DOCSLIB.ORG

Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostat

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostate Cancer Thomas A. White A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Peter S. Nelson, Chair Janet L. Stanford Raymond J. Monnat Jay A. Shendure Program Authorized to Offer Degree: Molecular and Cellular Biology ©Copyright 2013 Thomas A. White University of Washington Abstract Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostate Cancer Thomas A. White Chair of the Supervisory Committee: Peter S. Nelson, MD Novel functionally altered transcripts may be recurrent in prostate cancer (PCa) and may underlie lethal and advanced disease and the neuroendocrine small cell carcinoma (SCC) phenotype. We conducted an RNASeq survey of the LuCaP series of 24 PCa xenograft tumors from 19 men, and validated observations on metastatic tumors and PCa cell lines. Key findings include discovery and validation of 40 novel fusion transcripts including one recurrent chimera, many SCC-specific and castration resistance (CR) -specific novel splice isoforms, new observations on SCC-specific and TMPRSS2-ERG specific differential expression, the allele-specific expression of certain recurrent non- synonymous somatic single nucleotide variants (nsSNVs) previously discovered via exome sequencing of the same tumors, rgw ubiquitous A-to-I RNA editing of base excision repair (BER) gene NEIL1 as well as CDK13, a kinase involved in RNA splicing, and the SCC expression of a previously unannotated long noncoding RNA (lncRNA) at Chr6p22.2. Mechanistic investigation of the novel lncRNA indicates expression is regulated by derepression by master neuroendocrine regulator RE1-silencing transcription factor (REST), and may regulate some genes of axonogenesis and angiogenesis. Taken together these variant transcripts offer insight into aggressive metastatic PCa, both broadly and with regard to castration-resistant and neuroendocrine disease. TABLE OF CONTENTS Page List of Figures …………………………………………………………………………….ii List of Tables .………………………………………...…………...………………….… iii List of Abbreviations …………………………………...……………………………..…iv Acknowledgements ……………………………………..……………………………….vi Dedication ……………………………………………..…………………………….....viii Chapter 1: Introduction .…………………………………………………………………. 1 Significance ...…………………………………………………..…………..………….… 3 Prostate adenocarcinoma and neuroendocrine prostate cancer ………….....………….… 4 Risk factors for prostate cancer development …………………………...…......…..……. 6 Prevalence and roles of somatic mutations and transcript alterations in prostate cancer….............................................................................................................................. 9 LuCaP xenografts: surgically acquired models of metastatic prostate cancer ……......... 13 References ..…………………………………………………………...……………...… 16 Chapter 2: RNASeq of LuCaP prostate cancers reveals recurrent expression of novel functional variants ………………………………….…………...…………..………….. 20 Summary ………………………………………………………..……………………… 20 Introduction .………………………………………………………...………………….. 22 Results …………………………………………………………………..….…………... 24 Discussion ….……………………………………………………...………...…………. 30 Materials and Methods …..……………………………….…………………...……...… 35 References ..……………………………………………………………...…………...… 40 Chapter 3: lncRNA 6p22.2: A novel neuroendocrine PCa specific long noncoding RNA………………………………………………………………………………….… 54 Summary ..………………………………………………………………..………….… 55 Introduction ………………………………………………………………..…………... 55 Results …………………………………………………………………………….....… 56 Discussion ……….…………………………………………………………….........… 57 Materials and Methods …………………………………………………..…………..… 60 References ..……………………………………………………………………….....… 63 Chapter 4: Conclusions and Perspectives …..………………………………..……...… 66 i LIST OF FIGURES Page Chapter 2 Figure 1: Unsupervised clustering of expression of top 1,000 most variable transcripts..46 Figure 2: Differentially expressed genes in neuroendocrine LuCaPs vs Adenocarcinoma, by significantly enriched KEGG pathway ..……...…………………...……………..….47 Figure 3: Differentially expressed genes in TMPRSS2-ERG (+) vs (-) LuCaPs ………48 Figure 3: Neuroendocrine-specific lincRNA at chr6 p22.2 .……………………..….…. 49 Figure 4: STK39-COL5A2 rearrangement transcript …….…………….…...……….… 50 Figure 5: Proportion of expressed genes harboring somatic non-synonymous single nucleotide variants which display variant allele expression fraction ≥ 10%, by LuCaP. 51 Chapter 3 Figure 1: Genomic context of novel neuroendocrine-specific LincRNA ………...……. 61 Figure 2: RT-PCR of lncRNA and neuroendocrine markers in BPH-1 lincRNA overexpression ………………………………………………………………………..... 62 Figure 3: REST repressesion of lncRNA 6p22.2 expression ………………………..… 63 ii LIST OF TABLES Page Chapter 2 Table 1: Next-generation sequencing of prostate cancer xenografts …………………...40 Table 2: Expression of most frequently recurrent non-synonymous single nucleotide variants …………………………………………………………………..…………..… 41 Table 3: Novel rearrangement transcript expression in LuCaP prostate cancers (excluding TMPRSS2-ERG) ……………………………………………..………….… 43 Table 4: Neuroendocrine-specific novel splice junctions …………….…….……...….. 44 Table 5: Castration resistance specific novel splice junctions ………....…….…..……. 45 Table S1: Composite list of transcripts among the top 500 most abundant in one or more LuCaPs ………………………………………………………………………………..... 75 Table S2: Differential expression in neuroendocrine vs adenocarcinoma LuCaPs ..... 109 Table S3: Differential expression in TMPRSS2-ERG rearrangement (+) vs. (-) LuCaPs ......................................................................................................................................... 135 Chapter 3 Table 1: Annotated lncRNAs differentially expressed in neuroendocrine vs. adenocarcinoma LuCaPs………………………………………………….……..…...… 59 Table 2: REST-regulated gene expression in neuroendocrine vs. adenocarcinoma LuCaPs ……………………………………………………………………..…..………. 60 iii LIST OF ABBREVIATIONS ADT: androgen deprivation therapy AR: androgen receptor AS: alternate splicing BPH: benign prostatic hyperplasia CNV: copy number variation CR: castration resistant CRPC: castration resistant prostate cancer CS: castration sensitive DHT: dihydroxy testosterone DRE: digital rectal exam FISH: fluorescent in situ hybridization lncRNA: long noncoding RNA NCI: National Cancer Institute NEPC: neuroendocrine prostate cancer nsSNV: non-synonymous single nucleotide variant PCa: prostate cancer PCR: polymerase chain reaction PSA: prostate specific antigen RP: radical prostatectomy RPKM: reads per kilobase per million aligned reads RT-PCR: real-time PCR SCC: small cell carcinoma iv SCLC: small cell lung carcinoma SNV: single nucleotide variant XRT: external beam radiation therapy v Acknowledgements The author wishes to express sincere gratitude to his advisor Dr. Peter S. Nelson for his substantial support, miraculous patience and critical contribution to the development of this work. Professor Janet L. Stanford’s contribution of dual mentorship throughout this and prior work is also tremendously appreciated. The support and feedback of supervisory committee members Drs. Robert Eisenman, Ray Monnat and Jay Shendure are greatly valued. Regarding scientific accomplishments, this project would have been impossible without the efforts of Drs. Robert Vessella and Colm Morrisey and the selfless contributions of many victims of prostate cancer to the University of Washington Rapid Autopsy Program. Akash Kumar of the Shendure lab, who led the Exome sequencing sister study to this RNAseq project, and his lab colleagues Sarah Ng, Choli Lee and Alex MacKenzie contributed substantially to the foundation of this work. Matthew Fitzgibbon, Nigel Clegg and Jerry Davison of Dr. Martin McIntosh’s team made the analysis of RNAseq data possible, and made substantial intellectual contributions. Jeff Delrow and Jerry (Andy) Marty of the FHCRC Core Facilities, who performed high- throughput sequencing and their colleague Elizabeth Jensen who reliably performed Sanger sequencing made high quality data a matter of routine and are greatly appreciated. Drs. Larry True and Funda Vakar-Lopez provided invaluable pathology support and feedback. In the Nelson lab, virtually every member has made important contributions to this project, from expression microarray hybridization and analysis, to training or guidance on nearly every bench method, to moral support. This work would not have been completed without the support of Drs. Jared Lucas, Ilsa Coleman, Roger Coleman, vi Daniella Bianchi-Frias, Clint Matson, Robin Tharakan, Dapei Li, Roland Huber, Susana Hernandez-Lopez, Aric Zhao, Song Zhao as well as former members Drs. Eric Bluemn, James Dean, Ryan Gordon, Renee Chmelar, and Karl Thoreson and Andrew Morgan. The support of Ruthy Dumpit in particular spanned the breadth of the project and beyond, and was absolutely invaluable. The support of Alex Moreno both administrative and as a friend are greatly appreciated. Dr. Elahe Mostaghel and her lab members Arja Kaipainen, Qi Tain, Steven Mongovin and Ailin Zhang have also provided valuable support and feedback, as have countless other faculty, postdocs, scientists, students and staff at the FHCRC. The University of Washington Molecular and Cell Biology (MCB) Program provided a robust and flexible structure for the completion of this degree. MaryEllin
Recommended publications
  • Reprogramming of Trna Modifications Controls the Oxidative Stress Response by Codon-Biased Translation of Proteins

    Reprogramming of Trna Modifications Controls the Oxidative Stress Response by Codon-Biased Translation of Proteins

    Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Chan, Clement T.Y. et al. “Reprogramming of tRNA Modifications Controls the Oxidative Stress Response by Codon-biased Translation of Proteins.” Nature Communications 3 (2012): 937. As Published http://dx.doi.org/10.1038/ncomms1938 Publisher Nature Publishing Group Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/76775 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins Clement T.Y. Chan,1,2 Yan Ling Joy Pang,1 Wenjun Deng,1 I. Ramesh Babu,1 Madhu Dyavaiah,3 Thomas J. Begley3 and Peter C. Dedon1,4* 1Department of Biological Engineering, 2Department of Chemistry and 4Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; 3College of Nanoscale Science and Engineering, University at Albany, SUNY, Albany, NY 12203 * Corresponding author: PCD, Department of Biological Engineering, NE47-277, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139; tel 617-253-8017; fax 617-324-7554; email [email protected] 2 ABSTRACT Selective translation of survival proteins is an important facet of cellular stress response. We recently demonstrated that this translational control involves a stress-specific reprogramming of modified ribonucleosides in tRNA.
  • Download Ji Calendar Educator Guide

    Download Ji Calendar Educator Guide

    xxx Contents The Jewish Day ............................................................................................................................... 6 A. What is a day? ..................................................................................................................... 6 B. Jewish Days As ‘Natural’ Days ........................................................................................... 7 C. When does a Jewish day start and end? ........................................................................... 8 D. The values we can learn from the Jewish day ................................................................... 9 Appendix: Additional Information About the Jewish Day ..................................................... 10 The Jewish Week .......................................................................................................................... 13 A. An Accompaniment to Shabbat ....................................................................................... 13 B. The Days of the Week are all Connected to Shabbat ...................................................... 14 C. The Days of the Week are all Connected to the First Week of Creation ........................ 17 D. The Structure of the Jewish Week .................................................................................... 18 E. Deeper Lessons About the Jewish Week ......................................................................... 18 F. Did You Know? .................................................................................................................
  • Analysis of Gene Expression Data for Gene Ontology

    Analysis of Gene Expression Data for Gene Ontology

    ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins.
  • Allele-Specific Expression of Ribosomal Protein Genes in Interspecific Hybrid Catfish

    Allele-Specific Expression of Ribosomal Protein Genes in Interspecific Hybrid Catfish

    Allele-specific Expression of Ribosomal Protein Genes in Interspecific Hybrid Catfish by Ailu Chen A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama August 1, 2015 Keywords: catfish, interspecific hybrids, allele-specific expression, ribosomal protein Copyright 2015 by Ailu Chen Approved by Zhanjiang Liu, Chair, Professor, School of Fisheries, Aquaculture and Aquatic Sciences Nannan Liu, Professor, Entomology and Plant Pathology Eric Peatman, Associate Professor, School of Fisheries, Aquaculture and Aquatic Sciences Aaron M. Rashotte, Associate Professor, Biological Sciences Abstract Interspecific hybridization results in a vast reservoir of allelic variations, which may potentially contribute to phenotypical enhancement in the hybrids. Whether the allelic variations are related to the downstream phenotypic differences of interspecific hybrid is still an open question. The recently developed genome-wide allele-specific approaches that harness high- throughput sequencing technology allow direct quantification of allelic variations and gene expression patterns. In this work, I investigated allele-specific expression (ASE) pattern using RNA-Seq datasets generated from interspecific catfish hybrids. The objective of the study is to determine the ASE genes and pathways in which they are involved. Specifically, my study investigated ASE-SNPs, ASE-genes, parent-of-origins of ASE allele and how ASE would possibly contribute to heterosis. My data showed that ASE was operating in the interspecific catfish system. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5,420 (8.2%) and 13,390 (7.5%) SNPs were identified as significant ASE-SNPs, respectively.
  • Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas

    Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas

    Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo
  • March 2021 Adar / Nisan 5781

    March 2021 Adar / Nisan 5781

    March 2021 Adar / Nisan 5781 www.ti-stl.org Congregation Temple Israel is an inclusive community that supports your unique Jewish journey. TEMPLE NEWS SHABBAT WORSHIP SCHEDULE HIAS REFUGEE SHABBAT SERVICES WORSHIP SERVICE SCHEDULE Friday, March 5 @ 6:30 PM Throughout the month of March, Shabbat services will Temple Israel will be a proud participant in HIAS’ Refugee be available online only. Join us and watch services Shabbat, during which Jews in the United States and around the remotely on our website or on our Facebook page, where world will take action for refugees and asylum seekers. you can connect with other viewers in the comments section. Founded as the Hebrew Immigrant Aid Society in 1881 to assist Jews fleeing persecution in Russia and Eastern Europe, HIAS’s work is rooted in Jewish values and the belief that anyone fleeing WATCH SERVICES ONLINE hatred, bigotry and xenophobia, regardless of their faith or Services on our website: ethnicity, should be provided with a safe refuge. www.ti-stl.org/Watch Services on our Facebook page: Over the Shabbat of March 5-6, 2021, the Jewish community www.facebook.com/TempleIsraelStLouis will dedicate sacred time and space to refugees and asylum seekers. Now in its third year with hundreds of congregations and thousands of individuals participating, this Refugee Shabbat SERVICE SCHEDULE & PARSHA will be an opportunity to once again raise awareness in our 6:00 pm Weekly Pre-Oneg on Zoom communities, to recognize the work that has been done, and to (Link shared in our eNews each week.) reaffirm our commitment to welcoming refugees and asylum seekers.
  • The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase

    The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase

    Int. J. Mol. Sci. 2012, 13, 5375-5405; doi:10.3390/ijms13055375 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase Valerie J. Klema and Carrie M. Wilmot * Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-612-624-2406; Fax: +1-612-624-5121. Received: 6 April 2012; in revised form: 22 April 2012 / Accepted: 26 April 2012 / Published: 3 May 2012 Abstract: Copper amine oxidases (CAOs) are a ubiquitous group of enzymes that catalyze the conversion of primary amines to aldehydes coupled to the reduction of O2 to H2O2. These enzymes utilize a wide range of substrates from methylamine to polypeptides. Changes in CAO activity are correlated with a variety of human diseases, including diabetes mellitus, Alzheimer’s disease, and inflammatory disorders. CAOs contain a cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), that is required for catalytic activity and synthesized through the post-translational modification of a tyrosine residue within the CAO polypeptide. TPQ generation is a self-processing event only requiring the addition of oxygen and Cu(II) to the apoCAO. Thus, the CAO active site supports two very different reactions: TPQ synthesis, and the two electron oxidation of primary amines. Crystal structures are available from bacterial through to human sources, and have given insight into substrate preference, stereospecificity, and structural changes during biogenesis and catalysis.
  • Generated by SRI International Pathway Tools Version 25.0, Authors S

    Generated by SRI International Pathway Tools Version 25.0, Authors S

    An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
  • The Histone Deacetylase HDA15 Interacts with MAC3A and MAC3B to Regulate Intron

    The Histone Deacetylase HDA15 Interacts with MAC3A and MAC3B to Regulate Intron

    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 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. 1 The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron 2 retention of ABA-responsive genes 3 4 Yi-Tsung Tu1#, Chia-Yang Chen1#, Yi-Sui Huang1, Ming-Ren Yen2, Jo-Wei Allison Hsieh2,3, 5 Pao-Yang Chen2,3*and Keqiang Wu1* 6 7 1Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan 8 2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan 9 3 Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan 10 University, Taipei, Taiwan 11 12 # These authors contributed equally to this work. 13 * Corresponding authors: Keqiang Wu ([email protected], +886-2-3366-4546) and Pao-Yang 14 Chen ([email protected], +886-2-2787-1140) 15 16 Short title: HDA15 and MAC3A/MAC3B coregulate intron retention 17 One sentence summary: HDA15 and MAC3A/MAC3B coregulate intron retention and reduce 18 the histone acetylation level of the genomic regions near ABA-responsive retained introns. 19 20 The author responsible for distribution of materials integral to the findings presented in this 21 article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) 22 is: Keqiang Wu ([email protected]) 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020.
  • Passover Guide & March 2021

    Passover Guide & March 2021

    VIRTUAL SEDERS MARCH 27 5:00PM MARCH 28 5:00PM PAGE 3 PASSOVER GUIDE & MARCH 2021 ADAR / NISSAN1 5781 BULLETIN A MESSAGE FOR PASSOVER A Message for Passover Every year we remind the participants at the Passover table that the recounting of the experience is a “Haggadah,” a telling, and not a “Kriyah,” a reading. What’s the difference? A reading is simply going by the script of what’s on the page. A telling, on the other hand, requires both creativity, and the art, making the story pop. While the words on the page of the Haggadah have been the basis for the Passover Seder for thousands of years, they are merely jumping off points for rituals, conversations, and teaching the Passover narrative to our children and to each other. Taking part in a fulfilling Seder isn’t about reading every word on the page, but rather making the words that you do read come to life. Look no further than the famous Haggadah section of the Four Children to remind us of our responsibility to make the Seder interesting for every kind of participant. The Haggadah offers us four different types of Seder guests, the wise one, the rebellious one, the simple one, and the one who doesn’t know how to ask. We are given guidelines for how to explain the meaning of Passover to each of them. The four children remind us that each type of person at the table requires a different type of experience, and it’s the leader’s job to make the narrative relevant for each of them.
  • Apoptosis and Differentiation Commitment: Novel Insights Revealed by Gene Profiling Studies in Mouse Embryonic Stem Cells

    Apoptosis and Differentiation Commitment: Novel Insights Revealed by Gene Profiling Studies in Mouse Embryonic Stem Cells

    Cell Death and Differentiation (2006) 13, 564–575 & 2006 Nature Publishing Group All rights reserved 1350-9047/06 $30.00 www.nature.com/cdd Apoptosis and differentiation commitment: novel insights revealed by gene profiling studies in mouse embryonic stem cells D Duval1,2,4, M Trouillas3,4, C Thibault2, D Dembele´ 2, Introduction F Diemunsch2, B Reinhardt2, AL Mertz2, A Dierich2 Mouse embryonic stem (ES) cells, which are maintained and H Bœuf*,3 pluripotent in vitro with leukemia inhibitory factor (LIF) cytokine, are instrumental to study LIF-dependent cell 1 UMR5096-CNRS/UP/IRD, Perpignan, France 2 IGBMC/CNRS/INSERM, Strasbourg, France pluripotency as well as the first steps of differentiation 3 UMR-5164-CNRS-CIRID/Universite´ Bordeaux2, Bordeaux, France commitment triggered upon LIF starvation. As we recently 4 These authors contributed equally to this work reported, these cells could also be used to unravel the early * Corresponding author: H Bœuf, UMR-5164-CNRS-CIRID, Universite´ steps of apoptosis, a physiological cell death process Bordeaux2, Bat.1B, BP14, 146 rue Le´o Saignat, 33076 Bordeaux, France. occurring during the first embryogenesis stages. Indeed, the Tel: þ 05 57 57 46 33; Fax: þ 05 57 57 14 72; formation of the cavities, which starts at the blastocyst stage, E-mail:helene.bœ[email protected] is dependent on a specific cell death program, which includes caspase 3 cleavage and induction of the apoptosis-inducing Received 10.3.05; revised 01.9.05; accepted 01.9.05; published online 25.11.05 1 Edited by R De Maria factor (AIF)-complex proteins.
  • ASPA Gene Aspartoacylase

    ASPA Gene Aspartoacylase

    ASPA gene aspartoacylase Normal Function The ASPA gene provides instructions for making an enzyme called aspartoacylase. In the brain, this enzyme breaks down a compound called N-acetyl-L-aspartic acid (NAA) into aspartic acid (an amino acid that is a building block of many proteins) and another molecule called acetic acid. The production and breakdown of NAA appears to be critical for maintaining the brain's white matter, which consists of nerve fibers surrounded by a myelin sheath. The myelin sheath is the covering that protects nerve fibers and promotes the efficient transmission of nerve impulses. The precise function of NAA is unclear. Researchers had suspected that it played a role in the production of the myelin sheath, but recent studies suggest that NAA does not have this function. The enzyme may instead be involved in the transport of water molecules out of nerve cells (neurons). Health Conditions Related to Genetic Changes Canavan disease More than 80 mutations in the ASPA gene are known to cause Canavan disease, which is a rare inherited disorder that affects brain development. Researchers have described two major forms of this condition: neonatal/infantile Canavan disease, which is the most common and most severe form, and mild/juvenile Canavan disease. The ASPA gene mutations that cause the neonatal/infantile form severely impair the activity of aspartoacylase, preventing the breakdown of NAA and allowing this substance to build up to high levels in the brain. The mutations that cause the mild/juvenile form have milder effects on the enzyme's activity, leading to less accumulation of NAA.