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PA2G4 (proliferation-associated 2G4, 38kDa)

Written2011-09Anne Hamburger, Arundhati Ghosh, Smita Awasthi
University of Maryland School of Medicine, Department of Pathology, University of Maryland Greenebaum Cancer Center, Baltimore, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesproliferation-associated 2G4, 38kD
proliferation-associated 2G4, 38kDa
Other aliasEBP1
HG4-1
ITAF45
p38-2G4
HGNC (Hugo) PA2G4
LocusID (NCBI) 5036
Atlas_Id 41628
Location 12q13.2  [Link to chromosome band 12q13]
Location_base_pair Starts at 56104319 and ends at 56113910 bp from pter ( according to hg19-Feb_2009)  [Mapping PA2G4.png]
Fusion genes
(updated 2016)
PA2G4 (12q13.2) / JAK1 (1p31.3)PA2G4 (12q13.2) / PSMA7 (20q13.33)
Note PA2G4 encodes a cell-cycle regulated protein capable of interacting with DNA, RNA and protein. The gene was isolated as a DNA binding protein (p38-2g4) (Radomski and Jost, 1995) and also as an ErbB3-interacting protein (EBP1) (Yoo et al., 2000). Two different isoforms of EBP1 play a role in cell survival, cell cycle arrest and differentiation. The long form may have an oncogenic function when overexpressed, and the short form acts as a tumor suppressor (Liu et al., 2006). EPB1 also functions as a transcriptional repressor of E2F1-regulated genes (Zhang et al., 2004) and the androgen receptor (AR) (Zhang et al., 2005) through its interactions with histone deacetylases and Sin3A.

DNA/RNA

 
  The alignment of PA2G4 mRNA to its genomic sequence.
Description The PA2G4 gene contains 13 exons. The sizes of the exons 1-13 are 88, 128, 105, 69, 92, 63, 78, 78, 133, 94, 127, 53 and 65 bp (to the stop codon). Exon 1 contains the translation initiation ATG. Exon 13 contains the stop codon.
Transcription The human PA2G4 promoter contains several putative transcription factor binding sites. The major transcript length is 2643 nt. Two proteins are translated due to alternative splicing (Liu et al., 2006). An alternatively spliced version missing 29 NT between the first and third ATGs has been observed.
The PA2G4 promoter contains two tandem DNA elements that bind E2F1. E2F1 increases endogenous EBP1 mRNA levels in cancer cells, but decreases EBP1 mRNA abundance in non transformed cells (Judah et al., 2010).
Pseudogene Six pseudogenes, located on chromosomes 3, 6, 9, 18, 20 and X, have been identified.

Protein

 
  The linear schematic of EBP1. Functional domains, including Nucleolar Localization Signal (NuLS), σ70 RNA binding region (σ70), amphipathic helical domain (AHD), LXXLL nuclear receptor binding motif (LX) and demonstrated in vivo phosphorylation sites (*).
Description p38-2G4 was initially isolated as a DNA binding protein from mouse Ehrlich ascites cells (Radomski and Jost, 1995). The MW of this protein is predicted to be 38058 D, consisting of 340 amino acids. The human orthologue EBP1 was later identified as an ErbB3 binding protein of the same MW as the mouse protein (Yoo et al., 2000). This form migrates at approximately 42 kD in SDS-PAGE gels. Later, a larger 394 amino acid form (predicted MW 43787 D, migrating at 48 kD) was observed in mammalian cells (Xia et al., 2001). The two forms have been demonstrated to be the result of alternative splicing (Liu et al., 2006) or usage of alternative translation initiation sites (Xia et al., 2001). Amino acids 1-48 are required for nucleolar localization and the C terminal domain (aa 364-394) is required for interactions with nucleic acids (Moonie et al., 2007) and protein (Zhang et al., 2002).
EBP1 is post translationally modified at several phosphorylation sites (Ser 360 (Ahn et al., 2006), Ser 363 (Akinmade et al., 2007) and Thr 261 (Akinmade et al., 2008)) in vivo. The protein stability of the short form is regulated by ubiquitination (Liu et al., 2009). The short form is also sumoylated by the TLF/FUS E3 ligase and this sumoylation is required for the anti-proliferative effects of EBP1 (Oh et al., 2010).
The crystal structure of both murine (Monie et al., 2007) and human (Kowalinski et al., 2007) EBP1 has been solved. There is a core domain that is homologous to methionine aminopeptidases, although no enzymatic activity has been reported. The C terminal domain containing a Lys-rich nuclear hormone receptor binding motif (LKALL) was reported to mediate RNA binding (Monie et al., 2007).
Expression EBP1 has been found to be ubiquitously expressed with high expression levels in skeletal muscle (Yoo et al., 2000).
Localisation Under logarithmically growing conditions in cell culture, EBP1 localizes to the nucleolus and the cytoplasm (Xia et al., 2001; Squatrito et al., 2004). Upon stimulation with the ErbB3 ligand heregulin, the short form of EBP1 is recruited to the nucleus in AU565 breast cancer cells (Yoo et al., 2000). Sumoylation is required for nuclear translocation (Oh et al., 2010). In primary normal epithelial cells, EBP1 is confined to the cytoplasm (Zhang et al., 2008b).
Function EBP1 was initially isolated as a cell cycle-regulated DNA binding protein (Radomski and Jost, 1995) and has been shown to induce cell cycle arrest in the G2/M phase of the cell cycle (Zhang et al., 2005). EBP1 acts as a corepressor for several proliferation-associated genes including Cyclin D1, E2F1 (Zhang and Hamburger, 2004) and the androgen receptor (Zhang et al., 2005). EBP1 inhibits transcription of these genes by recruiting HDAC2 via Sin3A to the E2F1 and AR-regulated promoters (Zhang et al., 2005). EBP1 interacts with RB1 and the interaction is enhanced upon EBP1 dephosphorylation (Xia et al., 2001).
EBP1 was isolated as an ErbB3 binding protein using a yeast-two hybrid screen (Yoo et al., 2000). The interactions of EBP1 with ErbB3 is disrupted by the ErbB3 ligand heregulin, leading to EBP1 nuclear translocation. This leads to the eventual inhibition of heregulin-stimulated proliferation, presumably due to the repression of proliferation associated genes (Zhang et al., 2008a).
EBP1 also binds RNA and associates with 28S, 18S and 5.8S mature rRNAs, several rRNA precursors and probably U3 small nucleolar RNA. It has been implicated in the regulation of intermediate and late steps of rRNA processing (Squatrito et al., 2004; Squatrito et al., 2006). EBP1 also mediates cap-independent translation of specific viral IRES (internal ribosome entry site) (Pilipenko et al., 2000). EBP1 regulates translation of AR mRNA (Zhou et al., 2010).
EBP1 has also been implicated in protein stability via its interaction with the proteasome. Overexpression of EBP1 results in decreased stability of ErbB2 protein in breast cancer cells via a proteasome-mediated pathway (Lu et al., 2011). The long form of EBP1 binds to the p53 E3 ligase HDM2, enhancing HDM2-p53 interactions and promoting p53 degradation (Kim et al., 2011).
The long (p48) and short (p42) forms of EBP1 have opposing biological effects, with the longer form inducing cell survival and the shorter form inhibiting cell growth (Liu et al., 2006). The long form binds HDM2, promoting degradation of p53 (Kim et al., 2010).
Homology Similar (30% identity) to the 42 kDA DNA binding protein SF00553 in S. pombe yeast (Yamada et al., 1994) and StEBP1 in potato (Horvath et al., 2006). The orthologue in potatoes (StEBP1) has 69% sequence similarity to human EBP1 and can inhibit growth of human breast cancer cell lines and E2F1 expression in these cells.

Mutations

Germinal No mutations in the PA2G4 gene have been reported.
Somatic None reported.

Implicated in

Note
  
Entity Prostate cancer
Prognosis Decreased expression of EBP1 is associated with higher tumor grade and metastasis in prostate cancer (Zhang et al., 2008b). However, another study indicated EBP1 expression increased with disease progression (Gannon et al., 2008).
  
  
Entity Breast cancer
Prognosis Deletion of EBP1 results in tamoxifen resistance in breast cancer (Zhang et al., 2008a). However, patients with a high level of EBP1 protein have a poor clinical outcome (Ou et al., 2006).
  
  
Entity Glioblastoma
Prognosis Glioblastoma patients expressing a high level of p48 EBP1 have a worse prognosis than those expressing lower levels of the protein (Kim et al., 2010; Kwon and Ahn, 2011).
  

Bibliography

Nuclear Akt associates with PKC-phosphorylated Ebp1, preventing DNA fragmentation by inhibition of caspase-activated DNase.
Ahn JY, Liu X, Liu Z, Pereira L, Cheng D, Peng J, Wade PA, Hamburger AW, Ye K.
EMBO J. 2006 May 17;25(10):2083-95. Epub 2006 Apr 27.
PMID 16642037
 
Phosphorylation of the ErbB3 binding protein Ebp1 by p21-activated kinase 1 in breast cancer cells.
Akinmade D, Talukder AH, Zhang Y, Luo WM, Kumar R, Hamburger AW.
Br J Cancer. 2008 Mar 25;98(6):1132-40. Epub 2008 Feb 19.
PMID 18283314
 
Ebp1 expression in benign and malignant prostate.
Gannon PO, Koumakpayi IH, Le Page C, Karakiewicz PI, Mes-Masson AM, Saad F.
Cancer Cell Int. 2008 Nov 24;8:18.
PMID 19025630
 
EBP1 regulates organ size through cell growth and proliferation in plants.
Horvath BM, Magyar Z, Zhang Y, Hamburger AW, Bako L, Visser RG, Bachem CW, Bogre L.
EMBO J. 2006 Oct 18;25(20):4909-20. Epub 2006 Oct 5.
PMID 17024182
 
EBP1 is a novel E2F target gene regulated by transforming growth factor-beta.
Judah D, Chang WY, Dagnino L.
PLoS One. 2010 Nov 10;5(11):e13941.
PMID 21085677
 
Negative regulation of p53 by the long isoform of ErbB3 binding protein Ebp1 in brain tumors.
Kim CK, Nguyen TL, Joo KM, Nam DH, Park J, Lee KH, Cho SW, Ahn JY.
Cancer Res. 2010 Dec 1;70(23):9730-41. Epub 2010 Nov 23.
PMID 21098709
 
The crystal structure of Ebp1 reveals a methionine aminopeptidase fold as binding platform for multiple interactions.
Kowalinski E, Bange G, Bradatsch B, Hurt E, Wild K, Sinning I.
FEBS Lett. 2007 Sep 18;581(23):4450-4. Epub 2007 Aug 27.
PMID 17765895
 
P48 Ebp1 acts as a downstream mediator of Trk signaling in neurons, contributing neuronal differentiation.
Kwon IS, Ahn JY.
Neurochem Int. 2011 Feb;58(2):215-23. Epub 2010 Dec 8.
PMID 21145366
 
Ebp1 isoforms distinctively regulate cell survival and differentiation.
Liu Z, Ahn JY, Liu X, Ye K.
Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10917-22. Epub 2006 Jul 10.
PMID 16832058
 
Human BRE1 is an E3 ubiquitin ligase for Ebp1 tumor suppressor.
Liu Z, Oh SM, Okada M, Liu X, Cheng D, Peng J, Brat DJ, Sun SY, Zhou W, Gu W, Ye K.
Mol Biol Cell. 2009 Feb;20(3):757-68. Epub 2008 Nov 26.
PMID 19037095
 
The ErbB3 binding protein EBP1 regulates ErbB2 protein levels and tamoxifen sensitivity in breast cancer cells.
Lu Y, Zhou H, Chen W, Zhang Y, Hamburger AW.
Breast Cancer Res Treat. 2011 Feb;126(1):27-36. Epub 2010 Apr 9.
PMID 20379846
 
Structural insights into the transcriptional and translational roles of Ebp1.
Monie TP, Perrin AJ, Birtley JR, Sweeney TR, Karakasiliotis I, Chaudhry Y, Roberts LO, Matthews S, Goodfellow IG, Curry S.
EMBO J. 2007 Sep 5;26(17):3936-44. Epub 2007 Aug 9.
PMID 17690690
 
Ebp1 sumoylation, regulated by TLS/FUS E3 ligase, is required for its anti-proliferative activity.
Oh SM, Liu Z, Okada M, Jang SW, Liu X, Chan CB, Luo H, Ye K.
Oncogene. 2010 Feb 18;29(7):1017-30. Epub 2009 Nov 30.
PMID 19946338
 
Quantitative profiling of drug-associated proteomic alterations by combined 2-nitrobenzenesulfenyl chloride (NBS) isotope labeling and 2DE/MS identification.
Ou K, Kesuma D, Ganesan K, Yu K, Soon SY, Lee SY, Goh XP, Hooi M, Chen W, Jikuya H, Ichikawa T, Kuyama H, Matsuo E, Nishimura O, Tan P.
J Proteome Res. 2006 Sep;5(9):2194-206.
PMID 16944931
 
A cell cycle-dependent protein serves as a template-specific translation initiation factor.
Pilipenko EV, Pestova TV, Kolupaeva VG, Khitrina EV, Poperechnaya AN, Agol VI, Hellen CU.
Genes Dev. 2000 Aug 15;14(16):2028-45.
PMID 10950867
 
Molecular cloning of a murine cDNA encoding a novel protein, p38-2G4, which varies with the cell cycle.
Radomski N, Jost E.
Exp Cell Res. 1995 Oct;220(2):434-45.
PMID 7556453
 
Ebp1 is a dsRNA-binding protein associated with ribosomes that modulates eIF2alpha phosphorylation.
Squatrito M, Mancino M, Sala L, Draetta GF.
Biochem Biophys Res Commun. 2006 Jun 9;344(3):859-68. Epub 2006 Apr 19.
PMID 16631606
 
Ebp1, an ErbB-3 binding protein, interacts with Rb and affects Rb transcriptional regulation.
Xia X, Cheng A, Lessor T, Zhang Y, Hamburger AW.
J Cell Physiol. 2001 May;187(2):209-17.
PMID 11268000
 
A fission yeast gene encoding a protein that preferentially associates with curved DNA.
Yamada H, Mori H, Momoi H, Nakagawa Y, Ueguchi C, Mizuno T.
Yeast. 1994 Jul;10(7):883-94.
PMID 7985416
 
Interaction of the PA2G4 (EBP1) protein with ErbB-3 and regulation of this binding by heregulin.
Yoo JY, Wang XW, Rishi AK, Lessor T, Xia XM, Gustafson TA, Hamburger AW.
Br J Cancer. 2000 Feb;82(3):683-90.
PMID 10682683
 
Inhibition of heregulin mediated MCF-7 breast cancer cell growth by the ErbB3 binding protein EBP1.
Zhang Y, Akinmade D, Hamburger AW.
Cancer Lett. 2008a Jul 8;265(2):298-306. Epub 2008 Mar 19.
PMID 18355957
 
Heregulin regulates the ability of the ErbB3-binding protein Ebp1 to bind E2F promoter elements and repress E2F-mediated transcription.
Zhang Y, Hamburger AW.
J Biol Chem. 2004 Jun 18;279(25):26126-33. Epub 2004 Apr 8.
PMID 15073182
 
EBP1, an ErbB3-binding protein, is decreased in prostate cancer and implicated in hormone resistance.
Zhang Y, Linn D, Liu Z, Melamed J, Tavora F, Young CY, Burger AM, Hamburger AW.
Mol Cancer Ther. 2008b Oct;7(10):3176-86.
PMID 18852121
 
Post-transcriptional regulation of androgen receptor mRNA by an ErbB3 binding protein 1 in prostate cancer.
Zhou H, Mazan-Mamczarz K, Martindale JL, Barker A, Liu Z, Gorospe M, Leedman PJ, Gartenhaus RB, Hamburger AW, Zhang Y.
Nucleic Acids Res. 2010 Jun;38(11):3619-31. Epub 2010 Feb 16.
PMID 20159994
 

Citation

This paper should be referenced as such :
Hamburger, A ; Ghosh, A ; Awasthi, S
PA2G4 (proliferation-associated 2G4, 38kDa)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(2):131-134.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PA2G4ID41628ch12q13.html


External links

Nomenclature
HGNC (Hugo)PA2G4   8550
Cards
AtlasPA2G4ID41628ch12q13
Entrez_Gene (NCBI)PA2G4  5036  proliferation-associated 2G4
AliasesEBP1; HG4-1; p38-2G4
GeneCards (Weizmann)PA2G4
Ensembl hg19 (Hinxton)ENSG00000170515 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000170515 [Gene_View]  chr12:56104319-56113910 [Contig_View]  PA2G4 [Vega]
ICGC DataPortalENSG00000170515
TCGA cBioPortalPA2G4
AceView (NCBI)PA2G4
Genatlas (Paris)PA2G4
WikiGenes5036
SOURCE (Princeton)PA2G4
Genetics Home Reference (NIH)PA2G4
Genomic and cartography
GoldenPath hg38 (UCSC)PA2G4  -     chr12:56104319-56113910 +  12q13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PA2G4  -     12q13.2   [Description]    (hg19-Feb_2009)
EnsemblPA2G4 - 12q13.2 [CytoView hg19]  PA2G4 - 12q13.2 [CytoView hg38]
Mapping of homologs : NCBIPA2G4 [Mapview hg19]  PA2G4 [Mapview hg38]
OMIM602145   
Gene and transcription
Genbank (Entrez)AK291796 BC001951 BC007561 BC019222 BC032111
RefSeq transcript (Entrez)NM_006191
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PA2G4
Cluster EST : UnigeneHs.745109 [ NCBI ]
CGAP (NCI)Hs.745109
Alternative Splicing GalleryENSG00000170515
Gene ExpressionPA2G4 [ NCBI-GEO ]   PA2G4 [ EBI - ARRAY_EXPRESS ]   PA2G4 [ SEEK ]   PA2G4 [ MEM ]
Gene Expression Viewer (FireBrowse)PA2G4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5036
GTEX Portal (Tissue expression)PA2G4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UQ80   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UQ80  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UQ80
Splice isoforms : SwissVarQ9UQ80
PhosPhoSitePlusQ9UQ80
Domaine pattern : Prosite (Expaxy)MAP_2 (PS01202)   
Domains : Interpro (EBI)PA2G4    Pept_M24    Pept_M24A_MAP2_BS    WHTH_DNA-bd_dom   
Domain families : Pfam (Sanger)Peptidase_M24 (PF00557)   
Domain families : Pfam (NCBI)pfam00557   
Conserved Domain (NCBI)PA2G4
DMDM Disease mutations5036
Blocks (Seattle)PA2G4
PDB (SRS)2Q8K    3J2I   
PDB (PDBSum)2Q8K    3J2I   
PDB (IMB)2Q8K    3J2I   
PDB (RSDB)2Q8K    3J2I   
Structural Biology KnowledgeBase2Q8K    3J2I   
SCOP (Structural Classification of Proteins)2Q8K    3J2I   
CATH (Classification of proteins structures)2Q8K    3J2I   
SuperfamilyQ9UQ80
Human Protein AtlasENSG00000170515
Peptide AtlasQ9UQ80
HPRD03685
IPIIPI00299000   IPI00807557   IPI01022945   IPI01022476   IPI01022048   IPI01022806   IPI01021326   
Protein Interaction databases
DIP (DOE-UCLA)Q9UQ80
IntAct (EBI)Q9UQ80
FunCoupENSG00000170515
BioGRIDPA2G4
STRING (EMBL)PA2G4
ZODIACPA2G4
Ontologies - Pathways
QuickGOQ9UQ80
Ontology : AmiGODNA binding  transcription factor activity, sequence-specific DNA binding  RNA binding  protein binding  extracellular region  nucleus  nucleolus  cytoplasm  transcription, DNA-templated  rRNA processing  regulation of translation  cell cycle arrest  cell proliferation  membrane  intracellular ribonucleoprotein complex  ubiquitin protein ligase binding  azurophil granule lumen  negative regulation of apoptotic process  neutrophil degranulation  positive regulation of cell differentiation  negative regulation of transcription, DNA-templated  extracellular exosome  
Ontology : EGO-EBIDNA binding  transcription factor activity, sequence-specific DNA binding  RNA binding  protein binding  extracellular region  nucleus  nucleolus  cytoplasm  transcription, DNA-templated  rRNA processing  regulation of translation  cell cycle arrest  cell proliferation  membrane  intracellular ribonucleoprotein complex  ubiquitin protein ligase binding  azurophil granule lumen  negative regulation of apoptotic process  neutrophil degranulation  positive regulation of cell differentiation  negative regulation of transcription, DNA-templated  extracellular exosome  
REACTOMEQ9UQ80 [protein]
REACTOME PathwaysR-HSA-6798695 [pathway]   
NDEx NetworkPA2G4
Atlas of Cancer Signalling NetworkPA2G4
Wikipedia pathwaysPA2G4
Orthology - Evolution
OrthoDB5036
GeneTree (enSembl)ENSG00000170515
Phylogenetic Trees/Animal Genes : TreeFamPA2G4
HOVERGENQ9UQ80
HOGENOMQ9UQ80
Homologs : HomoloGenePA2G4
Homology/Alignments : Family Browser (UCSC)PA2G4
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPA2G4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PA2G4
dbVarPA2G4
ClinVarPA2G4
1000_GenomesPA2G4 
Exome Variant ServerPA2G4
ExAC (Exome Aggregation Consortium)PA2G4 (select the gene name)
Genetic variants : HAPMAP5036
Genomic Variants (DGV)PA2G4 [DGVbeta]
DECIPHERPA2G4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPA2G4 
Mutations
ICGC Data PortalPA2G4 
TCGA Data PortalPA2G4 
Broad Tumor PortalPA2G4
OASIS PortalPA2G4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPA2G4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPA2G4
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PA2G4
DgiDB (Drug Gene Interaction Database)PA2G4
DoCM (Curated mutations)PA2G4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PA2G4 (select a term)
intoGenPA2G4
NCG5 (London)PA2G4
Cancer3DPA2G4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602145   
Orphanet
MedgenPA2G4
Genetic Testing Registry PA2G4
NextProtQ9UQ80 [Medical]
TSGene5036
GENETestsPA2G4
Target ValidationPA2G4
Huge Navigator PA2G4 [HugePedia]
snp3D : Map Gene to Disease5036
BioCentury BCIQPA2G4
ClinGenPA2G4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5036
Chemical/Pharm GKB GenePA32877
Clinical trialPA2G4
Miscellaneous
canSAR (ICR)PA2G4 (select the gene name)
Probes
Litterature
PubMed98 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePA2G4
EVEXPA2G4
GoPubMedPA2G4
iHOPPA2G4
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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