and primers defining amplicons spanning such sequences were searched out. Supplementary Figure S3 gives the location of the amplicons used in each gene. 2. Obtaining the raw data and generating the BAM files for in silico analysis of the effects of EHMT2 and EZH2 silencing The data of siEZH2 (SRR6384524), siG9a (SRR6384526) and siNon-target (SRR6384521) in HCT116 cell line, were downloaded from SRA (Bioproject PRJNA422822, https://www.ncbi. nlm.nih.gov/bioproject/), using SRA-tolkit (https://ncbi.github.io/sra-tools/). All data correspond to RNAseq single end. doBasics = TRUE doAll = FALSE $ fastq-dump -I --split-files SRR6384524 Data quality was checked using the software fastqc (https://www.bioinformatics.babraham. ac.uk /projects/fastqc/). The first low quality removing nucleotides were removed using FASTX- Toolkit (http://hannonlab.cshl.edu/fastxtoolkit/).
    [Show full text]