DOCSLIB.ORG

Supplementary Tables

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Med Genet Supplementary tables Supplementary Table 1. List of 522 genes in the heart gene panel ABCC6 C5orf42 CUL3 FHL1 IGFBP7 MAT2A NR5A1 PTCH1 SKI TMEM43 ABCC9 CACNA1C CUL4B FIG4 IL10 MATR3 NRAS PTCH2 SLC19A2 TMEM67 ACE CACNA1D DAPK3 FKBP14 INVS MCTP2 NRXN1 PTEN SLC29A3 TNNC1 ACTA2 CACNA2D1 DCHS1 FKTN IRF6 MED12 NSD1 PTF1A SLC2A10 TNNI3 ACTB CACNB2 DDX11 FLNA IRX4 MED13L NSDHL PTH1R SLC35B2 TNNT2 ACTC1 CALM1 DDX3X FLNB JAG1 MEGF8 NUB1 PTPN11 SLCO2A1 TNS1 ACTG1 CALM2 DDX59 FOXC1 JPH2 MEOX1 OFD1 RAB10 SLMAP TP63 ACTN2 CALM3 DES FOXC2 JUP MESP1 ORC1 RAB23 SMAD2 TPM1 ACVR1 CALR3 DHCR24 FOXE3 KANSL1 MFAP5 ORC4 RAF1 SMAD3 TRDN ACVR2B CASQ2 DHCR7 FOXF1 KAT6B MGAT2 ORC6 RAI1 SMAD6 TRIM32 ADNP CAV3 DIS3L2 FOXH1 KCNA5 MGP PACS1 RANGRF SMARCA2 TRPM4 AGT CBL DLL3 FRAS1 KCND3 MIB1 PAFAH1B1 RARB SMARCA4 TRPV4 AKAP9 CCBE1 DLX5 FREM2 KCNE1 MID1 PAX1 RBM10 SMARCB1 TSR2 AKT3 CCDC103 DNAAF3 FTO KCNE1L MIR17HG PAX3 RBM20 SMARCE1 TTC37 ALDH18A1 CCDC114 DNAH11 G6PC3 KCNE2 MKKS PAX6 RBM8A SMC1A TTC8 ALDH1A2 CCDC151 DNAH5 GALNS KCNE3 MKS1 PCNT RECQL4 SNAI3 TTN ALG8 CCDC39 DNAI1 GATA3 KCNH2 MMP2 PDGFRB RELN SNRPB TTR ALPK3 CCDC40 DNMT3A GATA4 KCNJ2 MMP21 PDHA1 REN SNTA1 TUBA1A AMER1 CD96 DNMT3B GATA5 KCNJ5 MMP23A PDX1 RFX6 SOS1 TWIST1 ANK2 CDK13 DOCK6 GATA6 KCNJ8 MPDZ PEX1 RIT1 SOX10 TWIST2 ANKRD1 CDKN1C DSC2 GBA KCNQ1 MPLKIP PEX10 RMRP SOX2 UBE2B ANKRD11 CENPJ DSG1 GDF1 KDM5A MSX1 PEX2 RNF135 SOX9 UBR1 ARID1A CEP290 DSG2 GDF6 KDM5B MTCH1 PHF21A RNF20 SPRED1 USP34 ARID1B CEP57 DSP GEMIN2 KDM5C MYBPC3 PHGDH RNU4ATAC SRCAP USP44 ARL6 CFC1 DYNC2H1 GGCX KDM6A MYCN PIEZO2 ROR2 SRD5A3 VCL ASPH CHD4 DYRK1A GJA1 KIAA0196 MYH11 PIGF RPL35A STAMBP VEGFA ASXL1 CHD7 DYX1C1 GJA5 KIAA1279 MYH6 PIGL RPS11 STRA6 VEGFB ATIC CHRNA1 EBP GLA KIF11 MYH7 PIGN RPS17 SUPT5H VEGFC ATP7A CHRNB1 ECE1 GLB1 KIF7 MYH9 PIGT RPS19 SUV420H1 VIPAS39 ATR CHRNG EDN3 GLI3 KMT2A MYL2 PIGV RPS24 TAB2 VPS13B ATRX CHST3 EDNRB GLMN KMT2D MYL3 PIK3CA RPS5 TAF2 VPS33B AXIN1 CHUK EFEMP2 GPC3 KRAS MYLK PIK3R2 RPS7 TALDO1 WDR35 AXIN2 CITED2 EFTUD2 GPC6 KRT1 MYOZ2 PITX1 RRAS TAZ WDR5 B3GALT6 CNTNAP2 EHMT1 GPD1L LAMA4 MYPN PITX2 RUNX1 TBC1D24 WDR60 B3GALTL COG4 ELN GPX4 LAMP2 NAA15 PKD1 RYR2 TBC1D32 WNT4 B3GAT3 COG8 EMD GRHL3 LBR NEK1 PKD2 SALL1 TBX1 WNT5A BAG3 COL18A1 EMG1 HAND1 LDB3 NEXN PKP2 SALL4 TBX2 WNT7A BBS1 COL2A1 EOGT HAND2 LEFTY2 NFATC1 PLD1 SATB2 TBX20 WT1 BBS10 COL3A1 EP300 HCCS LIFR NFIX PLN SCLT1 TBX3 YAP1 BBS12 COLEC11 ESCO2 HCN4 LIG4 NIPBL PLXND1 SCN10A TBX5 ZBTB24 BBS2 COX7B EVC HES7 LMBR1 NKX2 PMM2 SCN1B TCAP ZEB2 BBS4 CREBBP EVC2 HEY2 LMCD1 NKX2-5 POLR1D SCN2B TCOF1 ZFPM2 BBS5 CRELD1 EZH2 HGD LMNA NKX2-6 PORCN SCN3B TCTN3 ZIC3 BBS9 CRELD2 FAM20C HGSNAT LMX1B NODAL PPA2 SCN4B TDGF1 ZMPSTE24 BCL9 CRKL FAM58A HOXA1 LRP2 NOS1 PPP3CA SCN5A TFAP2B ZNF236 BCOR CRYAA FBLN5 HPGD LRP5 NOTCH1 PQBP1 SDCCAG8 TGFB2 BHLHA9 CRYAB FBN1 HRAS LTBP4 NOTCH2 PRDM16 SETBP1 TGFB3 BMP4 CRYBB1 FBN2 HSPG2 LZTR1 NOTCH3 PRKAG2 SF3B4 TGFBR1 BMPR2 CRYGD FGD1 HUWE1 MAFB NPHP1 PRKD1 SH3PXD2B TGFBR2 BMS1 CSRP3 FGF16 IDH1 MAP2K1 NPHP3 PRKG1 SHANK3 TGIF1 BRAF CTCF FGF8 IDS MAP2K2 NPHP4 PRPS1 SHH TLL1 BUB1 CTNNA3 FGFR2 IFT122 MAP3K7 NPPA PSAT1 SHOC2 TMCO1 C12orf57 CTSA FGFR3 IFT80 MASP1 NR2F2 PSPH SHROOM3 TMEM216 van Wijngaarden AL, et al. J Med Genet 2020; 57:843–850. doi: 10.1136/jmedgenet-2019-106715 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Med Genet Supplementary Table 2. List of variants of uncertain significance found in 95 probands with mitral valve prolapse based on the heart gene panel ID Gene Exon Allele Nucleotide Amino acid change % HGMD ClinVar change GnomAD 49 ACTN2 10 Htz c.883G>T p.(Glu295*) - - - 56 COL18A1 39 Htz c.4931A>C p.(Asn1644Thr) - - - 93 DSP 2 Htz c.273+5G>A p.(?) 0.029 Class 5 Class 3 123 DSP 2 Htz c.273+5G>A p.(?) 0.029 Class 5 Class 3 32 FBN1 59 Htz c.7412C>G p.(Pro2471Arg) 0.003 Class 4? Class 3 63 FBN1 35 Htz c.4447G>A p.(Gly1483Arg) - - Class 4 75 FBN2 13 Htz c.1826C>G p.(Thr609Ser) - - - 86 FBN2 13 Htz c.1826C>G p.(Thr609Ser) - - - 87 FBN2 13 Htz c.1826C>G p.(Thr609Ser) - - - 99 FBN2 41 Htz c.5225G>A p.(Arg1742Gln) 0.002 - - 8 FLNA 25 Htz c.4288G>C p.(Gly1430Arg) 0.001 - - 69 FLNA 25 Htz c.4150G>A p.(Gly1384Ser) - - - 81 LZTR1 19 Htz c.2263C>T p.(Arg755Trp) 0.001 - - 13 MYH6 22 Htz c.2928+5G>A p.(?) 0.175 Class 5 Class 2 and class 3 29 MYH6 29 Htz c.4136C>T p.(Thr1379Met) 0.056 Class 5 Class 2 and class 3 44 MYH6 24 Htz c.3154C>T p.(Arg1052*) 0.001 - Class 3 114 MYH6 22 Htz c.2842G>A p.(Glu948Lys) 0.002 - - 28 NKX2-5 2c Htz c.545T>A p.(Val182Asp) - - - 92 NKX2-5 2c Htz c.413G>T p.(Arg138Leu) - - - 103 NOTCH1 24 Htz c.3905G>A p.(Arg1302His) 0.004 - - 3 NOTCH3 4 Htz c.625G>A p.(Gly209Arg) 0.002 - - 39 NOTCH3 33 Htz c.6097C>A p.(Pro2033Thr) 0.004 - - 63 NPM3 4 Htz c.343C>T p.(Gln115*) 0.000 - - 3 PRDM16 11 Htz c.2855C>A p.(Thr952Lys) 0.001 - Class 3 37 RYR2 103 Htz c.14757-7_14757- p.(?) - Class 5 - 6delTCinsAT 21 SMAD6 2 Htz c.841C>G p.(Arg281Gly) 0.014 - Class 2 21 SNAI3 3 Htz c.795C>A p.(Tyr265*) 0.003 - - 35 TCOF1 21 Htz c.3283C>T p.(Gln1095*) - - - 64 TNS1 24 Htz c.4223A>G p.(Asn1408Ser) 0.001 - - 69 TPM1 5 Htz c.549_563+10del p.(Glu184_Gly188del) - - - 4 TTN 327 Htz c.80414A>C p.(Glu26805Ala) 0.003 - Class 3 37 TTN 327 Htz c.80717G>A p.(Arg26906Gln) 0.003 - Class 3 77 TTN 327 Htz c.80717G>A p.(Arg26906Gln) 0.003 - Class 3 118 TTN 141 Htz c.33580G>A p.(Val1119Met) 0.001 - Class 3 46 VEGFA 1 Htz c.405_408del p.(Asp135Glufs*38) - - - * Class 2 = likely benign, Class 3 = variant of uncertain significance, Class 4 = likely pathogenic, Class 5 = pathogenic, and Htz = heterozygous 2 van Wijngaarden AL, et al. J Med Genet 2020; 57:843–850. doi: 10.1136/jmedgenet-2019-106715.
Recommended publications
  • Birthdating of Myenteric Neuron Subtypes in the Small Intestine of the Mouse

    Birthdating of Myenteric Neuron Subtypes in the Small Intestine of the Mouse

    RESEARCH ARTICLE Birthdating of Myenteric Neuron Subtypes in the Small Intestine of the Mouse Annette J. Bergner,1 Lincon A. Stamp,1 David G. Gonsalvez,1 Margaret B. Allison,2,3 David P. Olson,4 Martin G. Myers Jr,2,3,5 Colin R. Anderson,1 and Heather M. Young1* 1Department of Anatomy & Neuroscience, University of Melbourne, Victoria, Australia 2Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA 3Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA 4Division of Endocrinology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA 5Department of Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan, USA ABSTRACT vast majority of myenteric neurons had exited the cell There are many different types of enteric neurons. Pre- cycle by P10. We did not observe any EdU1/NOS11 vious studies have identified the time at which some myenteric neurons in the small intestine of adult mice enteric neuron subtypes are born (exit the cell cycle) in following EdU injection at E10.5 or E11.5, which was the mouse, but the birthdates of some major enteric unexpected, as previous studies have shown that NOS1 neuron subtypes are still incompletely characterized or neurons are present in E11.5 mice. Studies using the unknown. We combined 5-ethynynl-20-deoxyuridine proliferation marker Ki67 revealed that very few NOS1 (EdU) labeling with antibody markers that identify myen- neurons in the E11.5 and E12.5 gut were proliferating. teric neuron subtypes to determine when neuron sub- However, Cre-lox-based genetic fate-mapping revealed types are born in the mouse small intestine.
  • The Baseline Structure of the Enteric Nervous System and Its Role in Parkinson’S Disease

    The Baseline Structure of the Enteric Nervous System and Its Role in Parkinson’S Disease

    life Review The Baseline Structure of the Enteric Nervous System and Its Role in Parkinson’s Disease Gianfranco Natale 1,2,* , Larisa Ryskalin 1 , Gabriele Morucci 1 , Gloria Lazzeri 1, Alessandro Frati 3,4 and Francesco Fornai 1,4 1 Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; [email protected] (L.R.); [email protected] (G.M.); [email protected] (G.L.); [email protected] (F.F.) 2 Museum of Human Anatomy “Filippo Civinini”, University of Pisa, 56126 Pisa, Italy 3 Neurosurgery Division, Human Neurosciences Department, Sapienza University of Rome, 00135 Rome, Italy; [email protected] 4 Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuromed, 86077 Pozzilli, Italy * Correspondence: [email protected] Abstract: The gastrointestinal (GI) tract is provided with a peculiar nervous network, known as the enteric nervous system (ENS), which is dedicated to the fine control of digestive functions. This forms a complex network, which includes several types of neurons, as well as glial cells. Despite extensive studies, a comprehensive classification of these neurons is still lacking. The complexity of ENS is magnified by a multiple control of the central nervous system, and bidirectional communication between various central nervous areas and the gut occurs. This lends substance to the complexity of the microbiota–gut–brain axis, which represents the network governing homeostasis through nervous, endocrine, immune, and metabolic pathways. The present manuscript is dedicated to Citation: Natale, G.; Ryskalin, L.; identifying various neuronal cytotypes belonging to ENS in baseline conditions.
  • Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene

    Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene

    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R.
  • The Extracellular Matrix Phenome Across Species

    The Extracellular Matrix Phenome Across Species

    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.06.980169; this version posted March 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The extracellular matrix phenome across species Cyril Statzer1 and Collin Y. Ewald1* 1 Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach-Zürich CH-8603, Switzerland *Corresponding authors: [email protected] (CYE) Keywords: Phenome, genotype-to-phenotype, matrisome, extracellular matrix, collagen, data mining. Highlights • 7.6% of the human phenome originates from variations in matrisome genes • 11’671 phenotypes are linked to matrisome genes of humans, mice, zebrafish, Drosophila, and C. elegans • Expected top ECM phenotypes are developmental, morphological and structural phenotypes • Nonobvious top ECM phenotypes include immune system, stress resilience, and age-related phenotypes 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.06.980169; this version posted March 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Abstract 2 Extracellular matrices are essential for cellular and organismal function. Recent 3 genome-wide and phenome-wide association studies started to reveal a broad 4 spectrum of phenotypes associated with genetic variants. However, the phenome or 5 spectrum of all phenotypes associated with genetic variants in extracellular matrix 6 genes is unknown.
  • Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells

    Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells

    Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897
  • C-Myc Regulates Cell Proliferation During Lens Development

    C-Myc Regulates Cell Proliferation During Lens Development

    c-myc Regulates Cell Proliferation during Lens Development Gabriel R. Cavalheiro., Gabriel E. Matos-Rodrigues., Anielle L. Gomes, Paulo M. G. Rodrigues, Rodrigo A. P. Martins* Programa de Biologia Celular e do Desenvolvimento, Instituto de Cieˆncias Biome´dicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil Abstract Myc protooncogenes play important roles in the regulation of cell proliferation, growth, differentiation and survival during development. In various developing organs, c-myc has been shown to control the expression of cell cycle regulators and its misregulated expression is detected in many human tumors. Here, we show that c-myc gene (Myc) is highly expressed in developing mouse lens. Targeted deletion of c-myc gene from head surface ectoderm dramatically impaired ocular organogenesis, resulting in severe microphtalmia, defective anterior segment development, formation of a lens stalk and/or aphakia. In particular, lenses lacking c-myc presented thinner epithelial cell layer and growth impairment that was detectable soon after its inactivation. Defective development of c-myc-null lens was not caused by increased cell death of lens progenitor cells. Instead, c-myc loss reduced cell proliferation, what was associated with an ectopic expression of Prox1 and p27Kip1 proteins within epithelial cells. Interestingly, a sharp decrease in the expression of the forkhead box transcription factor Foxe3 was also observed following c-myc inactivation. These data represent the first description of the physiological roles played by a Myc family member in mouse lens development. Our findings support the conclusion that c- myc regulates the proliferation of lens epithelial cells in vivo and may, directly or indirectly, modulate the expression of classical cell cycle regulators in developing mouse lens.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • A Clinicopathological and Molecular Genetic Analysis of Low-Grade Glioma in Adults

    A Clinicopathological and Molecular Genetic Analysis of Low-Grade Glioma in Adults

    A CLINICOPATHOLOGICAL AND MOLECULAR GENETIC ANALYSIS OF LOW-GRADE GLIOMA IN ADULTS Presented by ANUSHREE SINGH MSc A thesis submitted in partial fulfilment of the requirements of the University of Wolverhampton for the degree of Doctor of Philosophy Brain Tumour Research Centre Research Institute in Healthcare Sciences Faculty of Science and Engineering University of Wolverhampton November 2014 i DECLARATION This work or any part thereof has not previously been presented in any form to the University or to any other body whether for the purposes of assessment, publication or for any other purpose (unless otherwise indicated). Save for any express acknowledgments, references and/or bibliographies cited in the work, I confirm that the intellectual content of the work is the result of my own efforts and of no other person. The right of Anushree Singh to be identified as author of this work is asserted in accordance with ss.77 and 78 of the Copyright, Designs and Patents Act 1988. At this date copyright is owned by the author. Signature: Anushree Date: 30th November 2014 ii ABSTRACT The aim of the study was to identify molecular markers that can determine progression of low grade glioma. This was done using various approaches such as IDH1 and IDH2 mutation analysis, MGMT methylation analysis, copy number analysis using array comparative genomic hybridisation and identification of differentially expressed miRNAs using miRNA microarray analysis. IDH1 mutation was present at a frequency of 71% in low grade glioma and was identified as an independent marker for improved OS in a multivariate analysis, which confirms the previous findings in low grade glioma studies.
  • A Forkhead Gene, Foxe3, Is Essential for Lens Epithelial Proliferation and Closure of the Lens Vesicle

    A Forkhead Gene, Foxe3, Is Essential for Lens Epithelial Proliferation and Closure of the Lens Vesicle

    Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press A forkhead gene, FoxE3, is essential for lens epithelial proliferation and closure of the lens vesicle Åsa Blixt,1 Margit Mahlapuu,1 Marjo Aitola,2 Markku Pelto-Huikko,2 Sven Enerba¨ck,1 and Peter Carlsson1,3 1Department of Molecular Biology, Go¨teborg University, The Lundberg Laboratory, Medicinaregatan 9C, Box 462, S-405 30 Go¨teborg, Sweden; 2Department of Developmental Biology, Medical School, University of Tampere, Tampere, Finland In the mouse mutant dysgenetic lens (dyl) the lens vesicle fails to separate from the ectoderm, causing a fusion between the lens and the cornea. Lack of a proliferating anterior lens epithelium leads to absence of secondary lens fibers and a dysplastic, cataractic lens. We report the cloning of a gene, FoxE3, encoding a forkhead/winged helix transcription factor, which is expressed in the developing lens from the start of lens placode induction and becomes restricted to the anterior proliferating cells when lens fiber differentiation begins. We show that FoxE3 is colocalized with dyl in the mouse genome, that dyl mice have mutations in the part of FoxE3 encoding the DNA-binding domain, and that these mutations cosegregate with the dyl phenotype. During embryonic development, the primordial lens epithelium is formed in an apparently normal way in dyl mutants. However, instead of the proliferation characteristic of a normal lens epithelium, the posterior of these cells fail to divide and show signs of premature differentiation, whereas the most anterior cells are eliminated by apoptosis. This implies that FoxE3 is essential for closure of the lens vesicle and is a factor that promotes survival and proliferation, while preventing differentiation, in the lens epithelium.
  • Profiling Data

    Profiling Data

    Compound Name DiscoveRx Gene Symbol Entrez Gene Percent Compound Symbol Control Concentration (nM) JNK-IN-8 AAK1 AAK1 69 1000 JNK-IN-8 ABL1(E255K)-phosphorylated ABL1 100 1000 JNK-IN-8 ABL1(F317I)-nonphosphorylated ABL1 87 1000 JNK-IN-8 ABL1(F317I)-phosphorylated ABL1 100 1000 JNK-IN-8 ABL1(F317L)-nonphosphorylated ABL1 65 1000 JNK-IN-8 ABL1(F317L)-phosphorylated ABL1 61 1000 JNK-IN-8 ABL1(H396P)-nonphosphorylated ABL1 42 1000 JNK-IN-8 ABL1(H396P)-phosphorylated ABL1 60 1000 JNK-IN-8 ABL1(M351T)-phosphorylated ABL1 81 1000 JNK-IN-8 ABL1(Q252H)-nonphosphorylated ABL1 100 1000 JNK-IN-8 ABL1(Q252H)-phosphorylated ABL1 56 1000 JNK-IN-8 ABL1(T315I)-nonphosphorylated ABL1 100 1000 JNK-IN-8 ABL1(T315I)-phosphorylated ABL1 92 1000 JNK-IN-8 ABL1(Y253F)-phosphorylated ABL1 71 1000 JNK-IN-8 ABL1-nonphosphorylated ABL1 97 1000 JNK-IN-8 ABL1-phosphorylated ABL1 100 1000 JNK-IN-8 ABL2 ABL2 97 1000 JNK-IN-8 ACVR1 ACVR1 100 1000 JNK-IN-8 ACVR1B ACVR1B 88 1000 JNK-IN-8 ACVR2A ACVR2A 100 1000 JNK-IN-8 ACVR2B ACVR2B 100 1000 JNK-IN-8 ACVRL1 ACVRL1 96 1000 JNK-IN-8 ADCK3 CABC1 100 1000 JNK-IN-8 ADCK4 ADCK4 93 1000 JNK-IN-8 AKT1 AKT1 100 1000 JNK-IN-8 AKT2 AKT2 100 1000 JNK-IN-8 AKT3 AKT3 100 1000 JNK-IN-8 ALK ALK 85 1000 JNK-IN-8 AMPK-alpha1 PRKAA1 100 1000 JNK-IN-8 AMPK-alpha2 PRKAA2 84 1000 JNK-IN-8 ANKK1 ANKK1 75 1000 JNK-IN-8 ARK5 NUAK1 100 1000 JNK-IN-8 ASK1 MAP3K5 100 1000 JNK-IN-8 ASK2 MAP3K6 93 1000 JNK-IN-8 AURKA AURKA 100 1000 JNK-IN-8 AURKA AURKA 84 1000 JNK-IN-8 AURKB AURKB 83 1000 JNK-IN-8 AURKB AURKB 96 1000 JNK-IN-8 AURKC AURKC 95 1000 JNK-IN-8
  • Supplementary Table 7. Characterization of Human Proteins Involved in the Prostate Cancer Pathway

    Supplementary Table 7. Characterization of Human Proteins Involved in the Prostate Cancer Pathway

    Supplementary Table 7. Characterization of human proteins involved in the prostate cancer pathway f Protein UniProt Protein PONDR-FIT MobiDB Location (length) Location (length) Nint ID length (%)b consensus of long disordered of AIBSse a c d (NAIBS) (%) regions BAD, Bcl2-associated Q92934 168 100.00 84.54 1-105 (105) 1-53 (53) 66 agonist of cell death (4/70.8) 122-147 (27) 57-80 (24) 158-168 (11) 100-129 (30) 146-157 (12) CREB5; cyclic AMP- Q02930 508 85.24 75.39 46-59 (14) 66-86 (21) 65 responsive element (7/67.9) 86-393 (308) 99-183 (85) binding protein 5 447-470 (24) 188-358 (171) 479-508 (31) 362-370 (9) 378-406 (29) 421-444 (24) 503-508 (6) CREB1, cyclic AMP- P16220 341 79.47 40.47 1-32 (32) 32-44 (13) 169 responsive element- (7/29.3) 40-50 (11) 89-104 (16) binding protein 1 102-132 (33) 128-145 (18) 138-171 (34) 166-191 (26) 271-285 (15) 265-270 (6) 307-314 (8) 329-341 (13) FOXO1, Forkhead box Q12778 655 78.63 72.82 1-69 (69) 1-32 (32) 68 protein O1 (19/56.9) 74-101 (28) 54-82 (29) 105-160 (56) 88-118 (31) 199-210 (12) 160-172 (13) 229-336 (107) 182-196 (15) 385-450 (66) 216-226 (11) 463-488 (26) 258-280 (23) 498-569 (72) 289-297 (9) 644-655 (12) 306-314 (9) 323-365 (43) 371-388 (18) 301-409 (8) 447-469 (23) 483-517 (35) 528-545 (18) 550-565 (16) 570-592 (23) 605-612 (8) TCF7L1, transcription Q9HCS4 588 77.04 61.90 1-104 (104) 1-46 (46) 4 factor 7 like 1 (16/54.5) 161-183 (23) 53-74 (22) 192-238 (47) 94-135 (42) 316-344 (29) 146-159 (14) 406-512 (107) 191-201 (11) 524-546 (21) 234-252 (19) 274-288 (15) 349-371 (23) 373-383 (11)
  • Molecular Classification of Patients with Unexplained Hamartomatous and Hyperplastic Polyposis

    Molecular Classification of Patients with Unexplained Hamartomatous and Hyperplastic Polyposis

    ORIGINAL CONTRIBUTION Molecular Classification of Patients With Unexplained Hamartomatous and Hyperplastic Polyposis Kevin Sweet, MS, CGC Context Significant proportions of patients with hamartomatous polyposis or with Joseph Willis, MD hyperplastic/mixed polyposis remain without specific clinical and molecular diagnosis Xiao-Ping Zhou, MD, PhD or present atypically. Assigning a syndromic diagnosis is important because it guides management, especially surveillance and prophylactic surgery. Carol Gallione, PhD Objective To systematically classify patients with unexplained hamartomatous or hy- Takeshi Sawada, MD, PhD perplastic/mixed polyposis by extensive molecular analysis in the context of central Pia Alhopuro, MD rereview of histopathology results. Sok Kean Khoo, PhD Design, Setting, and Patients Prospective, referral-based study of 49 unrelated patients from outside institutions (n=28) and at a comprehensive cancer center (n=21), Attila Patocs, MD, PhD conducted from May 2, 2002, until December 15, 2004. Germline analysis of PTEN, Cossette Martin, PhD BMPR1A, STK11 (sequence, deletion), SMAD4, and ENG (sequence), specific exon screen- Scott Bridgeman, BSc ing of BRAF, MYH, and BHD, and rereview of polyp histology results were performed. John Heinz, PhD Main Outcome Measures Molecular, clinical, and histopathological findings in pa- tients with unexplained polyposis. Robert Pilarski, MS, CGC Results Of the 49 patients, 11 (22%) had germline mutations. Of 14 patients with Rainer Lehtonen, BSc juvenile polyposis, 2 with early-onset disease had mutations in ENG, encoding endo- Thomas W. Prior, PhD glin, previously only associated with hereditary hemorrhagic telangiectasia; 1 had hemi- zygous deletion encompassing PTEN and BMPR1A; and 1 had an SMAD4 mutation. Thierry Frebourg, MD, PhD One individual previously classified with Peutz-Jeghers syndrome had a PTEN dele- Bin Tean Teh, MD, PhD tion.