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NDRG2 (NDRG family member 2)

Written2005-06Libo Yao, Lifeng Wang, Jiang Zhang, Na Liu
Department of Biochemistry, Molecular Biology, The State Key Laboratory of Cancer Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)KIAA1248
SYLD
Other aliasDKFZp781G1938
HGNC:14460
HGNC (Hugo) NDRG2
LocusID (NCBI) 57447
Atlas_Id 41513
Location 14q11.2  [Link to chromosome band 14q11]
Location_base_pair Starts at 21016763 and ends at 21070872 bp from pter ( according to hg19-Feb_2009)  [Mapping NDRG2.png]
Fusion genes
(updated 2016)
ATL2 (2p22.2) / NDRG2 (14q11.2)CRYL1 (13q12.11) / NDRG2 (14q11.2)NDRG2 (14q11.2) / BAG6 (6p21.33)
NDRG2 (14q11.2) / CALR (19p13.2)NDRG2 (14q11.2) / DDIT4 (10q22.1)NDRG2 (14q11.2) / ERC1 (12p13.33)
NDRG2 (14q11.2) / KIF3A (5q31.1)NDRG2 (14q11.2) / NDRG2 (14q11.2)NDRG2 (14q11.2) / RABEP1 (17p13.2)
NDRG2 (14q11.2) / RPL38 (17q25.1)NDRG2 (14q11.2) / SEC63 (6q21)NDRG2 (14q11.2) / TRAF4 (17q11.2)
PAPLN (14q24.2) / NDRG2 (14q11.2)

DNA/RNA

Description The gene encompasses 9013 bp of DNA; 16 or 17 exons (the first and second are non-coding).
Transcription Eight splicing mRNAs are found.
  • 2142 bp mRNA; CDS: 174-1289bp ;1113 bp open reading frame
  • 2100 bp mRNA; CDS: 174-1247bp ;1071 bp open reading frame
  • 2033 bp mRNA; CDS: 107-1180bp ;1071 bp open reading frame
  • 2075 bp mRNA; CDS: 107-1222bp ;1113 bp open reading frame
  • 2010 bp mRNA; CDS: 84-1157bp ;1071 bp open reading frame
  • 2052 bp mRNA; CDS: 84-1199bp ;1113 bp open reading frame
  • 2119 bp mRNA; CDS: 151-1266bp ;1113 bp open reading frame
  • 2077 bp mRNA; CDS: 151-1224bp ;1071 bp open reading frame.
  • Protein

    Description 357 amino acids ; another isoform has 371 amino acids ; 40 or 43 kDa ; Thr348 is a Akt phosphorylation site, Ser332 is a PKC teta-phosphorylation site. NDRG2 has the alpha/beta hydrolase fold motif.
    Expression Widely expressed, especially in brain, heart, skeletal muscle and kidney.
    Localisation cytosol
    Function A candidate tumor suppressor gene. Ndrg2 expressed much higher in normal tissues than the tumors (brain, liver, pancreas tissues etc) . Overexpression of ndrg2 can inhibit the proliferation of glioblastoma U373 and U138 cells. NDRG2 upregulation is associated with disease pathogenesis in the human brain. Ndrg2 is expressed during the differentiation of DCs, and the expression is differentially regulated by maturation-inducing stimuli such as LPS and CD40. The expression of ndrg2 in rat frontal cortex was decreased by chronic antidepressant treatment.
    Homology At the amino acid level, human NDRG2 shows 57% identical to NDRG1 and NDRG3, 65% identical to NDRG4-B, 63% identical to NDRG4-Bvar and 61% identical to NDRG4-H respectively. Also human NDRG2 shows 92% identical to mouse NDRG2.

    Implicated in

    Note
      
    Entity Alzheimer's disease
    Disease Alzheimer's disease is the most common cause of dementia. Dementia is a collective name for progressive degenerative brain syndromes, which affect memory, thinking, behavior and emotion. Symptoms may include: 1) lose of memory ; 2) difficulty in finding the right words or understanding what people are saying; 3) difficulty in performing previously routine tasks; 4) personality and mood changes.
    Prognosis The probable outcome is poor. The disorder is usually not acute, but progresses steadily. Total disability is common. Death normally occurs within 15 years, usually from an infection or a failure of other body systems. The duration of illness, from onset of symptoms to death, averages 8 to 10 years
    Hybrid/Mutated Gene NDRG2 is upregulated at both the RNA and protein levels in AD brains. Expression of NDRG2 in affected brains was revealed in : (1) cortical pyramidal neurons, (2) senile plaques and (3) cellular processes of dystrophic neurons. NDRG2 upregulation is associated with disease pathogenesis in the human brain
      
      
    Entity Liver cancers
    Disease Liver cancers are primary liver tumors (hepatoma/hepatocellular carcinoma, bile duct cancer/cholangio-carcinoma) or metastatic liver tumor.
    Oncogenesis Compared with adjacent normal tissues, the expression levels of NDRG2 mRNA in liver cancer tissues reduced significantly, but the mutation in the whole coding region of NDRG2 was not found.
      
      
    Entity Glioblastoma
    Disease Glioblastoma multiforme (GBM) is the most aggressive form of the primary brain tumors known collectively as gliomas. These tumors arise from the supporting, glial cells of the brain during childhood and in adults. These growths do not spread throughout the body like other forms of cancer, but cause symptoms by invading the brain.NDRG2 gene was first found in this tissue by using subtraction cloning.
    Oncogenesis Ndrg2 is present at low levels in human GBM tissues and glioblastoma cell lines comparing with normal tissue and cells. Transient transfection exogenous NDRG2 gene will inhibits glioblastoma U373 and U138 cells proliferation.
      
      
    Entity Gastric cancer
    Disease Gastric cancer is the result of cell changes in the lining of the stomach. The most common types of stomach cancer start in the glandular cells of the stomach lining and are known as adenocarcinomas. These are rare cancers that usually start from the cells of the muscle layer of the stomach. The most common type of sarcoma to affect the stomach is a leiomyosarcoma. Another type of sarcoma is a gastrointestinal stromal tumour (GIST).
    Oncogenesis Ndrg2 is present at low level in some stomach cancer tissue and cell lines.
      

    Bibliography

    Embryonic lethality in mice homozygous for a targeted disruption of the N-myc gene.
    Charron J, Malynn BA, Fisher P, Stewart V, Jeannotte L, Goff SP, Robertson EJ, Alt FW
    Genes & development. 1992 ; 6 (12A) : 2248-2257.
    PMID 1459450
     
    N-Myc downstream-regulated gene 2 (NDRG2) inhibits glioblastoma cell proliferation.
    Deng Y, Yao L, Chau L, Ng SS, Peng Y, Liu X, Au WS, Wang J, Li F, Ji S, Han H, Nie X, Li Q, Kung HF, Leung SY, Lin MC
    International journal of cancer. Journal international du cancer. 2003 ; 106 (3) : 342-347.
    PMID 12845671
     
    NDRG2 expression and mutation in human liver and pancreatic cancers.
    Hu XL, Liu XP, Lin SX, Deng YC, Liu N, Li X, Yao LB
    World journal of gastroenterology : WJG. 2004 ; 10 (23) : 3518-3521.
    PMID 15526377
     
    Homocysteine-respondent genes in vascular endothelial cells identified by differential display analysis. GRP78/BiP and novel genes.
    Kokame K, Kato H, Miyata T
    The Journal of biological chemistry. 1996 ; 271 (47) : 29659-29665.
    PMID 8939898
     
    Inhibition of tumor cell growth by RTP/rit42 and its responsiveness to p53 and DNA damage.
    Kurdistani SK, Arizti P, Reimer CL, Sugrue MM, Aaronson SA, Lee SW
    Cancer research. 1998 ; 58 (19) : 4439-4444.
    PMID 9766676
     
    NDRG2: a novel Alzheimer's disease associated protein.
    Mitchelmore C, Büchmann-M&oring; S, Rask L, West MJ, Troncoso JC, Jensen NA
    Neurobiology of disease. 2004 ; 16 (1) : 48-58.
    PMID 15207261
     
    Identification of new genes ndr2 and ndr3 which are related to Ndr1/RTP/Drg1 but show distinct tissue specificity and response to N-myc.
    Okuda T, Kondoh H
    Biochemical and biophysical research communications. 1999 ; 266 (1) : 208-215.
    PMID 10581191
     
    Characterization and expression of three novel differentiation-related genes belong to the human NDRG gene family.
    Qu X, Zhai Y, Wei H, Zhang C, Xing G, Yu Y, He F
    Molecular and cellular biochemistry. 2002 ; 229 (1-2) : 35-44.
    PMID 11936845
     
    N-myc-dependent repression of ndr1, a gene identified by direct subtraction of whole mouse embryo cDNAs between wild type and N-myc mutant.
    Shimono A, Okuda T, Kondoh H
    Mechanisms of development. 1999 ; 83 (1-2) : 39-52.
    PMID 10381566
     
    Loss of N-myc function results in embryonic lethality and failure of the epithelial component of the embryo to develop.
    Stanton BR, Perkins AS, Tessarollo L, Sassoon DA, Parada LF
    Genes & development. 1992 ; 6 (12A) : 2235-2247.
    PMID 1459449
     
    Characterization of the human NDRG gene family: a newly identified member, NDRG4, is specifically expressed in brain and heart.
    Zhou RH, Kokame K, Tsukamoto Y, Yutani C, Kato H, Miyata T
    Genomics. 2001 ; 73 (1) : 86-97.
    PMID 11352569
     
    A novel gene which is up-regulated during colon epithelial cell differentiation and down-regulated in colorectal neoplasms.
    van Belzen N, Dinjens WN, Diesveld MP, Groen NA, van der Made AC, Nozawa Y, Vlietstra R, Trapman J, Bosman FT
    Laboratory investigation; a journal of technical methods and pathology. 1997 ; 77 (1) : 85-92.
    PMID 9251681
     

    Citation

    This paper should be referenced as such :
    Yao, L ; Wang, L ; Zhang, J ; Na, Liu N
    NDRG2 (NDRG family member 2)
    Atlas Genet Cytogenet Oncol Haematol. 2005;9(4):278-279.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/NDRG2ID41513ch14q11.html


    External links

    Nomenclature
    HGNC (Hugo)NDRG2   14460
    Cards
    AtlasNDRG2ID41513ch14q11
    Entrez_Gene (NCBI)NDRG2  57447  NDRG family member 2
    AliasesSYLD
    GeneCards (Weizmann)NDRG2
    Ensembl hg19 (Hinxton)ENSG00000165795 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000165795 [Gene_View]  chr14:21016763-21070872 [Contig_View]  NDRG2 [Vega]
    ICGC DataPortalENSG00000165795
    TCGA cBioPortalNDRG2
    AceView (NCBI)NDRG2
    Genatlas (Paris)NDRG2
    WikiGenes57447
    SOURCE (Princeton)NDRG2
    Genetics Home Reference (NIH)NDRG2
    Genomic and cartography
    GoldenPath hg38 (UCSC)NDRG2  -     chr14:21016763-21070872 -  14q11.2   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)NDRG2  -     14q11.2   [Description]    (hg19-Feb_2009)
    EnsemblNDRG2 - 14q11.2 [CytoView hg19]  NDRG2 - 14q11.2 [CytoView hg38]
    Mapping of homologs : NCBINDRG2 [Mapview hg19]  NDRG2 [Mapview hg38]
    OMIM605272   
    Gene and transcription
    Genbank (Entrez)###############################################################################################################################################################################################################################################################
    RefSeq transcript (Entrez)NM_001282211 NM_001282212 NM_001282213 NM_001282214 NM_001282215 NM_001282216 NM_001320329 NM_016250 NM_201535 NM_201536 NM_201537 NM_201538 NM_201539 NM_201540 NM_201541
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)NDRG2
    Cluster EST : UnigeneHs.525205 [ NCBI ]
    CGAP (NCI)Hs.525205
    Alternative Splicing GalleryENSG00000165795
    Gene ExpressionNDRG2 [ NCBI-GEO ]   NDRG2 [ EBI - ARRAY_EXPRESS ]   NDRG2 [ SEEK ]   NDRG2 [ MEM ]
    Gene Expression Viewer (FireBrowse)NDRG2 [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)57447
    GTEX Portal (Tissue expression)NDRG2
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ9UN36   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ9UN36  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ9UN36
    Splice isoforms : SwissVarQ9UN36
    PhosPhoSitePlusQ9UN36
    Domains : Interpro (EBI)AB_hydrolase    NDRG    NDRG2   
    Domain families : Pfam (Sanger)Ndr (PF03096)   
    Domain families : Pfam (NCBI)pfam03096   
    Conserved Domain (NCBI)NDRG2
    DMDM Disease mutations57447
    Blocks (Seattle)NDRG2
    PDB (SRS)2XMQ    2XMR    2XMS   
    PDB (PDBSum)2XMQ    2XMR    2XMS   
    PDB (IMB)2XMQ    2XMR    2XMS   
    PDB (RSDB)2XMQ    2XMR    2XMS   
    Structural Biology KnowledgeBase2XMQ    2XMR    2XMS   
    SCOP (Structural Classification of Proteins)2XMQ    2XMR    2XMS   
    CATH (Classification of proteins structures)2XMQ    2XMR    2XMS   
    SuperfamilyQ9UN36
    Human Protein AtlasENSG00000165795
    Peptide AtlasQ9UN36
    HPRD17630
    IPI###############################################################################################################################################################################################################################################################   
    Protein Interaction databases
    DIP (DOE-UCLA)Q9UN36
    IntAct (EBI)Q9UN36
    FunCoupENSG00000165795
    BioGRIDNDRG2
    STRING (EMBL)NDRG2
    ZODIACNDRG2
    Ontologies - Pathways
    QuickGOQ9UN36
    Ontology : AmiGOnegative regulation of cytokine production  molecular_function  protein binding  nucleus  Golgi apparatus  cytosol  regulation of vascular endothelial growth factor production  Wnt signaling pathway  substantia nigra development  cell differentiation  growth cone  perinuclear region of cytoplasm  negative regulation of smooth muscle cell proliferation  extracellular exosome  negative regulation of ERK1 and ERK2 cascade  regulation of platelet-derived growth factor production  
    Ontology : EGO-EBInegative regulation of cytokine production  molecular_function  protein binding  nucleus  Golgi apparatus  cytosol  regulation of vascular endothelial growth factor production  Wnt signaling pathway  substantia nigra development  cell differentiation  growth cone  perinuclear region of cytoplasm  negative regulation of smooth muscle cell proliferation  extracellular exosome  negative regulation of ERK1 and ERK2 cascade  regulation of platelet-derived growth factor production  
    NDEx NetworkNDRG2
    Atlas of Cancer Signalling NetworkNDRG2
    Wikipedia pathwaysNDRG2
    Orthology - Evolution
    OrthoDB57447
    GeneTree (enSembl)ENSG00000165795
    Phylogenetic Trees/Animal Genes : TreeFamNDRG2
    HOVERGENQ9UN36
    HOGENOMQ9UN36
    Homologs : HomoloGeneNDRG2
    Homology/Alignments : Family Browser (UCSC)NDRG2
    Gene fusions - Rearrangements
    Fusion : MitelmanNDRG2/KIF3A [14q11.2/5q31.1]  
    Fusion : MitelmanNDRG2/RABEP1 [14q11.2/17p13.2]  [t(14;17)(q11;p13)]  
    Fusion : MitelmanNDRG2/SEC63 [14q11.2/6q21]  [t(6;14)(q21;q11)]  
    Fusion: TCGANDRG2 14q11.2 KIF3A 5q31.1 LGG
    Fusion: TCGANDRG2 14q11.2 RABEP1 17p13.2 LGG
    Fusion: TCGANDRG2 14q11.2 SEC63 6q21 LGG
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerNDRG2 [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)NDRG2
    dbVarNDRG2
    ClinVarNDRG2
    1000_GenomesNDRG2 
    Exome Variant ServerNDRG2
    ExAC (Exome Aggregation Consortium)NDRG2 (select the gene name)
    Genetic variants : HAPMAP57447
    Genomic Variants (DGV)NDRG2 [DGVbeta]
    DECIPHERNDRG2 [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisNDRG2 
    Mutations
    ICGC Data PortalNDRG2 
    TCGA Data PortalNDRG2 
    Broad Tumor PortalNDRG2
    OASIS PortalNDRG2 [ Somatic mutations - Copy number]
    Somatic Mutations in Cancer : COSMICNDRG2  [overview]  [genome browser]  [tissue]  [distribution]  
    Mutations and Diseases : HGMDNDRG2
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    BioMutasearch NDRG2
    DgiDB (Drug Gene Interaction Database)NDRG2
    DoCM (Curated mutations)NDRG2 (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)NDRG2 (select a term)
    intoGenNDRG2
    NCG5 (London)NDRG2
    Cancer3DNDRG2(select the gene name)
    Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM605272   
    Orphanet
    MedgenNDRG2
    Genetic Testing Registry NDRG2
    NextProtQ9UN36 [Medical]
    TSGene57447
    GENETestsNDRG2
    Target ValidationNDRG2
    Huge Navigator NDRG2 [HugePedia]
    snp3D : Map Gene to Disease57447
    BioCentury BCIQNDRG2
    ClinGenNDRG2
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD57447
    Chemical/Pharm GKB GenePA31483
    Clinical trialNDRG2
    Miscellaneous
    canSAR (ICR)NDRG2 (select the gene name)
    Probes
    Litterature
    PubMed117 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineNDRG2
    EVEXNDRG2
    GoPubMedNDRG2
    iHOPNDRG2
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

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    indexed on : Wed Jun 7 12:09:20 CEST 2017

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