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PDE11A (phosphodiesterase 11A)

Written2010-01Rossella Libé, Jérôme Bertherat
INSERM U567, CNRS 8104, Institut Cochin, Service de Maladies Endocriniennes et Metabolique, Hopital Cochin, Paris, France

(Note : for Links provided by Atlas : click)

Identity

Other aliasFLJ23693
MGC133355
MGC133356
PDE11A1
PDE11A2
PDE11A3
PPNAD2
HGNC (Hugo) PDE11A
LocusID (NCBI) 50940
Atlas_Id 44448
Location 2q31.2  [Link to chromosome band 2q31]
Location_base_pair Starts at 177623249 and ends at 177888739 bp from pter ( according to hg19-Feb_2009)  [Mapping PDE11A.png]
 
Fusion genes
(updated 2016)
ITGAV (2q32.1) / PDE11A (2q31.2)NFE2L2 (2q31.2) / PDE11A (2q31.2)

DNA/RNA

 
Description PDE11A is the most recently discovered PDE enzyme family. In this family, only one gene, PDE11A, has been identified. It is a dual phosphodiesterase that hydrolyzes both cAMP and cGMP.
Transcription Four different isoforms of PDE11A (PDE11A1→A4) have been identified. The longest variant, PDE11A4 is composed of 20 coding exons of varying length, separated by introns, giving the gene a total length of 4441 bps.

Protein

Description PDE11A4 is a protein of 104 kDa: it contains two N-terminal GAF domains (between exons 3-12) and one C-terminal catalytic domain (between exons 14-22).
Expression Isoform 1 is present in prostate, pituitary, heart, liver and skeletal muscle. Isoform 2 and 3 are expressed in the testis. Isoform 4 is the only isoform of the enzyme expressed in the adrenal cortex, where it is expressed substantially less than in the prostate.
Localisation Cytoplasm > cytosol.
Function PDE11A enzymes catalyze the hydrolysis of both cAMP and cGMP to 5'-AMP and 5'-GMP, respectively. This takes part in the down-regulation of the cAMP and cGMP signaling.
Inactive mutations of the isoform PDE11A4 gene have been identified in patients with adrenal Cushing syndrome due to micronodular adrenocortical hyperplasia. An association of PDE11A4 variants and other neoplasms is suggested since a higher frequency of PDE11A4 missense mutations is observed in patients with macronodular adrenal hyperplasia and testicular tumors than in the controls.
Homology The catalytic domain is conserved among the 4 isoforms of PDE11A.
A high sequence similarity of 42-51% is found within the amino acid sequences of the catalytic regions of PDEs containing a Gaf sequence (i.e. PDE2A, PDE5A, PDE6B, PDE6C, PDE10A and PDE11A).
Gene conserved among species: Pan troglodytes: 98.6%; Canis lupus familiaris: 96.4%; Bos taurus: 95.9%; Mus musculus: 94.6%; Rattus norvegicus: 94.5%; Gallus gallus: 90%; Danio rerio: 90%.

Mutations

 
  Non-sense mutations (yellow) and missense mutations (green) described in adrenocortical tumor (PPNAD, AIMAH, ACA and ACC).
Germinal Non sense.
Three PDE11A nonsense mutations leading to a premature stop codon were identified in 3 kindreds with adrenal Cushing syndrome due to micronodular adrenocortical hyperplasia.
Other missense mutations (genetic variants) are described in adrenocortical tumor, as macronodular adrenal hyperplasia (AIMAH), adrenocortical adenoma (ACA), adrenocortical carcinoma (ACC) and testicular tumors.
Somatic Loss of heterozygosity with loss of wild type allele have been reported in adrenocortical tumor (benign and malignant) with PDE11A4 missense mutations.

Implicated in

Note
  
Entity Adrenal Cushing syndrome due to micronodular adrenocortical hyperplasia
Disease ACTH-independant chronic oversecretion of cortisol due to bilateral adrenal involvement. Pathological examination demonstrates diffuse micronodular hyperaplasia of the cortex of both adrenal. These nodules can be pigmented as observed in primary pigmented nodular adrenocortical disease (PPNAD).
Prognosis Morbidity and mortality of non treated Cushing syndrome is high. However after treatment (bilateral adrenalectomy in most cases) there is a clear improvement and the overall prognosis is good, the main side effect of the treatment being adrenal deficiency.
Oncogenesis In the patients with non-sense mutations a loss of the wild type allele was demonstrated in the adrenal nodes, supporting the hypothesis that PDE11A4 is a tumor suppressor gene.
  
  
Entity ACTH-independent macronodular adrenal hyperplasia (AIMAH)
Disease AIMAH is a rare form of benign bilateral adrenocortical tumor. It can be associated to an overt Cushing's syndrome (CS). Nowadays, the most frequent clinical presentation is that of bilateral adrenal incidentalomas. The initial endocrine evaluation usually demonstrates subtle abnormalities of cortisol secretion, suggesting a subclinical CS.
Prognosis Morbidity and mortality of non treated Cushing syndrome is high. However after treatment (bilateral adrenalectomy in most cases) there is a clear improvement and the overall prognosis is good, the main side effect of the treatment being adrenal deficiency.
Cytogenetics A higher frequency of missense PDE11A mutations (genetic variants) than in healthy subjects are found.
Oncogenesis The higher frequency of PDE11A missense mutations suggests a role of PDE11A in the genetic predisposition to adrenal tumors.
  
  
Entity Testicular germ cells tumors (TGCT)
Disease It is the most common malignancy in Caucasian men aged from 15 to 45 years old. A genetic basis for TGCT is supported by familial clustering, younger-than-usual age at diagnosis, and an increased risk of bilateral disease.
Prognosis More than 90% of patients with newly diagnosed TGCT are cured, and delay in diagnosis correlates with a higher stage at presentation for treatment.
Cytogenetics Recently, PDE11A missense mutations (genetic variants) have been reported in TGCT. The frequency was significantly higher in patients with TGCT than in healthy subjects.
Oncogenesis PDE11A variants are involved in the testicular tumorigenesis and may modify the risk of familial and bilateral TGCT.
  
  
Entity Adrenocortical carcinoma (ACC)
Disease ACC is a rare malignant tumor, with an estimated prevalence between 4 and 12 per million in adults.
Prognosis The overall survival varies according to tumor stage. However the overall survival is poor and below 30% at 5 years in most series.
Cytogenetics A higher frequency of a polymorphism in exon 6 (E421E) and of three associated polymorphisms located in intron 10-exon 11-intron 11 is found in ACCs than in healthy subjects.
Oncogenesis The synonymous E421E variant and the intron 10/intron 11 variants could play a role in the predisposition to ACC development.
  

Bibliography

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PMID 16767104
 
A cAMP-specific phosphodiesterase (PDE8B) that is mutated in adrenal hyperplasia is expressed widely in human and mouse tissues: a novel PDE8B isoform in human adrenal cortex.
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PMID 18431404
 
Functional phosphodiesterase 11A mutations may modify the risk of familial and bilateral testicular germ cell tumors.
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PMID 19549888
 
Unraveling the molecular basis of micronodular adrenal hyperplasia.
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PMID 18438169
 
Clinical and genetic heterogeneity, overlap with other tumor syndromes, and atypical glucocorticoid hormone secretion in adrenocorticotropin-independent macronodular adrenal hyperplasia compared with other adrenocortical tumors.
Hsiao HP, Kirschner LS, Bourdeau I, Keil MF, Boikos SA, Verma S, Robinson-White AJ, Nesterova M, Lacroix A, Stratakis CA.
J Clin Endocrinol Metab. 2009 Aug;94(8):2930-7. Epub 2009 Jun 9.
PMID 19509103
 
PDE9A, PDE10A, and PDE11A expression in rat trigeminovascular pain signalling system.
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Brain Res. 2009 Jul 24;1281:25-34. Epub 2009 May 13.
PMID 19445908
 
Pharmacogenetics studies in STAR*D: strengths, limitations, and results.
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PMID 19880459
 
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PMID 18559625
 
3',5'-cyclic nucleotide phosphodiesterase 11A: localization in human tissues.
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PMID 15800651
 
ACTH-independent Cushing's syndrome with bilateral micronodular adrenal hyperplasia and ectopic adrenocortical adenoma.
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PMID 19915020
 
Association of PDE11A global haplotype with major depression and antidepressant drug response.
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Neuropsychiatr Dis Treat. 2009;5:163-70. Epub 2009 Apr 8.
PMID 19557111
 
Binding of cyclic nucleotides to phosphodiesterase 10A and 11A GAF domains does not stimulate catalytic activity.
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PMID 19689430
 
Identification, synthesis and SAR of amino substituted pyrido[3,2b]pyrazinones as potent and selective PDE5 inhibitors.
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PMID 19540112
 
Analysis of genetic variants of phosphodiesterase 11A in acromegalic patients.
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PMID 19671705
 
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PMID 17544419
 
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PMID 16094044
 
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PMID 19063937
 
Detection of somatic beta-catenin mutations in primary pigmented nodular adrenocortical disease (PPNAD).
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PMID 18419788
 
Variants in PDE11A and PDE1A are not associated with citalopram response.
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PMID 19068395
 
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PMID 18706893
 
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Int J Impot Res. 2005 May-Jun;17(3):216-23.
PMID 15800654
 
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PMID 19641165
 
High biochemical selectivity of tadalafil, sildenafil and vardenafil for human phosphodiesterase 5A1 (PDE5) over PDE11A4 suggests the absence of PDE11A4 cross-reaction in patients.
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Phosphodiesterase genes are associated with susceptibility to major depression and antidepressant treatment response.
Wong ML, Whelan F, Deloukas P, Whittaker P, Delgado M, Cantor RM, McCann SM, Licinio J.
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PMID 17008408
 
Genomic organization of the human phosphodiesterase PDE11A gene. Evolutionary relatedness with other PDEs containing GAF domains.
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PMID 11121118
 
Isolation and characterization of two novel phosphodiesterase PDE11A variants showing unique structure and tissue-specific expression.
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Identification of rat cyclic nucleotide phosphodiesterase 11A (PDE11A): comparison of rat and human PDE11A splicing variants.
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PMID 11134002
 

Citation

This paper should be referenced as such :
Lib&eacute, R ; Bertherat, J
PDE11A (phosphodiesterase 11A)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(11):1027-1031.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PDE11AID44448ch2q31.html


External links

Nomenclature
HGNC (Hugo)PDE11A   8773
Cards
AtlasPDE11AID44448ch2q31
Entrez_Gene (NCBI)PDE11A  50940  phosphodiesterase 11A
AliasesPPNAD2
GeneCards (Weizmann)PDE11A
Ensembl hg19 (Hinxton)ENSG00000128655 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000128655 [Gene_View]  chr2:177623249-177888739 [Contig_View]  PDE11A [Vega]
ICGC DataPortalENSG00000128655
TCGA cBioPortalPDE11A
AceView (NCBI)PDE11A
Genatlas (Paris)PDE11A
WikiGenes50940
SOURCE (Princeton)PDE11A
Genetics Home Reference (NIH)PDE11A
Genomic and cartography
GoldenPath hg38 (UCSC)PDE11A  -     chr2:177623249-177888739 -  2q31.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDE11A  -     2q31.2   [Description]    (hg19-Feb_2009)
EnsemblPDE11A - 2q31.2 [CytoView hg19]  PDE11A - 2q31.2 [CytoView hg38]
Mapping of homologs : NCBIPDE11A [Mapview hg19]  PDE11A [Mapview hg38]
OMIM604961   610475   
Gene and transcription
Genbank (Entrez)AB036704 AB038041 AF281865 AI919276 AJ251509
RefSeq transcript (Entrez)NM_001077196 NM_001077197 NM_001077358 NM_016953
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PDE11A
Cluster EST : UnigeneHs.570273 [ NCBI ]
CGAP (NCI)Hs.570273
Alternative Splicing GalleryENSG00000128655
Gene ExpressionPDE11A [ NCBI-GEO ]   PDE11A [ EBI - ARRAY_EXPRESS ]   PDE11A [ SEEK ]   PDE11A [ MEM ]
Gene Expression Viewer (FireBrowse)PDE11A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)50940
GTEX Portal (Tissue expression)PDE11A
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9HCR9   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9HCR9  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9HCR9
Splice isoforms : SwissVarQ9HCR9
Catalytic activity : Enzyme3.1.4.35 [ Enzyme-Expasy ]   3.1.4.353.1.4.35 [ IntEnz-EBI ]   3.1.4.35 [ BRENDA ]   3.1.4.35 [ KEGG ]   
PhosPhoSitePlusQ9HCR9
Domaine pattern : Prosite (Expaxy)PDEASE_I (PS00126)   
Domains : Interpro (EBI)GAF    GAF_dom-like    HD/PDEase_dom    PDEase    PDEase_catalytic_dom    PDEase_CS   
Domain families : Pfam (Sanger)GAF (PF01590)    PDEase_I (PF00233)   
Domain families : Pfam (NCBI)pfam01590    pfam00233   
Domain families : Smart (EMBL)GAF (SM00065)  HDc (SM00471)  
Conserved Domain (NCBI)PDE11A
DMDM Disease mutations50940
Blocks (Seattle)PDE11A
SuperfamilyQ9HCR9
Human Protein AtlasENSG00000128655
Peptide AtlasQ9HCR9
HPRD05391
IPIIPI00784419   IPI00783388   IPI00784056   IPI00917797   IPI01010718   IPI00073708   IPI00917066   IPI00917380   
Protein Interaction databases
DIP (DOE-UCLA)Q9HCR9
IntAct (EBI)Q9HCR9
FunCoupENSG00000128655
BioGRIDPDE11A
STRING (EMBL)PDE11A
ZODIACPDE11A
Ontologies - Pathways
QuickGOQ9HCR9
Ontology : AmiGOcyclic-nucleotide phosphodiesterase activity  3',5'-cyclic-nucleotide phosphodiesterase activity  3',5'-cyclic-AMP phosphodiesterase activity  cGMP-stimulated cyclic-nucleotide phosphodiesterase activity  cellular_component  cytosol  cAMP catabolic process  signal transduction  cAMP binding  cGMP binding  perikaryon  cGMP catabolic process  metal ion binding  3',5'-cyclic-GMP phosphodiesterase activity  
Ontology : EGO-EBIcyclic-nucleotide phosphodiesterase activity  3',5'-cyclic-nucleotide phosphodiesterase activity  3',5'-cyclic-AMP phosphodiesterase activity  cGMP-stimulated cyclic-nucleotide phosphodiesterase activity  cellular_component  cytosol  cAMP catabolic process  signal transduction  cAMP binding  cGMP binding  perikaryon  cGMP catabolic process  metal ion binding  3',5'-cyclic-GMP phosphodiesterase activity  
Pathways : KEGGPurine metabolism    Morphine addiction   
REACTOMEQ9HCR9 [protein]
REACTOME PathwaysR-HSA-418555 [pathway]   
NDEx NetworkPDE11A
Atlas of Cancer Signalling NetworkPDE11A
Wikipedia pathwaysPDE11A
Orthology - Evolution
OrthoDB50940
GeneTree (enSembl)ENSG00000128655
Phylogenetic Trees/Animal Genes : TreeFamPDE11A
HOVERGENQ9HCR9
HOGENOMQ9HCR9
Homologs : HomoloGenePDE11A
Homology/Alignments : Family Browser (UCSC)PDE11A
Gene fusions - Rearrangements
Fusion : MitelmanITGAV/PDE11A [2q32.1/2q31.2]  [t(2;2)(q31;q32)]  
Fusion : MitelmanNFE2L2/PDE11A [2q31.2/2q31.2]  [t(2;2)(q31;q31)]  
Fusion: TCGAITGAV 2q32.1 PDE11A 2q31.2 LUAD
Fusion: TCGANFE2L2 2q31.2 PDE11A 2q31.2 LUSC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDE11A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDE11A
dbVarPDE11A
ClinVarPDE11A
1000_GenomesPDE11A 
Exome Variant ServerPDE11A
ExAC (Exome Aggregation Consortium)PDE11A (select the gene name)
Genetic variants : HAPMAP50940
Genomic Variants (DGV)PDE11A [DGVbeta]
DECIPHERPDE11A [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDE11A 
Mutations
ICGC Data PortalPDE11A 
TCGA Data PortalPDE11A 
Broad Tumor PortalPDE11A
OASIS PortalPDE11A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDE11A  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDE11A
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 PDE11A
DgiDB (Drug Gene Interaction Database)PDE11A
DoCM (Curated mutations)PDE11A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDE11A (select a term)
intoGenPDE11A
NCG5 (London)PDE11A
Cancer3DPDE11A(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604961    610475   
Orphanet18376   
MedgenPDE11A
Genetic Testing Registry PDE11A
NextProtQ9HCR9 [Medical]
TSGene50940
GENETestsPDE11A
Target ValidationPDE11A
Huge Navigator PDE11A [HugePedia]
snp3D : Map Gene to Disease50940
BioCentury BCIQPDE11A
ClinGenPDE11A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD50940
Chemical/Pharm GKB GenePA33121
Clinical trialPDE11A
Miscellaneous
canSAR (ICR)PDE11A (select the gene name)
Probes
Litterature
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