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HNRNPD (heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa))

Written2009-11Carsten Sekulla, Bogusz Trojanowicz, Cuong Hoang-Vu
AG Experimentelle, Chirurgische Onkologie, Universitatsklinik und Poliklinik fur Allgemein-, Viszeral- und Gefasschirurgie, Martin-Luther Universitat, Magdeburger Strasse 18, 06097 Halle/S, Germany (CS, BT, CHV); AG Experimentelle, Chirurgische Onkologie, Universitatsklinik und Poliklinik fur Kinderchirurgie, Martin-Luther Universitat, Magdeburger Strasse 18, 06097 Halle/S, Germany (BT)

(Note : for Links provided by Atlas : click)

Identity

Alias_namesAUF1
HNRPD
heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)
AU-rich element RNA binding protein 1, 37kDa
Other aliasAUF1A
P37
hnRNPD0
HGNC (Hugo) HNRNPD
LocusID (NCBI) 3184
Atlas_Id 40840
Location 4q21.22  [Link to chromosome band 4q21]
Location_base_pair Starts at 82353314 and ends at 82373996 bp from pter ( according to hg19-Feb_2009)  [Mapping HNRNPD.png]
Fusion genes
(updated 2016)
GRHL2 (8q22.3) / HNRNPD (4q21.22)HNRNPD (4q21.22) / ELL (19p13.11)HNRNPD (4q21.22) / HNRNPD (4q21.22)
HNRNPD (4q21.22) / NOL6 (9p13.3)HNRNPD (4q21.22) / TMEM67 (8q22.1)HNRNPD (4q21.22) / VAMP2 (17p13.1)
LAMB2 (3p21.31) / HNRNPD (4q21.22)NFE2L2 (2q31.2) / HNRNPD (4q21.22)PDCD10 (3q26.1) / HNRNPD (4q21.22)
PPDPF (20q13.33) / HNRNPD (4q21.22)RASGRF1 (15q25.1) / HNRNPD (4q21.22)RILPL2 (12q24.31) / HNRNPD (4q21.22)
SNU13 (22q13.2) / HNRNPD (4q21.22)

DNA/RNA

Note Differential splicing of a single HNRNPD transcript results in four isoforms: p37, p40, p42 and p45.
 
  Structure of the human HNRNPD gene. Exon positions (red) and sizes (nt-nucleotides) are labelled.
Description HNRNPD gene is composed of 10 exons, ranging in size from 57 to 497 nt. Eight of 10 exons are localised within the coding region. Exon 1 contains 5' UTR and encodes N-terminal part of the AUF1 protein. Exon 2 encodes the 19-aminoacid insertion of the N-terminal part of the first RNA-binding domain (RBD). This insertion is localised only in isoforms p40 and p45. Exons 3-6 encode the rest of the first RBD, the N-terminal half of the second RBD, the C-terminal half of the second RBD and the glutamine rich region, respectively. Exon 7 encodes the 49-aminoacid insertion localised only in isoforms p42 and p45. The smallest isoform p37, lacks exon 2 and 7. Exon 8 encodes the C-terminal part common to all isoforms and part of the 3' UTR. A TAA nonsense codon is also localised within this exon. Exon 9 contains two additional in-frame stop codons and encodes an alternatively spliced, 107 nt part of the 3' UTR. Exon 10 encodes the rest of 3' UTR and contains an AATAAA polyadenylation signal.
Transcription Transcription initiation sites were not exactly identified, but there is a TATAA box 175 nt upstream of the 5' end of the human cDNA clone with the longest 5' UTR. The first ATG codon is located in exon 1, at least 250 nt from the 5' end of mRNA.
Pseudogene One pseudogene according to RefSeq was localised. Localisation: Xq12

Protein

 
  Structure of HNRNPD (AUF1) proteins; RBD1-2, RNA binding domains; Q, glutamine rich element; HNS, Exon 2, 19 amino acids; Exon 7, 49 amino acids.
Description The family of HNRNPD (AUF1) proteins distinguishes a 37 kDa (p37) core protein, a 40 kDa protein (p40) containing an N-terminal 19 amino acid insertion (exon 2), a 42 kDa protein (p42) exhibiting a C-terminal 49 amino acids insertion (exon 7), and a 45 kDa protein (p45) with insertions of both exon 2 and exon 7. Presence or absence of these alternatively spliced exons confers distinct biological properties to individual AUF1 isoforms. Presence of exon 7 not only affects nucleo-cytoplasmic distribution, but also blocks ubiquitination of p42 and p45. In contrast, the lack of exon 7 targets p37 and p40 to the ubiquitin proteasome pathway, where both isoforms serve as substrates in decay reaction. This results in rapid and selected decay of adenylate-uridylate rich elements (AREs) containing mRNAs. Importantly, absence of exon 2 in p37 and p42 is associated with high affinity binding of these isoforms. The smallest AUF1 isoform p37 posses the strongest mRNA binding affinity, which for other isoforms decreases in following rank of order: p37>p42>p45>p40.
Expression AUF1 is expressed early in the development. High levels of AUF1 proteins were found in lymphoid tissues, such as spleen and thymus, and lower levels in brain and fetal liver. In adult liver AUF1 was undetectable. In spleen and thymus extracts, isoforms p40 and p45 were more abundant than p37. Isoforms p45 and p40 were most abundant in brain and in fetal liver, respectively. Both mentioned organs lacked expression of p37.
Localisation AUF1 is predominantly nuclear and is able to shuttle between nucleus and cytoplasm. In the nucleus, AUF1 is found within stable ribonucleoprotein complexes; in the cytoplasm, AUF1 binds to target mRNAs and is often co-localised with the exosome.
The triggering of AUF1-mediated degradation is consistent with changes of cellular localisation of this protein. Previous studies demonstrated that blocking of ARE-mediated mRNA decay by heat shock, down-regulation of the ubiquitin-proteasome pathway or by inactivation of the E1 ubiquitinating enzyme all resulted in hnRNPD movement to the nucleus of human HeLa cells. However, the cellular factors and/or events involved in regulating these different activities for AUF1 remain to be defined.
Function AUF1 is involved in processes of apoptosis, tumorigenesis and development by its interactions with AREs bearing mRNAs. It is able to bind both single stranded DNA and RNA, especially transcripts bearing AREs in their 3' UTR. AUF1 may bind AREs of all classes (I, II and III) and its over-expression noticeably influences the stability of ARE containing mRNAs. AUF1 appears to enhance target mRNA decay, a process that is closely related to the ubiquitination and targeting of AUF1 to the proteasome. AUF1 target mRNAs encode mitogenic, immune response, cancer-associated, stress response, and cell cycle regulatory proteins such as c-fos, c-jun, c-myc, egr-1, interleukins, iNOS, DNMT1, p21, p27, hsp70, MnSOD, catalase, cyclin D1, and cdc25. It was reported that increased level of AUF1 in human erythroleukemic K562 cells, especially isoforms p37AUF1 and p42AUF1, induced ARE-directed mRNA degradation.
AUF1 itself does not possess enzymatic activity but may interact and recruit other proteins, including lactate dehydrogenase (LDH), stratifin, ubiquitin-conjugating enzyme E2I, RNA binding proteins NSEP-1, NSAP-1 and IMP-2. NSEP-1 was demonstrated to possess an endoribonuclease activity.
Homology The human and murine HNRNPD proteins are highly conserved and revealed similarity of 98.9%. The differences are mainly restricted to the N-terminal portion of the protein. The human HNRNPD locus maps to 4q21, and the murine Hnrnpd locus maps to the F region of chromosome 3.

Mutations

Note Not known in human.

Implicated in

Note
  
Entity Oral squamous cell carcinoma (OSCC)
Note The higher expression of HNRNPD, HNRNPK, MutS homolog 2 (MSH2) and grainyhead-like 2 (GRHL2), and subsequently increased activity of human telomerase reverse transcriptase (hTERT) were detected in OSCC cells when compared to normal cells, which do not exhibit hTERT activity. RNAi mediated knock-down of HNRNPD, MSH2 and GRHL2 resulted in decreased proliferation rates and hTERT promoter activity. Down-regulation of HNRNPK reduced only proliferation of the cells without affecting the hTERT promoter activity.
  
  
Entity Mediated growth arrest of cancer cells
Note Prostaglandin A2 (PGA2) is an experimental anti-cancer agent associated with reduced levels of cyclin D1 and decreased proliferation of cancer cells. Employment of PGA2 induced AUF1 expression and resulted in destabilisation of cyclin D1 mRNA in non small cell lung cancer (H1299) and breast carcinoma (MCF-7) cells. The other breast carcinoma cell line MDA-MB-453, bearing a large deletion in cyclin's D1 3'UTR, responded with unaltered cyclin D1 mRNA upon PGA2 treatment.
  
  
Entity Thyroid carcinoma
Note AUF1 was demonstrated as a new, additional marker for thyroid carcinoma. Increased cytoplasmic AUF1 levels were found in dividing thyroid carcinoma cell lines and in most malignant thyroid carcinoma tissues. Furthermore, by immunohistochemistry and subcellular fractionation of thyroid tissues it has been shown that cytoplasmic expression of AUF1 in benign and malignant tissues was significantly increased when compared to normal thyroid tissues. Furthermore, logarithmic nuclear/cytoplasmic ratio of total AUF1 expression in normal, goiter, adenoma and follicular thyroid carcinoma decreased with tissue malignancy. Stable and transient suppression of AUF1 by RNAi in thyroid carcinoma cells resulted in decreased proliferation rates accompanied by increased levels of cell cycle inhibitors and reduced expression of cell cycle promoters.
  
  
Entity Lung cancer
Note Cytosolic levels of AUF1 and HuR proteins were found to be significantly increased in lung hyperplasia and neoplasia, both in vitro and in vivo. Normal peripheral lung tissues expressed significantly lower levels of cytosolic AUF1 and HuR when compared with lung tumors.
  
  
Entity Sarcomas
Note Overexpression of AUF1 isoform p37 led to development of sarcomas accompanied by induction of c-myc, c-fos, c-jun and cyclin D1 mRNAs in tumor tissues comparing with non-neoplastic control tissues. Furthermore, sarcomas revealed decreased levels of TNFa and GM-CSF mRNAs, and no significant differences in VEGF expression were detectable.
  
  
Entity Melanoma with increased expression of interleukin 10 (IL-10)
Note Elevated levels of IL-10 in melanoma cells resulted in decreased cytosolic AUF1 levels as compared with normal melanocytes.
  
  
Entity Hepatitis C virus (HCV) mediated hepatitis, liver cirrhosis and hepatocellular carcinoma
Note Overexpression of HNRNPD (especially isoforms p37 and p45) resulted in enhanced translation of internal ribosome entry site (IRES) of HCV, further processed into 10 or more viral proteins. In contrast, HNRNPD knock-down significantly reduced its translation and hampered infection by HCV.
  
  
Entity Anaplastic large cell lymphoma (ALCL)
Note Approximately 80% of anaplastic lymphoma kinase (ALK)-positive lymphomas express the fusion protein called nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) causing constitutive activation of ALK tyrosine kinase and abnormal induction of down-stream signaling resulting in malignant transformation. It was demonstrated that AUF1 is co-localised with NPM-ALK in the same cytoplasmic loci and was hyperphosphorylated in NPM-ALK expressing cells. AUF1 hyperphosphorylation was associated with elevated stability of several target mRNAs encoding proteins crucial for cell proliferation and cell survival such as c-myc, and cyclin D1, cyclin A2, cyclin B1, and cyclin D3.
  
  
Entity Cardiac hypertrophy and heart failure
Note Experimental animals and patients with cardiac hypertrophy and heart failure revealed abnormalities in myocardial relaxation, which are related with reduced levels of sarco(endo)plasmic reticulum calcium ATPase 2a (SERCA2a) gene expression. AUF1 was identified to interact with SERCA2a 3' UTR predominantly in nucleus. This suggests that AUF1-mediated decay of SERCA2a mRNA starts within the nucleus and further continues during shuttling to the cytoplasm.
Expression of cardiac myocyte Kv4 channels is reduced in hypertrophy and leads to reduce in the transient outward current. Studies in vitro demonstrated that employment of angiotensin II may recapitulate these effects and is accompanied by up-regulation of AUF1, which in turn binds and destabilises Kv4 mRNA.
  
  
Entity Secondary hyperparathyroidism
Note It was demonstrated that AUF1 mRNA levels were repressed in secondary hyperparathyroidism patients with nodular growth of the gland. It is worth to notice that secondary hyperparathyroidism results in increased levels of parathyroid hormone (PTH), demonstrated to be a target for AUF1. PTH mRNA contains AREs in its 3' UTR.
  
  
Entity Replicative senescence
Note AUF1 was identified as a critical mediator of senescence events. Reduction of AUF1 level occurred with replicative senescence and contributed to stabilisation and elevated expression of ARE-bearing p16 mRNA in senescence-phenotype cells.
  
  
Entity UVC irradiation-induced apoptosis
Note AUF1 levels increased upon UVC irradiation-induced apoptosis and correlated with reduction of ARE-containing bcl-2 mRNA.
  
  
Entity Mammary gland differentiation
Note It was demonstrated that AUF1 translocation from cytoplasm to the nucleus correlates with mammary gland differentiation, induction of milk production and inhibition of proliferation. Participation of AUF1 in those processes was lactogenic hormone signals-dependent.
  
  
Entity Systemic rheumatic diseases
Note AUF1 proteins were identified as novel autoantigens in systemic lupus erythematosus (SLE) and other associated autoimmune rheumatic disorders. Autoantibodies to AUF1 were found in 33% of SLE patients, 20% of patients with rheumatioid arthritis, 17% of patients with mixed connective tissue disorders and below 10% of patients with other related rheumatic diseases. Healthy controls were AUF1 autoantibodies negative.
  

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Citation

This paper should be referenced as such :
Sekulla, C ; Trojanowicz, B ; Hoang-Vu, C
HNRNPD (heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa))
Atlas Genet Cytogenet Oncol Haematol. 2010;14(9):817-821.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/HNRNPDID40840ch4q21.html


External links

Nomenclature
HGNC (Hugo)HNRNPD   5036
Cards
AtlasHNRNPDID40840ch4q21
Entrez_Gene (NCBI)HNRNPD  3184  heterogeneous nuclear ribonucleoprotein D
AliasesAUF1; AUF1A; HNRPD; P37; 
hnRNPD0
GeneCards (Weizmann)HNRNPD
Ensembl hg19 (Hinxton)ENSG00000138668 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000138668 [Gene_View]  chr4:82353314-82373996 [Contig_View]  HNRNPD [Vega]
ICGC DataPortalENSG00000138668
TCGA cBioPortalHNRNPD
AceView (NCBI)HNRNPD
Genatlas (Paris)HNRNPD
WikiGenes3184
SOURCE (Princeton)HNRNPD
Genetics Home Reference (NIH)HNRNPD
Genomic and cartography
GoldenPath hg38 (UCSC)HNRNPD  -     chr4:82353314-82373996 -  4q21.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HNRNPD  -     4q21.22   [Description]    (hg19-Feb_2009)
EnsemblHNRNPD - 4q21.22 [CytoView hg19]  HNRNPD - 4q21.22 [CytoView hg38]
Mapping of homologs : NCBIHNRNPD [Mapview hg19]  HNRNPD [Mapview hg38]
OMIM601324   
Gene and transcription
Genbank (Entrez)AF039575 AK057836 AK292707 AK300149 AK303552
RefSeq transcript (Entrez)NM_001003810 NM_002138 NM_031369 NM_031370
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HNRNPD
Cluster EST : UnigeneHs.480073 [ NCBI ]
CGAP (NCI)Hs.480073
Alternative Splicing GalleryENSG00000138668
Gene ExpressionHNRNPD [ NCBI-GEO ]   HNRNPD [ EBI - ARRAY_EXPRESS ]   HNRNPD [ SEEK ]   HNRNPD [ MEM ]
Gene Expression Viewer (FireBrowse)HNRNPD [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3184
GTEX Portal (Tissue expression)HNRNPD
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14103   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14103  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14103
Splice isoforms : SwissVarQ14103
PhosPhoSitePlusQ14103
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)CARG-binding_factor_N    Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)CBFNT (PF08143)    RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam08143    pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
Conserved Domain (NCBI)HNRNPD
DMDM Disease mutations3184
Blocks (Seattle)HNRNPD
PDB (SRS)1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
PDB (PDBSum)1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
PDB (IMB)1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
PDB (RSDB)1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
Structural Biology KnowledgeBase1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
SCOP (Structural Classification of Proteins)1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
CATH (Classification of proteins structures)1HD0    1HD1    1IQT    1WTB    1X0F    2Z5N    5IM0   
SuperfamilyQ14103
Human Protein AtlasENSG00000138668
Peptide AtlasQ14103
HPRD03206
IPIIPI00028888   IPI00220683   IPI00220684   IPI00220685   IPI01014602   IPI01012829   IPI00903278   IPI00967841   IPI00963980   IPI00965952   IPI00968092   IPI00967562   IPI00964648   
Protein Interaction databases
DIP (DOE-UCLA)Q14103
IntAct (EBI)Q14103
FunCoupENSG00000138668
BioGRIDHNRNPD
STRING (EMBL)HNRNPD
ZODIACHNRNPD
Ontologies - Pathways
QuickGOQ14103
Ontology : AmiGOmRNA splicing, via spliceosome  liver development  AT DNA binding  chromatin binding  RNA binding  RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  transcription, DNA-templated  regulation of transcription, DNA-templated  RNA processing  RNA catabolic process  transcription factor binding  gene expression  cerebellum development  intracellular ribonucleoprotein complex  regulation of telomere maintenance  mRNA 3'-UTR AU-rich region binding  telomeric DNA binding  response to drug  regulation of circadian rhythm  histone deacetylase binding  regulation of mRNA stability  positive regulation of translation  positive regulation of transcription, DNA-templated  mRNA stabilization  response to calcium ion  response to electrical stimulus  3'-UTR-mediated mRNA destabilization  extracellular exosome  cellular response to amino acid stimulus  cellular response to estradiol stimulus  cellular response to nitric oxide  circadian regulation of translation  response to rapamycin  positive regulation of telomere capping  response to sodium phosphate  cellular response to putrescine  positive regulation of telomerase RNA reverse transcriptase activity  hepatocyte dedifferentiation  
Ontology : EGO-EBImRNA splicing, via spliceosome  liver development  AT DNA binding  chromatin binding  RNA binding  RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  transcription, DNA-templated  regulation of transcription, DNA-templated  RNA processing  RNA catabolic process  transcription factor binding  gene expression  cerebellum development  intracellular ribonucleoprotein complex  regulation of telomere maintenance  mRNA 3'-UTR AU-rich region binding  telomeric DNA binding  response to drug  regulation of circadian rhythm  histone deacetylase binding  regulation of mRNA stability  positive regulation of translation  positive regulation of transcription, DNA-templated  mRNA stabilization  response to calcium ion  response to electrical stimulus  3'-UTR-mediated mRNA destabilization  extracellular exosome  cellular response to amino acid stimulus  cellular response to estradiol stimulus  cellular response to nitric oxide  circadian regulation of translation  response to rapamycin  positive regulation of telomere capping  response to sodium phosphate  cellular response to putrescine  positive regulation of telomerase RNA reverse transcriptase activity  hepatocyte dedifferentiation  
REACTOMEQ14103 [protein]
REACTOME PathwaysR-HSA-72203 [pathway]   
NDEx NetworkHNRNPD
Atlas of Cancer Signalling NetworkHNRNPD
Wikipedia pathwaysHNRNPD
Orthology - Evolution
OrthoDB3184
GeneTree (enSembl)ENSG00000138668
Phylogenetic Trees/Animal Genes : TreeFamHNRNPD
HOVERGENQ14103
HOGENOMQ14103
Homologs : HomoloGeneHNRNPD
Homology/Alignments : Family Browser (UCSC)HNRNPD
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHNRNPD [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HNRNPD
dbVarHNRNPD
ClinVarHNRNPD
1000_GenomesHNRNPD 
Exome Variant ServerHNRNPD
ExAC (Exome Aggregation Consortium)HNRNPD (select the gene name)
Genetic variants : HAPMAP3184
Genomic Variants (DGV)HNRNPD [DGVbeta]
DECIPHERHNRNPD [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHNRNPD 
Mutations
ICGC Data PortalHNRNPD 
TCGA Data PortalHNRNPD 
Broad Tumor PortalHNRNPD
OASIS PortalHNRNPD [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHNRNPD  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHNRNPD
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HNRNPD
DgiDB (Drug Gene Interaction Database)HNRNPD
DoCM (Curated mutations)HNRNPD (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HNRNPD (select a term)
intoGenHNRNPD
NCG5 (London)HNRNPD
Cancer3DHNRNPD(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601324   
Orphanet
MedgenHNRNPD
Genetic Testing Registry HNRNPD
NextProtQ14103 [Medical]
TSGene3184
GENETestsHNRNPD
Target ValidationHNRNPD
Huge Navigator HNRNPD [HugePedia]
snp3D : Map Gene to Disease3184
BioCentury BCIQHNRNPD
ClinGenHNRNPD
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3184
Chemical/Pharm GKB GenePA29361
Clinical trialHNRNPD
Miscellaneous
canSAR (ICR)HNRNPD (select the gene name)
Probes
Litterature
PubMed176 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHNRNPD
EVEXHNRNPD
GoPubMedHNRNPD
iHOPHNRNPD
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 1 17:28:01 CEST 2017

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