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GLIS2 (GLIS family zinc finger 2)

Written2013-04Clarisse Thiollier
Gustave Roussy Institute, Villejuif, France

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)NPHP7
Other aliasNKL
HGNC (Hugo) GLIS2
LocusID (NCBI) 84662
Atlas_Id 44598
Location 16p13.3  [Link to chromosome band 16p13]
Location_base_pair Starts at 4364762 and ends at 4389598 bp from pter ( according to hg19-Feb_2009)  [Mapping GLIS2.png]
Fusion genes
(updated 2016)
CBFA2T3 (16q24.3) / GLIS2 (16p13.3)GLIS2 (16p13.3) / EIF1AX (Xp22.12)GLIS2 (16p13.3) / PHF21A (11p11.2)
PHF21A (11p11.2) / GLIS2 (16p13.3)

DNA/RNA

Note Size: 7383 b; 6 coding exons.
Transcription 2 transcripts: 3,7 kb RNA and 4,469 kb RNA (Ensembl).

Protein

Note 524 amino acids; molecular weight: 55,688 kD.
Member of the Krüppel-like zinc finger proteins family, forming a subfamily with Glis1 and Glis3 closely related to Gli and Zic protein families.
Description Similarly to Gli and Zic proteins, Glis2 contains 5 Cys2-His2 zinc finger motifs separated by a conserved consensus region T/SGEKPY/FX (Zhang et al., 2002).
Expression In mouse tissues: high expression level of Glis2 in kidney, moderate level in heart, lung, low level in prostate, brain, colon (Zhang et al., 2002).
In rat embryos: high expression in embryonic kidneys (particularly within the ureteric bud in 16-dpc and 19-dpc rat).
Expression of Glis2 detected in caudal somites and in the neural tubes of 13-dpc in rat embryos (Zhang et al., 2002); high expression level in neural tube in Xenopus, mouse and chick embryos (Lamar et al., 2001).
In human: GLIS2 mRNA is highly expressed in kidney, low level in heart, lung and placenta (Zhang and Jetten, 2001).
Localisation Nuclear localization (Zhang et al., 2002); the 3rd Zinc Finger motif contains a region required for the nuclear localization (Vasanth et al., 2011).
Function Krüppel-like zinc finger family proteins can act as activator or repressor of gene transcription. They are involved in regulation of embryonic development and various physiological mechanisms in adults (Dang et al., 2000).
Kang and colleagues described the regulation of gene expression by Glis1-3 through the interaction with transcriptional mediators that are recruited by specific repressor and activation domains within the respective Glis protein.
According to cell context, Glis2 can thus act as a transcriptional activator or repressor. Glis2 is especially implicated in the maintenance of normal kidney structure and function; both activation and repression roles are involved during embryonic development and adult kidney (Zhang et al., 2002; Attanasio et al., 2007).
GLIS2 has also been described as NKL (neuronal Krüppel-like protein): NKL is broadly expressed in the neural tube and peripheral nervous system when neural precursors are differentiating. NKL is implicated in neurogenesis, promoting neuronal differentiation (Lamar et al., 2001).
In mice, Zhang and colleagues (Zhang et al., 2002) highlighted the presence of an activation domain located between Gly71 and Gly137. Two repressor domains were identified: one is located between Ser148 and Arg171 and the other is located within the first zinc finger motif. CtBP1 (C-terminal binding protein 1) and HDAC3 (histone deacetylase 3) are two co-repressor recruited by Glis2 for its repression activity, though a repression complex (Kim et al., 2005).
Homology GLI proteins are homologous of Cubitus interruptus (Ci) in Drosophila melanogaster which plays an important role in wing development. Ci and GLI are involved in Sonic-Hedgehog pathway in Dosophila and vertebrates. (Zhang and Jetten, 2001).
Glis2 shows high homologies with Gli and Zic Krüppel-like protein families.
In mice highest homology is observed in the zinc finger motifs: 57%, 56%, 56% and 49% homology with Gli1, Gli2, Gli3 and Zic1 respectively. 3rd and 5th zinc finger domains show the highest homology with Gli proteins (70 and 88% homology) (Zhang et al., 2002).
In human: highest homology is observed with GLI1: 58% between Zinc Finger domains. 3rd, 4th and 5th Zinc Finger show the highest homology: 65-80% homology when compared to those of GLI and ZIC proteins (Zhang and Jetten, 2001).
This suggests that Glis2 interacts with DNA in the way Gli and Zic proteins do (Zhang et al., 2002).
In both human and mouse, little homology with Gli and Zic protein family is observed outside the zinc finger domain, which show that Glis2 belongs to another subfamily of Krüppel-like zinc finger proteins (Zhang et al., 2002; Zhang and Jetten, 2001).

Implicated in

Note
  
Entity Acute megakaryoblastic leukemia (AMKL, AML-M7 (FAB classification))
Note CBFA2T3-GLIS2 or ETO2-GLIS2 fusion oncogene (Thiollier et al., 2012; Gruber et al., 2012; Masetti et al., 2013).
For the first time, GLIS2 has been implicated in the haematological context. GLIS2 is indeed not expressed in normal hematopoietic cells. Its fusion to CBFA2T3 leads to the expression of GLIS2 in blasts.
Prognosis Worse overall survival at 5 years than other pediatric AMKL patients.
Cytogenetics The ETO2-GLIS2 fusion oncogene results from a chromosomal inversion inv(16)(p13.3q24.3). This is a cryptic inversion not visible by on a karyotype.
Abnormal Protein Different fusions points have been described: 1) between exon 11 of CBFA2T3 and exon 3 of GLIS2 (most frequent); 2) between exon 10 of CBFA2T3 and exon 2 of GLIS2; 3) between exon 12 of CBFA2T3 and exon 1 of GLIS2. All fusion proteins are predicted to contain the GLIS2 DNA binding C-terminal Zinc Finger domains and the three CBFA2T3 N-terminal nervy homology regions that mediate protein interactions.
  
  
Entity Nephronophthisis (NPHP)
Disease Nephronophthisis, an autosomal recessive kidney disease.
Cytogenetics Mutation in GLIS2 gene: homozygous transversion IVS5+1G>T that leads to an abrogation of the obligatory splice site and to a non-functional protein. This mutation defines a new cause of NPHP (Attanasio et al., 2007).
  

Bibliography

Loss of GLIS2 causes nephronophthisis in humans and mice by increased apoptosis and fibrosis.
Attanasio M, Uhlenhaut NH, Sousa VH, O'Toole JF, Otto E, Anlag K, Klugmann C, Treier AC, Helou J, Sayer JA, Seelow D, Nurnberg G, Becker C, Chudley AE, Nurnberg P, Hildebrandt F, Treier M.
Nat Genet. 2007 Aug;39(8):1018-24. Epub 2007 Jul 8.
PMID 17618285
 
The biology of the mammalian Kruppel-like family of transcription factors.
Dang DT, Pevsner J, Yang VW.
Int J Biochem Cell Biol. 2000 Nov-Dec;32(11-12):1103-21. (REVIEW)
PMID 11137451
 
An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia.
Gruber TA, Larson Gedman A, Zhang J, Koss CS, Marada S, Ta HQ, Chen SC, Su X, Ogden SK, Dang J, Wu G, Gupta V, Andersson AK, Pounds S, Shi L, Easton J, Barbato MI, Mulder HL, Manne J, Wang J, Rusch M, Ranade S, Ganti R, Parker M, Ma J, Radtke I, Ding L, Cazzaniga G, Biondi A, Kornblau SM, Ravandi F, Kantarjian H, Nimer SD, Dohner K, Dohner H, Ley TJ, Ballerini P, Shurtleff S, Tomizawa D, Adachi S, Hayashi Y, Tawa A, Shih LY, Liang DC, Rubnitz JE, Pui CH, Mardis ER, Wilson RK, Downing JR.
Cancer Cell. 2012 Nov 13;22(5):683-97. doi: 10.1016/j.ccr.2012.10.007.
PMID 23153540
 
Kruppel-like zinc finger protein Gli-similar 2 (Glis2) represses transcription through interaction with C-terminal binding protein 1 (CtBP1).
Kim SC, Kim YS, Jetten AM.
Nucleic Acids Res. 2005 Dec 2;33(21):6805-15. Print 2005.
PMID 16326862
 
Identification of NKL, a novel Gli-Kruppel zinc-finger protein that promotes neuronal differentiation.
Lamar E, Kintner C, Goulding M.
Development. 2001 Apr;128(8):1335-46.
PMID 11262234
 
CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype.
Masetti R, Pigazzi M, Togni M, Astolfi A, Indio V, Manara E, Casadio R, Pession A, Basso G, Locatelli F.
Blood. 2013 Apr 25;121(17):3469-72. doi: 10.1182/blood-2012-11-469825. Epub 2013 Feb 13.
PMID 23407549
 
Characterization of novel genomic alterations and therapeutic approaches using acute megakaryoblastic leukemia xenograft models.
Thiollier C, Lopez CK, Gerby B, Ignacimouttou C, Poglio S, Duffourd Y, Guegan J, Rivera-Munoz P, Bluteau O, Mabialah V, Diop M, Wen Q, Petit A, Bauchet AL, Reinhardt D, Bornhauser B, Gautheret D, Lecluse Y, Landman-Parker J, Radford I, Vainchenker W, Dastugue N, de Botton S, Dessen P, Bourquin JP, Crispino JD, Ballerini P, Bernard OA, Pflumio F, Mercher T.
J Exp Med. 2012 Oct 22;209(11):2017-31. doi: 10.1084/jem.20121343. Epub 2012 Oct 8.
PMID 23045605
 
Identification of nuclear localization, DNA binding, and transactivating mechanisms of Kruppel-like zinc finger protein Gli-similar 2 (Glis2).
Vasanth S, ZeRuth G, Kang HS, Jetten AM.
J Biol Chem. 2011 Feb 11;286(6):4749-59. doi: 10.1074/jbc.M110.165951. Epub 2010 Dec 2.
PMID 21127075
 
Genomic structure of the gene encoding the human GLI-related, Kruppel-like zinc finger protein GLIS2.
Zhang F, Jetten AM.
Gene. 2001 Dec 12;280(1-2):49-57.
PMID 11738817
 
Characterization of Glis2, a novel gene encoding a Gli-related, Kruppel-like transcription factor with transactivation and repressor functions. Roles in kidney development and neurogenesis.
Zhang F, Nakanishi G, Kurebayashi S, Yoshino K, Perantoni A, Kim YS, Jetten AM.
J Biol Chem. 2002 Mar 22;277(12):10139-49. Epub 2001 Dec 12.
PMID 11741991
 

Citation

This paper should be referenced as such :
Thiollier, C
GLIS2 (GLIS family zinc finger 2)
Atlas Genet Cytogenet Oncol Haematol. 2013;17(10):687-688.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/GLIS2ID44598ch16p13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  inv(16)(p13q24) CBFA2T3/GLIS2


External links

Nomenclature
HGNC (Hugo)GLIS2   29450
Cards
AtlasGLIS2ID44598ch16p13
Entrez_Gene (NCBI)GLIS2  84662  GLIS family zinc finger 2
AliasesNKL; NPHP7
GeneCards (Weizmann)GLIS2
Ensembl hg19 (Hinxton)ENSG00000126603 [Gene_View]  chr16:4364762-4389598 [Contig_View]  GLIS2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000126603 [Gene_View]  chr16:4364762-4389598 [Contig_View]  GLIS2 [Vega]
ICGC DataPortalENSG00000126603
TCGA cBioPortalGLIS2
AceView (NCBI)GLIS2
Genatlas (Paris)GLIS2
WikiGenes84662
SOURCE (Princeton)GLIS2
Genetics Home Reference (NIH)GLIS2
Genomic and cartography
GoldenPath hg19 (UCSC)GLIS2  -     chr16:4364762-4389598 +  16p13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)GLIS2  -     16p13.3   [Description]    (hg38-Dec_2013)
EnsemblGLIS2 - 16p13.3 [CytoView hg19]  GLIS2 - 16p13.3 [CytoView hg38]
Mapping of homologs : NCBIGLIS2 [Mapview hg19]  GLIS2 [Mapview hg38]
OMIM608539   611498   
Gene and transcription
Genbank (Entrez)AF325914 AK095566 AK096936 AK124985 AK126918
RefSeq transcript (Entrez)NM_001318918 NM_032575
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_016391 NT_010393 NT_187608 NW_004929400
Consensus coding sequences : CCDS (NCBI)GLIS2
Cluster EST : UnigeneHs.592087 [ NCBI ]
CGAP (NCI)Hs.592087
Alternative Splicing GalleryENSG00000126603
Gene ExpressionGLIS2 [ NCBI-GEO ]   GLIS2 [ EBI - ARRAY_EXPRESS ]   GLIS2 [ SEEK ]   GLIS2 [ MEM ]
Gene Expression Viewer (FireBrowse)GLIS2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)84662
GTEX Portal (Tissue expression)GLIS2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BZE0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BZE0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BZE0
Splice isoforms : SwissVarQ9BZE0
PhosPhoSitePlusQ9BZE0
Domaine pattern : Prosite (Expaxy)ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)GLIS2
DMDM Disease mutations84662
Blocks (Seattle)GLIS2
SuperfamilyQ9BZE0
Human Protein AtlasENSG00000126603
Peptide AtlasQ9BZE0
HPRD12256
IPIIPI00000274   IPI00884094   
Protein Interaction databases
DIP (DOE-UCLA)Q9BZE0
IntAct (EBI)Q9BZE0
FunCoupENSG00000126603
BioGRIDGLIS2
STRING (EMBL)GLIS2
ZODIACGLIS2
Ontologies - Pathways
QuickGOQ9BZE0
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  protein binding  nucleus  cytoplasm  transcription from RNA polymerase II promoter  nervous system development  nuclear speck  cell differentiation  negative regulation of sequence-specific DNA binding transcription factor activity  transcription regulatory region DNA binding  negative regulation of smoothened signaling pathway  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  protein binding  nucleus  cytoplasm  transcription from RNA polymerase II promoter  nervous system development  nuclear speck  cell differentiation  negative regulation of sequence-specific DNA binding transcription factor activity  transcription regulatory region DNA binding  negative regulation of smoothened signaling pathway  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  
NDEx NetworkGLIS2
Atlas of Cancer Signalling NetworkGLIS2
Wikipedia pathwaysGLIS2
Orthology - Evolution
OrthoDB84662
GeneTree (enSembl)ENSG00000126603
Phylogenetic Trees/Animal Genes : TreeFamGLIS2
HOVERGENQ9BZE0
HOGENOMQ9BZE0
Homologs : HomoloGeneGLIS2
Homology/Alignments : Family Browser (UCSC)GLIS2
Gene fusions - Rearrangements
Fusion : MitelmanCBFA2T3/GLIS2 [16q24.3/16p13.3]  [inv(16)(p13q24)]  
Fusion : MitelmanGLIS2/PHF21A [16p13.3/11p11.2]  [t(11;16)(p11;p13)]  
Fusion : MitelmanPHF21A/GLIS2 [11p11.2/16p13.3]  [t(11;16)(p11;p13)]  
Fusion : COSMICCBFA2T3 [16q24.3]  -  GLIS2 [16p13.3]  [fusion_2287]  [fusion_2288]  [fusion_2289]  [fusion_2290]  [fusion_2293]  [fusion_2295]  [fusion_2296]  
Fusion: TCGAPHF21A 11p11.2 GLIS2 16p13.3 HNSC LAML
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerGLIS2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)GLIS2
dbVarGLIS2
ClinVarGLIS2
1000_GenomesGLIS2 
Exome Variant ServerGLIS2
ExAC (Exome Aggregation Consortium)GLIS2 (select the gene name)
Genetic variants : HAPMAP84662
Genomic Variants (DGV)GLIS2 [DGVbeta]
DECIPHER (Syndromes)16:4364762-4389598  ENSG00000126603
CONAN: Copy Number AnalysisGLIS2 
Mutations
ICGC Data PortalGLIS2 
TCGA Data PortalGLIS2 
Broad Tumor PortalGLIS2
OASIS PortalGLIS2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICGLIS2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDGLIS2
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
LOVD (Leiden Open Variation Database)Eye diseases - LOVD
BioMutasearch GLIS2
DgiDB (Drug Gene Interaction Database)GLIS2
DoCM (Curated mutations)GLIS2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)GLIS2 (select a term)
intoGenGLIS2
NCG5 (London)GLIS2
Cancer3DGLIS2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608539    611498   
Orphanet21935    12427   
MedgenGLIS2
Genetic Testing Registry GLIS2
NextProtQ9BZE0 [Medical]
TSGene84662
GENETestsGLIS2
Huge Navigator GLIS2 [HugePedia]
snp3D : Map Gene to Disease84662
BioCentury BCIQGLIS2
ClinGenGLIS2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD84662
Chemical/Pharm GKB GenePA134919876
Clinical trialGLIS2
Miscellaneous
canSAR (ICR)GLIS2 (select the gene name)
Probes
Litterature
PubMed16 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineGLIS2
EVEXGLIS2
GoPubMedGLIS2
iHOPGLIS2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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