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CCDC6 (coiled-coil domain containing 6)

Written2001-06Nick.C P Cross
Wessex Regional Genetics Laboratory Salisbury District Hospital Salisbury, SP2 8BJ, UK
Updated2015-06Francesco Morra, Caterina Miro, Virginia Napolitano, Francesco Merolla, Angela Celetti
Istituto per l'Endocrinologia e l'Oncologia Sperimentale, IEOS, CNR, via Pansini 5, 80131, Naples, Italy. francesco_morra@hotmail.it, caterinamiro@hotmail.it, virnap87@hotmail.it, merollafra@gmail.com, celetti@unina.it.

Abstract CCDC6 gene product is a pro-apoptotic protein substrate of ATM whose loss or inactivation enhances tumor progression. In primary tumors the impaired function of CCDC6 protein has been ascribed to CCDC6 rearrangements, to somatic mutations and to CCDC6 different levels in several neoplasia. The CCDC6 turnover is regulated in a cell cycle dependent manner upon post-translational modification events. The impairment of CCDC6 turnover may affect cells behaviour and drug response.

(Note : for Links provided by Atlas : click)

Identity

Other namesD10S170
H4
TST1
HGNC (Hugo) CCDC6
LocusID (NCBI) 8030
Atlas_Id 280
Location 10q21.2  [Link to chromosome band 10q21]
Location_base_pair Starts at 61548506 and ends at 61666414 bp from pter ( according to hg19-Feb_2009)  [Mapping CCDC6.png]
Fusion genes
(updated 2016)
CCDC6 (10q21.2) / ANK3 (10q21.2)CCDC6 (10q21.2) / CCDC6 (10q21.2)CCDC6 (10q21.2) / CTNNA3 (10q21.3)
CCDC6 (10q21.2) / KCNH8 (3p24.3)CCDC6 (10q21.2) / LIPI (21q11.2)CCDC6 (10q21.2) / PDGFRB (5q32)
CCDC6 (10q21.2) / RAD1 (5p13.2)CCDC6 (10q21.2) / RET (10q11.21)CCDC6 (10q21.2) / ROS1 (6q22.1)
CCDC6 (10q21.2) / UBE2D1 (10q21.1)FGFR2 (10q26.13) / CCDC6 (10q21.2)KCNH8 (3p24.3) / CCDC6 (10q21.2)
KITLG (12q21.32) / CCDC6 (10q21.2)PDGFRB (5q32) / CCDC6 (10q21.2)RET (10q11.21) / CCDC6 (10q21.2)
ROS1 (6q22.1) / CCDC6 (10q21.2)VPS13B (8q22.2) / CCDC6 (10q21.2)

DNA/RNA

Description The CCDC6 gene (Coiled Coil Containing 6) has been identified upon its frequent rearrangement with the RET proto-oncogene in papillary thyroid carcinomas (Fusco et al., 1987; Grieco et al., 1990), and with genes other than RET in solid and not solid tumours (Drechsler et al., 2007). Recently, by using an integrated molecular- and histopathology- based screening, the fusion CCDC6/RET has been also detected in lung adenocarcinoma, even at low frequency (Takeuchi et al., 2012).
The CCDC6 gene is located on the long arm of chromosome 10 (10q21), and contains 9 exons that encode a transcript of 3 Kb showing an open reading frame (ORF) of 475 aa. The CCDC6 gene promoter, localized within 259 bp upstream of the ATG site, drives the gene expression ubiquitously in various human tissue (Tong et al., 1995). In tumors harboring the RET/PTC1 rearrangement, the activation of RET involves chromosomal inversion of the long arm of chromosome 10 that juxtaposes the tyrosine kinase-encoding domain of RET, mapped at 10q11.2, to the promoter and the first exon of the CCDC6 gene, originally named H4(D10S170) (Pierotti et al., 1992).
Pseudogene None reported

Protein

Description 474 amino acid coiled coil protein. Its predicted amino-acid (aa) sequence contains a long coiled coil region and a putative binding domain for SH3-proteins, suggesting its possible involvement in protein-protein interactions (Grieco et al., 1994). CCDC6 gene product shows extensive regions of alpha helices which have a high potential to adopt a coiled-coil conformation. Coiled-coils are formed by two or three alpha-helices that are strongly amphipathic and supercoil around each other, crossing at an angle of about 20- (Lupas et al., 1991). It has been demonstrate that such region can be involved in protein dimerization or oligomerization. CCDC6 protein is an ubiquitously expressed 65 KDa nuclear and cytosolic protein phosphorylated by ERK1/2 at serine 244 upon serum induction (Grieco et al., 1994; Celetti et al., 2004). In the last years, several large-scale phosphorylation site-mapping studies have recognized CCDC6 as a phosphoprotein (Beausoleil et al., 2004; Brill et al., 2004) (Figure 1).
CCDC6 has been recognized as a pro-apoptotic protein, while the CCDC6 protein truncated at the carboxyterminus, such as in the fusion with different oncogenes, acts as dominant negative on nuclear localization and apoptosis induced by the wild-type protein (Celetti et al., 2004). CCDC6 is phosphorylated at T434 by the ATM kinase that stabilizes the protein in the nucleus in response to DNA damage. The loss of the CCDC6 region recognised by ATM kinase or the full protein deficiency determines an increase in cell survival, allows for DNA synthesis and permits cell to progress into mitosis, following the exposure to genotoxic stress (Merolla et al., 2007).
CCDC6 gene product undergoes multiple post-translational modifications such as sumoylation (Luise et al., 2012), ubiquitination (Povlsen et al., 2012; Morra et al., 2015), and phosphorylation (Celetti et al., 2004; Beausoleil et al., 2004; Brill et al., 2004; Morra et al., 2015), suggesting that CCDC6 protein activity is highly regulated (Figure 3).
 
  Fig. 1: Putative phosphorylation sites in CCDC6 protein. The arrows indicate the ERK1/2 and the ATM kinases predicted phosphorylation sites.
Expression Widely expressed, cell cycle regulated, post translational modified
Function Proapoptotic and cell cycle regulated protein, involved in DNA damage and repair.
Further supporting a role of CCDC6 in control of cell proliferation, it has been reported that CCDC6 interacts with CREB1 and inhibits its cAMP-dependent transcriptional activity (Leone et al., 2010) in a SUMO-dependent manner (Luise et al., 2012). Interestingly, CCDC6 knock-in mice develop thyroid hyperplasia associated to an enhanced CREB1 activity (Leone V et al., 2015), supporting a likely role of the haploinsufficiency of CCDC6 expression in the development of thyroid papillary carcinomas carrying the RET/PTC1 rearrangements.
High-throughput proteomic screening predicted the interaction between CCDC6 and the catalytic subunit of Protein Phosphatase 4 (PP4c) (Ewing et al., 2007) that has been confirmed in vitro and in vivo (Merolla et al., 2012). Moreover, it has been demonstrate that cells depleted of CCDC6 have an enhanced phosphatase activity directed toward the phosphorylation of the H2AX protein in response to ionizing radiation (IR). Loss of CCDC6 also affects the DNA damage induced G2 arrest, promoting the overcome of G2/M checkpoint. Furthermore, loss of CCDC6 affects the DNA repair mechanisms in G2 and increases the levels of the error prone mechanism of repair, 'Non Homologous End Joining', (NHEJ ) (Merolla et al., 2012). In recent studies it has been reported that the E3 ubiquitin ligase FBXW7 specifically interacts with CCDC6 driving its degradation in a proteasomal dependent manner (Zhao et al., 2012). Moreover, CCDC6 degradation is impaired in response to DNA damage. The post translational events that regulate the phosphorylation status and the abundance of CCDC6 during the cell cycle have been also investigated (Morra et al., 2015a).
In human cancers, it has been recently reported that the loss of CCDC6 in the Testicular Germ Cell Tumors (TGCTs) might aid the spermatogonial cells to benefit from a pro-survival pathway in order to evade the toxic effects of endogenous oxidants and then promote testicular neoplastic growth (Staibano et al., 2013). Furthermore, in NSCLC, TMA immunostaining for CCDC6 revealed low CCDC6 expression in about 30% of the NSCLC analyzed (45 out of 138), besides the low penetrance of reported CCDC6 mutations or CCDC6/RET rearrangements. The defective expression of CCDC6 in NSCLC has been negatively correlated to DFS and OS (Morra et al., 2015b). Moreover, the defective expression of CCDC6 causes an impairment of DNA repair by homologous recombination (HR) in NSCLC cells, making these cells sensitive to PARP inhibitors. Finally, it has been reported that beside the CCDC6 sporadic mutations, molecular alterations in CCDC6 modifiers, such as Fbxw7 E3 ubiquitin ligase or USP7 de-ubiquitinating enzyme, may also account for the impairment of the CCDC6 turnover and may be critical in optimizing personalized therapy. About 20% of primary NSCLC exhibit reduced USP7 expression and also show barely detectable levels of CCDC6 that may increase their sensitivity to PARP inhibitors (Morra et al., 2015a). Therefore, the indication of CCDC6 as a novel USP7 substrate provides the rational for novel personalized therapy in NSCLC patients carrying USP7 deficiency.
Therefore, as the loss of CCDC6 causes an impairment of DNA repair by homologous recombination, in tumors that harbor low levels of USP7, the detection of low levels of its substrate CCDC6 should provide the indications for the PARP inhibitors treatment (Morra et al., 2015b).
 
  Fig. 2: CCDC6 interactors and modifiers.
Homology Sequencing analysis of CCDC6 cDNA shows that CCDC6 has not significant homology to know genes. Weak but significant homology to the myosin superfamily.

Mutations

 
  Fig. 3 : CCDC6 rearrangements. The red arrow shows the RET/PTC1 and the black one shows the CCDC6/PDGFRB breakpoint.
Germinal None
Somatic Fusions: CCDC6/PDGFRB, CCDC6/ROS1; VPS13B/CCDC6; CCDC6/RET; CCDC6/ANK3; CCDC6/UBE2D1; CCDC6/PTEN; FGFR2/CCDC6; KITLG/CCDC6; CCDC6/LIPI
Point mutations: TCGAcbioPortal& Cosmic -CCDC6 - dist

Implicated in

Note The 60 amino acid fragment of the CCDC6 coiled coil domain, included in the RET/PTC1 gene product rearrangement, has been shown to be necessary for homodimerization, constitutive activation and transforming ability of the oncoprotein (Tong et al., 1997; Jhiang, 2000) (Figure 2).
In few cases of atypical chronic myelogeneous leukaemia (aCML) the first 368 aa of CCDC6 has been found fused to the tyrosine kinase domain of the PDGFRB. The chromosomal event is a t(5;10) translocation. In atypical CMLs carrying the CCDC6/PDGFRB rearrangement, the fusion protein is a product of 948 aa containing most of the coiled-coil domain of CCDC6 and the transmembrane and the tyrosine kinase domains of the PDGFRB. The reciprocal product of the translocation has not been found (Kulkarni et al., 2000; Schwaller et al., 2001).
Finally, CCDC6/PTEN rearrangements have also been identified in irradiated thyroid cell lines. Sequence analysis revealed a transcript consisting of exon 1 and 2 of CCDC6 fused to exon 3 and 6 of PTEN (Puxeddu et al., 2005) (Figure 3).
Notably, in most cancer harboring the CCDC6 gene rearrangements, the product of the normal allele is absent or functionally inactivated by a dominant negative mechanism (Celetti et al., 2004).
Entity Papillary thyroid carcinoma
Cytogenetics inv(10)(q11.2q21) or t(10;10)(q11;q21) CCDC6/RET
t(10;10)(q21;q23) CCDC6/PTEN
t(8;10)(q22;q21) VPS13B/CCDC6
Hybrid/Mutated Gene CCDC6/RET
CCDC6/PTEN
VPS13B/CCDC6
Abnormal Protein The fusion protein CCDC6/RET contains the first 101 aminoacids including part of CCDC6 coiled coil domain and the entire tyrosine kinase domain of RET. The fusion is a constitutively active tyrosine kinase.
Oncogenesis In transgenic mice the fusion CCDC6/RET gave rise to mammary adenocarcinomas and, less frequently, hyperplasia of sebaceous glands and rare benign skin tumors. CCDC6 knock in mice develop thyroid hyperplasia associated with an enhanced CREB1 activity.
The simultaneous occurrence of CCDC6/PTEN, RET/PTC and BRAF mutations have been reported in papillary thyroid carcinomas.
  
Entity negative chronic myeloid leukaemia / chronic myelomonocytic leukemia
Disease atypical chronic myeloid leukemia
Prognosis Too few cases reported but likely to be similar to CML
Cytogenetics t(5;10)(q33;q21.2)
Hybrid/Mutated Gene CCDC6/PDGFRB. In a single case analyzed the translocation was found to be complex at the molecular level.
Abnormal Protein Contains the first 368 amminoacids including part of CCDC6 coiled coil domain of CCDC6 and the leucine zipper of H4 and the entire tyrosine kinase domain and transmembrane domain of PDGFRB
  
Entity Non-small-cell lung cancer (NSCLC)
Disease Adenocarcinoma (NSCLC)
Cytogenetics inv(10)(q11.2q21) or t(10;10)(q11;q21) CCDC6/RET
t(6;10)(q22;q21) CCDC6/ROS1
t(10;10)(q21;q21) CCDC6/CTNNA3
t(10;12)(q21;q21) KITLG/CCDC6
t(10;21)(q21;q11) CCDC6/LIPI
Hybrid/Mutated Gene CCDC6/RET CCDC6/ROS1 CCDC6/CTNNA3 KITLG/CCDC6 CCDC6/LIPI
Abnormal Protein Contains the first 101 amino acids including part of CCDC6 coiled coil domain of CCDC6
  
Entity Breast cancer
Cytogenetics t(10;10)(q21;q26) FGFR2/CCDC6
t(10;10)(q21;q21) CCDC6/UBE2D1
Hybrid/Mutated Gene FGFR2/CCDC6
CCDC6/UBE2D1
  
Entity Ovarian epithelial tumor
Cytogenetics t(10;10)(q21;q21) CCDC6/ANK3
Hybrid/Mutated Gene CCDC6/ANK3
  

Breakpoints

 

Bibliography

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Citation

This paper should be referenced as such :
Morra F, Miro C, Napolitano V, Merolla F, Celetti A
CCDC6 (coiled-coil domain containing 6);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/H4ID280.html
History of this paper:
Cross, NCP. CCDC6 (coiled-coil domain containing 6). Atlas Genet Cytogenet Oncol Haematol. 2001;5(3):186-187.
http://documents.irevues.inist.fr/bitstream/handle/2042/37754/06-2001-H4ID280.pdf


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  Atypical Chronic Myeloid Leukemia (aCML)
t(5;10)(q33;q21) CCDC6/PDGFB

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  Thyroid: Papillary carcinoma/Adenocarcinoma
Lung: Translocations in Adenocarcinoma
Lung: Translocations in Small Cell Carcinoma

External links

Nomenclature
HGNC (Hugo)CCDC6   18782
Cards
AtlasH4ID280
Entrez_Gene (NCBI)CCDC6  8030  coiled-coil domain containing 6
AliasesD10S170; H4; PTC; TPC; 
TST1
GeneCards (Weizmann)CCDC6
Ensembl hg19 (Hinxton)ENSG00000108091 [Gene_View]  chr10:61548506-61666414 [Contig_View]  CCDC6 [Vega]
Ensembl hg38 (Hinxton)ENSG00000108091 [Gene_View]  chr10:61548506-61666414 [Contig_View]  CCDC6 [Vega]
ICGC DataPortalENSG00000108091
TCGA cBioPortalCCDC6
AceView (NCBI)CCDC6
Genatlas (Paris)CCDC6
WikiGenes8030
SOURCE (Princeton)CCDC6
Genomic and cartography
GoldenPath hg19 (UCSC)CCDC6  -     chr10:61548506-61666414 -  10q21.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CCDC6  -     10q21.2   [Description]    (hg38-Dec_2013)
EnsemblCCDC6 - 10q21.2 [CytoView hg19]  CCDC6 - 10q21.2 [CytoView hg38]
Mapping of homologs : NCBICCDC6 [Mapview hg19]  CCDC6 [Mapview hg38]
OMIM188550   601985   
Gene and transcription
Genbank (Entrez)AA112388 AK024913 AK055515 AK056848 AK292593
RefSeq transcript (Entrez)NM_005436
RefSeq genomic (Entrez)NC_000010 NC_018921 NG_027819 NT_030059 NW_004929376
Consensus coding sequences : CCDS (NCBI)CCDC6
Cluster EST : UnigeneHs.591360 [ NCBI ]
CGAP (NCI)Hs.591360
Alternative Splicing GalleryENSG00000108091
Gene ExpressionCCDC6 [ NCBI-GEO ]   CCDC6 [ EBI - ARRAY_EXPRESS ]   CCDC6 [ SEEK ]   CCDC6 [ MEM ]
Gene Expression Viewer (FireBrowse)CCDC6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8030
GTEX Portal (Tissue expression)CCDC6
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ16204 (Uniprot)
NextProtQ16204  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ16204
Splice isoforms : SwissVarQ16204 (Swissvar)
PhosPhoSitePlusQ16204
Domains : Interpro (EBI)DUF2046   
Domain families : Pfam (Sanger)DUF2046 (PF09755)   
Domain families : Pfam (NCBI)pfam09755   
DMDM Disease mutations8030
Blocks (Seattle)CCDC6
SuperfamilyQ16204
Human Protein AtlasENSG00000108091
Peptide AtlasQ16204
HPRD09064
IPIIPI00807498   IPI00956015   
Protein Interaction databases
DIP (DOE-UCLA)Q16204
IntAct (EBI)Q16204
FunCoupENSG00000108091
BioGRIDCCDC6
STRING (EMBL)CCDC6
ZODIACCCDC6
Ontologies - Pathways
QuickGOQ16204
Ontology : AmiGOstructural constituent of cytoskeleton  protein binding  cytoplasm  cytoskeleton  biological_process  SH3 domain binding  
Ontology : EGO-EBIstructural constituent of cytoskeleton  protein binding  cytoplasm  cytoskeleton  biological_process  SH3 domain binding  
Pathways : KEGGPathways in cancer    Thyroid cancer   
NDEx Network
Atlas of Cancer Signalling NetworkCCDC6
Wikipedia pathwaysCCDC6
Orthology - Evolution
OrthoDB8030
GeneTree (enSembl)ENSG00000108091
Phylogenetic Trees/Animal Genes : TreeFamCCDC6
Homologs : HomoloGeneCCDC6
Homology/Alignments : Family Browser (UCSC)CCDC6
Gene fusions - Rearrangements
Fusion : MitelmanCCDC6/ANK3 [10q21.2/10q21.2]  
Fusion : MitelmanCCDC6/CTNNA3 [10q21.2/10q21.3]  [t(10;10)(q21;q21)]  
Fusion : MitelmanCCDC6/LIPI [10q21.2/21q11.2]  [t(10;21)(q21;q11)]  
Fusion : MitelmanCCDC6/PDGFRB [10q21.2/5q32]  [t(5;10)(q32;q21)]  
Fusion : MitelmanCCDC6/RET [10q21.2/10q11.21]  [inv(10)(p11q11)]  [inv(10)(q11q11)]  
[inv(10)(q11q21)]  [t(10;17)(q11;q24)]  
Fusion : MitelmanCCDC6/ROS1 [10q21.2/6q22.1]  [t(6;10)(q22;q21)]  
Fusion : MitelmanCCDC6/UBE2D1 [10q21.2/10q21.1]  [t(10;10)(q21;q21)]  
Fusion : MitelmanFGFR2/CCDC6 [10q26.13/10q21.2]  [t(10;10)(q21;q26)]  
Fusion : MitelmanKITLG/CCDC6 [12q21.32/10q21.2]  [t(10;12)(q21;q21)]  
Fusion : MitelmanRET/CCDC6 [10q11.21/10q21.2]  [t(10;10)(q11;q21)]  
Fusion : MitelmanVPS13B/CCDC6 [8q22.2/10q21.2]  [t(8;10)(q22;q21)]  
Fusion : COSMICCCDC6 [10q21.2]  -  RET [10q11.21]  [fusion_1271]  [fusion_1272]  [fusion_1480]  [fusion_1515]  [fusion_1516]  [fusion_1518]  [fusion_1532]  
[fusion_1533]  
Fusion: TCGACCDC6 10q21.2 ANK3 10q21.2 BRCA LUAD OV
Fusion: TCGACCDC6 10q21.2 LIPI 21q11.2 LUAD
Fusion: TCGACCDC6 10q21.2 RET 10q11.21 THCA
Fusion: TCGACCDC6 10q21.2 UBE2D1 10q21.1 BRCA
Fusion: TCGAFGFR2 10q26.13 CCDC6 10q21.2 BRCA
Fusion: TCGAKITLG 12q21.32 CCDC6 10q21.2 LUSC
Fusion: TCGARET 10q11.21 CCDC6 10q21.2 THCA
Fusion: TCGAVPS13B 8q22.2 CCDC6 10q21.2 THCA
Fusion : TICdbCCDC6 [10q21.2]  -  PDGFRB [5q32]
Fusion : TICdbCCDC6 [10q21.2]  -  RET [10q11.21]
Fusion Cancer (Beijing)CCDC6 [10q21.2]  -  ROS1 [6q22.1]  [FUSC002622]  [FUSC002622]
Fusion Cancer (Beijing)ROS1 [6q22.1]  -  CCDC6 [10q21.2]  [FUSC002665]  [FUSC002665]
Polymorphisms : SNP, variants
NCBI Variation ViewerCCDC6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CCDC6
dbVarCCDC6
ClinVarCCDC6
1000_GenomesCCDC6 
Exome Variant ServerCCDC6
ExAC (Exome Aggregation Consortium)CCDC6 (select the gene name)
Genetic variants : HAPMAP8030
Genomic Variants (DGV)CCDC6 [DGVbeta]
Mutations
ICGC Data PortalCCDC6 
TCGA Data PortalCCDC6 
Broad Tumor PortalCCDC6
OASIS PortalCCDC6 [ Somatic mutations - Copy number]
Cancer Gene: CensusCCDC6 
Somatic Mutations in Cancer : COSMICCCDC6 
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 CCDC6
DgiDB (Drug Gene Interaction Database)CCDC6
DoCM (Curated mutations)CCDC6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CCDC6 (select a term)
intoGenCCDC6
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)10:61548506-61666414  ENSG00000108091
CONAN: Copy Number AnalysisCCDC6 
Mutations and Diseases : HGMDCCDC6
OMIM188550    601985   
MedgenCCDC6
Genetic Testing Registry CCDC6
NextProtQ16204 [Medical]
TSGene8030
GENETestsCCDC6
Huge Navigator CCDC6 [HugePedia]
snp3D : Map Gene to Disease8030
BioCentury BCIQCCDC6
ClinGenCCDC6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8030
Chemical/Pharm GKB GenePA134904022
Clinical trialCCDC6
Miscellaneous
canSAR (ICR)CCDC6 (select the gene name)
Probes
Litterature
PubMed54 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCCDC6
EVEXCCDC6
GoPubMedCCDC6
iHOPCCDC6
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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