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PSIP1 (PC4 and SFRS1 interacting protein 1)

Written2007-03Cristina Morerio, Claudio Panarello
Dipartimento di Ematologia ed Oncologia Pediatrica, IRCCS Istituto Giannina Gaslini, Largo G. Gaslini 5, 16147 Genoa, Italy

(Note : for Links provided by Atlas : click)

Identity

Other namesLEDGF (lens epithelium-derived growth factor)
p75
p52
HGNC (Hugo) PSIP1
LocusID (NCBI) 11168
Atlas_Id 405
Location 9p22.3  [Link to chromosome band 9p22]
Location_base_pair Starts at 15464065 and ends at 15511017 bp from pter ( according to hg19-Feb_2009)  [Mapping PSIP1.png]
Fusion genes
(updated 2016)
LYRM4 (6p25.1) / PSIP1 (9p22.3)NUP98 (11p15.4) / PSIP1 (9p22.3)PSIP1 (9p22.3) / MYL6 (12q13.2)
PSIP1 (9p22.3) / NUP98 (11p15.4)PSIP1 (9p22.3) / PSIP1 (9p22.3)QPCTL (19q13.32) / PSIP1 (9p22.3)

DNA/RNA

Description The gene contains at least 15 exons and 14 introns.
Transcription Two alternative splice variants: p75 and p52.

Protein

Description 530 amino acids (p75), 333 amino acids (p52); N-term - PWWP (proline-tryptophan-tryptophan-proline) domain   NLS (nuclear localization signal)   AT-hook-like   Coiled coil   IBD (integrase binding domain)   HTH1 (helix-turn-helix DNA binding motif)   HTH2   C-term.
Expression Expression of PSIP1 has been reported to be increased in human breast and bladder cancer, prostate tumorsand benign prostate hyperplasia.
Localisation nuclear.
Function Transcriptional regulation of stress-associated genes, mRNA splicing and cell survival. The involvement of PSIP1 (LEDGF) has been reported in human immunodeficiency virus type-1 (HIV-1) integration, autoimmune disorders, and neurogenesis. Recent data reveal LEDGF as an oncogenic protein that controls a caspase-independent lysosomal cell death pathway.
Homology PSIP1 belongs to the hepatoma-derived growth factor (HDGF) family of proteins that contain a well conserved N-terminal amino acid sequence known as the HATH (homologous to amino terminus of HDGF) region.

Implicated in

Note
Entity t(9;11)(p22;p15) NUP98-PSIP1
Note acute non lymphoblastic leukemia (AML), one case of transformed .
Hybrid/Mutated Gene 5'NUP98 - 3'PSIP1.
Abnormal Protein fuses the GLFG repeat domains of NUP98 to the COOH-terminus of PSIP1.
  

Bibliography

t(9;11)(p22;p15) in acute myeloid leukemia results in a fusion between NUP98 and the gene encoding transcriptional coactivators p52 and p75-lens epithelium-derived growth factor (LEDGF).
Ahuja HG, Hong J, Aplan PD, Tcheurekdjian L, Forman SJ, Slovak ML
Cancer research. 2000 ; 60 (22) : 6227-6229.
PMID 11103774
 
Lens epithelium-derived growth factor (LEDGF/p75) and p52 are derived from a single gene by alternative splicing.
Singh DP, Kimura A, Chylack LT Jr, Shinohara T
Gene. 2000 ; 242 (1-2) : 265-273.
PMID 10721720
 
Fusion of the NUP98 gene with the LEDGF/p52 gene defines a recurrent acute myeloid leukemia translocation.
Hussey DJ, Moore S, Nicola M, Dobrovic A
BMC genetics. 2001 ; 2 : page 20.
PMID 11737860
 
Caspase cleavage of the nuclear autoantigen LEDGF/p75 abrogates its pro-survival function: implications for autoimmunity in atopic disorders.
Wu X, Daniels T, Molinaro C, Lilly MB, Casiano CA
Cell death and differentiation. 2002 ; 9 (9) : 915-925.
PMID 12181742
 
HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells.
Cherepanov P, Maertens G, Proost P, Devreese B, Van Beeumen J, Engelborghs Y, De Clercq E, Debyser Z
The Journal of biological chemistry. 2003 ; 278 (1) : 372-381.
PMID 12407101
 
Antinuclear autoantibodies in prostate cancer: immunity to LEDGF/p75, a survival protein highly expressed in prostate tumors and cleaved during apoptosis.
Daniels T, Zhang J, Gutierrez I, Elliot ML, Yamada B, Heeb MJ, Sheets SM, Wu X, Casiano CA
The Prostate. 2005 ; 62 (1) : 14-26.
PMID 15389814
 
NUP98-LEDGF fusion and t(9;11) in transformed chronic myeloid leukemia.
Grand FH, Koduru P, Cross NC, Allen SL
Leukemia research. 2005 ; 29 (12) : 1469-1472.
PMID 15982735
 
t(9;11)(p22;p15) with NUP98-LEDGF fusion gene in pediatric acute myeloid leukemia.
Morerio C, Acquila M, Rosanda C, Rapella A, Tassano E, Micalizzi C, Panarello C
Leukemia research. 2005 ; 29 (4) : 467-470.
PMID 15725483
 
DNA binding domains and nuclear localization signal of LEDGF: contribution of two helix-turn-helix (HTH)-like domains and a stretch of 58 amino acids of the N-terminal to the trans-activation potential of LEDGF.
Singh DP, Kubo E, Takamura Y, Shinohara T, Kumar A, Chylack LT Jr, Fatma N
Journal of molecular biology. 2006 ; 355 (3) : 379-394.
PMID 16318853
 
Disruption of Ledgf/Psip1 results in perinatal mortality and homeotic skeletal transformations.
Sutherland HG, Newton K, Brownstein DG, Holmes MC, Kress C, Semple CA, Bickmore WA
Molecular and cellular biology. 2006 ; 26 (19) : 7201-7210.
PMID 16980622
 
Lens epithelium-derived growth factor is an Hsp70-2 regulated guardian of lysosomal stability in human cancer.
Daugaard M, Kirkegaard-S&oring;rensen T, Ostenfeld MS, Aaboe M, H&oring;yer-Hansen M, Orntoft TF, Rohde M, Jäättelä M
Cancer research. 2007 ; 67 (6) : 2559-2567.
PMID 17363574
 

Citation

This paper should be referenced as such :
Panarello, C ; Morerio, C
PSIP1 (PC4, SFRS1 interacting protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(3):237-238.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PSIP1ID405ch9q22.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(4;11)(q21;p15) NUP98/RAP1GDS1
t(9;11)(p22;p15) NUP98/PSIP1

External links

Nomenclature
HGNC (Hugo)PSIP1   9527
Cards
AtlasPSIP1ID405ch9q22
Entrez_Gene (NCBI)PSIP1  11168  PC4 and SFRS1 interacting protein 1
AliasesDFS70; LEDGF; PAIP; PSIP2; 
p52; p75
GeneCards (Weizmann)PSIP1
Ensembl hg19 (Hinxton)ENSG00000164985 [Gene_View]  chr9:15464065-15511017 [Contig_View]  PSIP1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000164985 [Gene_View]  chr9:15464065-15511017 [Contig_View]  PSIP1 [Vega]
ICGC DataPortalENSG00000164985
TCGA cBioPortalPSIP1
AceView (NCBI)PSIP1
Genatlas (Paris)PSIP1
WikiGenes11168
SOURCE (Princeton)PSIP1
Genomic and cartography
GoldenPath hg19 (UCSC)PSIP1  -     chr9:15464065-15511017 -  9p22.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PSIP1  -     9p22.2   [Description]    (hg38-Dec_2013)
EnsemblPSIP1 - 9p22.2 [CytoView hg19]  PSIP1 - 9p22.2 [CytoView hg38]
Mapping of homologs : NCBIPSIP1 [Mapview hg19]  PSIP1 [Mapview hg38]
OMIM603620   
Gene and transcription
Genbank (Entrez)AF063020 AF098482 AF098483 AF432220 AK096405
RefSeq transcript (Entrez)NM_001128217 NM_001317898 NM_001317900 NM_021144 NM_033222
RefSeq genomic (Entrez)NC_000009 NC_018920 NT_008413 NW_004929342
Consensus coding sequences : CCDS (NCBI)PSIP1
Cluster EST : UnigeneHs.658434 [ NCBI ]
CGAP (NCI)Hs.658434
Alternative Splicing GalleryENSG00000164985
Gene ExpressionPSIP1 [ NCBI-GEO ]   PSIP1 [ EBI - ARRAY_EXPRESS ]   PSIP1 [ SEEK ]   PSIP1 [ MEM ]
Gene Expression Viewer (FireBrowse)PSIP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)11168
GTEX Portal (Tissue expression)PSIP1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75475 (Uniprot)
NextProtO75475  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75475
Splice isoforms : SwissVarO75475 (Swissvar)
PhosPhoSitePlusO75475
Domaine pattern : Prosite (Expaxy)PWWP (PS50812)   
Domains : Interpro (EBI)LEDGF    PWWP_dom    Treacle-like_TCS   
Domain families : Pfam (Sanger)LEDGF (PF11467)    PWWP (PF00855)   
Domain families : Pfam (NCBI)pfam11467    pfam00855   
Domain families : Smart (EMBL)PWWP (SM00293)  
DMDM Disease mutations11168
Blocks (Seattle)PSIP1
PDB (SRS)1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
PDB (PDBSum)1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
PDB (IMB)1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
PDB (RSDB)1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
Structural Biology KnowledgeBase1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
SCOP (Structural Classification of Proteins)1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
CATH (Classification of proteins structures)1Z9E    2B4J    2M16    2MSR    2MTN    2N3A    3F9K    3HPG    3HPH    3U88    3ZEH    4FU6   
SuperfamilyO75475
Human Protein AtlasENSG00000164985
Peptide AtlasO75475
HPRD04688
IPIIPI00028122   IPI00333317   IPI00643781   
Protein Interaction databases
DIP (DOE-UCLA)O75475
IntAct (EBI)O75475
FunCoupENSG00000164985
BioGRIDPSIP1
STRING (EMBL)PSIP1
ZODIACPSIP1
Ontologies - Pathways
QuickGOO75475
Ontology : AmiGOmRNA 5'-splice site recognition  RNA polymerase II transcription coactivator activity  chromatin binding  protein binding  nucleus  nucleoplasm  nucleoplasm  nuclear heterochromatin  nucleolus  cytosol  transcription, DNA-templated  regulation of transcription, DNA-templated  response to oxidative stress  response to heat  activating transcription factor binding  nuclear periphery  transcriptionally active chromatin  poly(A) RNA binding  positive regulation of transcription from RNA polymerase II promoter  nuclear transport  establishment of integrated proviral latency  supercoiled DNA binding  
Ontology : EGO-EBImRNA 5'-splice site recognition  RNA polymerase II transcription coactivator activity  chromatin binding  protein binding  nucleus  nucleoplasm  nucleoplasm  nuclear heterochromatin  nucleolus  cytosol  transcription, DNA-templated  regulation of transcription, DNA-templated  response to oxidative stress  response to heat  activating transcription factor binding  nuclear periphery  transcriptionally active chromatin  poly(A) RNA binding  positive regulation of transcription from RNA polymerase II promoter  nuclear transport  establishment of integrated proviral latency  supercoiled DNA binding  
REACTOMEO75475 [protein]
REACTOME PathwaysR-HSA-177539 Autointegration results in viral DNA circles [pathway]
REACTOME PathwaysR-HSA-180910 Vpr-mediated nuclear import of PICs [pathway]
REACTOME PathwaysR-HSA-162592 Integration of provirus [pathway]
REACTOME PathwaysR-HSA-164843 2-LTR circle formation [pathway]
REACTOME PathwaysR-HSA-175567 Integration of viral DNA into host genomic DNA [pathway]
REACTOME PathwaysR-HSA-180689 APOBEC3G mediated resistance to HIV-1 infection [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkPSIP1
Wikipedia pathwaysPSIP1
Orthology - Evolution
OrthoDB11168
GeneTree (enSembl)ENSG00000164985
Phylogenetic Trees/Animal Genes : TreeFamPSIP1
Homologs : HomoloGenePSIP1
Homology/Alignments : Family Browser (UCSC)PSIP1
Gene fusions - Rearrangements
Fusion : MitelmanNUP98/PSIP1 [11p15.4/9p22.3]  [t(9;11)(p22;p15)]  
Fusion : MitelmanPSIP1/NUP98 [9p22.3/11p15.4]  [t(9;11)(p22;p15)]  
Fusion : TICdbNUP98 [11p15.4]  -  PSIP1 [9p22.3]
Polymorphisms : SNP, variants
NCBI Variation ViewerPSIP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PSIP1
dbVarPSIP1
ClinVarPSIP1
1000_GenomesPSIP1 
Exome Variant ServerPSIP1
ExAC (Exome Aggregation Consortium)PSIP1 (select the gene name)
Genetic variants : HAPMAP11168
Genomic Variants (DGV)PSIP1 [DGVbeta]
Mutations
ICGC Data PortalPSIP1 
TCGA Data PortalPSIP1 
Broad Tumor PortalPSIP1
OASIS PortalPSIP1 [ Somatic mutations - Copy number]
Cancer Gene: CensusPSIP1 
Somatic Mutations in Cancer : COSMICPSIP1 
intOGen PortalPSIP1
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)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch PSIP1
DgiDB (Drug Gene Interaction Database)PSIP1
DoCM (Curated mutations)PSIP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PSIP1 (select a term)
intoGenPSIP1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)9:15464065-15511017  ENSG00000164985
CONAN: Copy Number AnalysisPSIP1 
Mutations and Diseases : HGMDPSIP1
OMIM603620   
MedgenPSIP1
Genetic Testing Registry PSIP1
NextProtO75475 [Medical]
TSGene11168
GENETestsPSIP1
Huge Navigator PSIP1 [HugePedia]
snp3D : Map Gene to Disease11168
BioCentury BCIQPSIP1
ClinGenPSIP1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD11168
Chemical/Pharm GKB GenePA33872
Clinical trialPSIP1
Miscellaneous
canSAR (ICR)PSIP1 (select the gene name)
Probes
Litterature
PubMed241 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePSIP1
EVEXPSIP1
GoPubMedPSIP1
iHOPPSIP1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Jun 11 13:01:02 CEST 2016

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