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PASD1 (PAS domain containing 1)

Written2013-04Ghazala Khan, Barbara-Ann Guinn
Department of Life Sciences, University of Bedfordshire, Park Square, Luton, UK (GK); Department of Life Sciences, University of Bedfordshire, Park Square, Luton, UK, Cancer Sciences Unit, University of Southampton, Southampton, UK, Department of Haematological Medicine, Kings College London, London, UK (BAG)

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)CT63
Other aliasOXTES1
HGNC (Hugo) PASD1
LocusID (NCBI) 139135
Atlas_Id 44567
Location Xq28  [Link to chromosome band Xq28]
Location_base_pair Starts at 150732007 and ends at 150845211 bp from pter ( according to hg19-Feb_2009)  [Mapping PASD1.png]
Fusion genes
(updated 2016)
DCX (Xq23) / PASD1 (Xq28)TEC (4p12) / PASD1 (Xq28)
Note PASD1 gene encodes a protein thought to be a transcription factor (Entrez Gene). In normal tissues expression is restricted to immunologically protected sites (which lack MHC class I expression) such as the testes, however the demonstration of expression in haematological malignancies and a range of solid tumour cell lines indicates it is a cancer-testis antigen (Liggins et al., 2004a; Liggins et al., 2004b; Guinn et al., 2005; Cooper et al., 2006; Sahota et al., 2006).

DNA/RNA

 
  Structure of the PASD1 gene from which (A) PASD1_v1 and (B) PASD1_v2 and transcribed. Lines indicate introns, boxes exons, the filled box the retained intron in PASD1_v1, "atg" the predicted start site and "tga" the predicted stop site (Liggins et al., 2004a).
Description 113205 bases.
Transcription The PASD1 gene is alternatively spliced into two transcripts named PASD1_v1 and PASD1_v2. PASD1_v2 lacks intron 14 and a retained stop signal (Liggins et al., 2004a). Differential splicing is predicted to create additional novel PASD1 isoforms as a protein smaller than PASD1_v1 and PASD1_v2 has been detected in OCi-Ly3 and FEPD cells (Cooper et al., 2006).
Transcripts found in 33% (4 of 12) acute myeloid leukaemia patients, 1 of 6 chronic myeloid leukaemia patients and 4 of 16 cell lines (Guinn et al., 2005).
Transcripts have been found in 5 of 11 multiple myeloma cell lines including THIEL and RPMI8226, and 14 of 16 primary multiple myeloma samples (Sahota et al., 2006), 22 of 25 B- and T-cell malignancy cell lines (Liggins et al., 2010).

Protein

 
  Schematic illustration of the functional domains within the PASD1 protein. PASD1a protein translated from PASD1_v1 (A) and PASD1b translated from PASD1_v2 (B) are shown (Liggins et al., 2004a).
Description Contains a Per Arnt Sim (PAS) domains in the N-terminal regions between aa 32-94 and aa 41-137 (Liggins et al., 2004a).
Expression Expression highest in G361 (melanoma) and SW480 (colorectal adenocarcinoma) cell lines of a panel of nine tested. Expression in 25 of 68 solid tumours on matched tumour/normal arrays (Liggins et al., 2004a).
Expression restricted in normal tissues, placenta and testes, not detected in panel of normal tissue cDNAs. Expression also found in K562, Jurkats (T-cell leukaemia), Hn5 (head and neck cancer) and highest in H1299 (lung cancer) cell lines by real-time PCR (Guinn et al., 2005).
Of the normal tissues expression was restricted to testes and not found in a range of normal tissues including brain, liver, kidney, placenta, breast, uterus or ovary (Guinn et al., 2005; Cooper et al., 2006).
Expression of PASD1 was demonstrated in OCI-Ly3 (non-germinal centre diffuse large B-cell lymphoma-derived cells), FEDP (ALK-negative anaplastic large-cell lymphoma), Granta519 (mantle cell lymphoma) KM-H2 (Hodgkin's lymphoma), K562 (chronic myeloid leukaemia) and Thiel (multiple myeloma) cell lines and 21/51 diffuse large B-cell lymphoma patients, 4/9 mantle cell lymphoma, 4/15 follicular lymphomas and a range of other tumour cells from patients with haematological malignancies (Cooper et al., 2006).
Expression has been detected in the multiple myeloma cell lines THIEL and RPMI8226, in the testis and in two of four primary multiple myeloma tumour samples (Sahota et al., 2006).
Not found in 78 basal cell carcinoma by real-time PCR (Ghafouri-Fard et al., 2010).
Localisation In normal tissues expression was only found in the nuclei of a subpopulation of spermatogonia near the basal membrane in the testicular tubules (Cooper et al., 2006).
PASD1 protein has shown variable expression. In OCI-Ly3 cells, PASD1 expression was found on the membrane and in the cytoplasm. Nuclear staining of KM-H2, K562 and Thiel cells, nuclear and cytoplasmic staining of Granta519 (Cooper et al., 2006).
Function The protein is thought to be a transcription factor (Entrez Gene). No role in human cell cycle (Denniss and Guinn, unpublished data). Detected by virtue of patient humoral responses (Liggins et al., 2004b; Guinn et al., 2005), it has shown to stimulate CD3+ (Guinn et al., 2005), CD4+ (Ait-Tahar et al., 2011) and CD8+ T cell responses (Ait-Tahar et al., 2009; Joseph-Pietras et al., 2010; Hardwick et al., submitted) in mixed lymphocyte reactions (MLR) and cytotoxic T lymphocyte (CTL) assays.
Homology PASD1 has been identified in cow, chicken and mouse where it is known as GM1141 (Entrez Gene). Similarity to the CLOCK gene in mice which is essential for circadian behaviour.

Implicated in

Note
  
Entity Diffuse large B-cell lymphoma (DLBCL)
Note DLBCL is the most common type of non-Hodgkins lymphoma and is caused by malignant mature B lymphocytes. Around half the number of patients diagnosed die from the disease (Alizadeh et al., 2000). Using gene expression patterns two types of DLBCL have been identified, 'germinal centre B-like DLBCL' and 'activated B-like DLBCL' (Alizadeh et al., 2000). PASD1 antigen is recognized by DLBCL patient sera (Liggins et al., 2004b)
Prognosis Germinal centre markers CD10, BCL6 and non-germinal centre marker MUM1 have been used to identify prognosis and survival of DLBCL patients. CD10 or BCL6 expression predicted better overall survival but MUM1 expression suggested worse overall survival (Hans et al., 2004). Germinal centre type associated with good prognosis. Patients with non-germinal centre type showed serum reactivity with PASD1, and PASD1_v2 expression was restricted to non-germinal cell lines (Liggins et al., 2004a).
  
  
Entity Acute myeloid leukaemia (AML) and chronic myeloid leukaemia (CML)
Note PASD1 was recognized by 35% of AML, 6% of CML and 10% of DLBCL sera but not the normal donor sera. Expression was found in 33% (4 of 12) AML and 17% (1 of 6) chronic myeloid leukaemia patient samples (Guinn et al., 2005) by RT-PCR and confirmed by RQ-PCR.
  
  
Entity Multiple myeloma
Note Cancer of the plasma cells in bone marrow. PASD1 expression has been seen in multiple myeloma cell lines by RT-PCR and in primary multiple myeloma samples by Q-PCR at presentation and previously treated cases (Sahota et al., 2006).
  

Bibliography

CD4-positive T-helper cell responses to the PASD1 protein in patients with diffuse large B-cell lymphoma.
Ait-Tahar K, Liggins AP, Collins GP, Campbell A, Barnardo M, Cabes M, Lawrie CH, Moir D, Hatton C, Banham AH, Pulford K.
Haematologica. 2011 Jan;96(1):78-86. doi: 10.3324/haematol.2010.028241. Epub 2010 Sep 17.
PMID 20851862
 
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM.
Nature. 2000 Feb 3;403(6769):503-11.
PMID 10676951
 
PASD1, a DLBCL-associated cancer testis antigen and candidate for lymphoma immunotherapy.
Cooper CD, Liggins AP, Ait-Tahar K, Roncador G, Banham AH, Pulford K.
Leukemia. 2006 Dec;20(12):2172-4. Epub 2006 Oct 5.
PMID 17024112
 
Elevated expression levels of testis-specific genes TEX101 and SPATA19 in basal cell carcinoma and their correlation with clinical and pathological features.
Ghafouri-Fard S, Abbasi A, Moslehi H, Faramarzi N, Taba Taba Vakili S, Mobasheri MB, Modarressi MH.
Br J Dermatol. 2010 Apr;162(4):772-9. doi: 10.1111/j.1365-2133.2009.09568.x. Epub 2009 Nov 3.
PMID 19886887
 
Humoral detection of leukaemia-associated antigens in presentation acute myeloid leukaemia.
Guinn BA, Bland EA, Lodi U, Liggins AP, Tobal K, Petters S, Wells JW, Banham AH, Mufti GJ.
Biochem Biophys Res Commun. 2005 Oct 7;335(4):1293-304.
PMID 16112646
 
Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray.
Hans CP, Weisenburger DD, Greiner TC, Gascoyne RD, Delabie J, Ott G, Muller-Hermelink HK, Campo E, Braziel RM, Jaffe ES, Pan Z, Farinha P, Smith LM, Falini B, Banham AH, Rosenwald A, Staudt LM, Connors JM, Armitage JO, Chan WC.
Blood. 2004 Jan 1;103(1):275-82. Epub 2003 Sep 22.
PMID 14504078
 
DNA vaccines to target the cancer testis antigen PASD1 in human multiple myeloma.
Joseph-Pietras D, Gao Y, Zojer N, Ait-Tahar K, Banham AH, Pulford K, Rice J, Savelyeva N, Sahota SS.
Leukemia. 2010 Nov;24(11):1951-9. doi: 10.1038/leu.2010.196. Epub 2010 Sep 23.
PMID 20861911
 
A panel of cancer-testis genes exhibiting broad-spectrum expression in haematological malignancies.
Liggins AP, Lim SH, Soilleux EJ, Pulford K, Banham AH.
Cancer Immun. 2010 Aug 23;10:8.
PMID 20726502
 
PASD1 is a potential multiple myeloma-associated antigen.
Sahota SS, Goonewardena CM, Cooper CD, Liggins AP, Ait-Tahar K, Zojer N, Stevenson FK, Banham AH, Pulford K.
Blood. 2006 Dec 1;108(12):3953-5.
PMID 17114574
 

Citation

This paper should be referenced as such :
Khan, G ; Guinn, BA
PASD1 (PAS domain containing 1)
Atlas Genet Cytogenet Oncol Haematol. 2013;17(9):630-632.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PASD1ID44567chXq28.html


External links

Nomenclature
HGNC (Hugo)PASD1   20686
Cards
AtlasPASD1ID44567chXq28
Entrez_Gene (NCBI)PASD1  139135  PAS domain containing 1
AliasesCT63; OXTES1
GeneCards (Weizmann)PASD1
Ensembl hg19 (Hinxton)ENSG00000166049 [Gene_View]  chrX:150732007-150845211 [Contig_View]  PASD1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000166049 [Gene_View]  chrX:150732007-150845211 [Contig_View]  PASD1 [Vega]
ICGC DataPortalENSG00000166049
TCGA cBioPortalPASD1
AceView (NCBI)PASD1
Genatlas (Paris)PASD1
WikiGenes139135
SOURCE (Princeton)PASD1
Genetics Home Reference (NIH)PASD1
Genomic and cartography
GoldenPath hg19 (UCSC)PASD1  -     chrX:150732007-150845211 +  Xq28   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PASD1  -     Xq28   [Description]    (hg38-Dec_2013)
EnsemblPASD1 - Xq28 [CytoView hg19]  PASD1 - Xq28 [CytoView hg38]
Mapping of homologs : NCBIPASD1 [Mapview hg19]  PASD1 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK097552 AM393031 AY270020 AY623425 BC040301
RefSeq transcript (Entrez)NM_173493
RefSeq genomic (Entrez)NC_000023 NC_018934 NG_021218 NT_011681 NW_004929448
Consensus coding sequences : CCDS (NCBI)PASD1
Cluster EST : UnigeneHs.160594 [ NCBI ]
CGAP (NCI)Hs.160594
Alternative Splicing GalleryENSG00000166049
Gene ExpressionPASD1 [ NCBI-GEO ]   PASD1 [ EBI - ARRAY_EXPRESS ]   PASD1 [ SEEK ]   PASD1 [ MEM ]
Gene Expression Viewer (FireBrowse)PASD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)139135
GTEX Portal (Tissue expression)PASD1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8IV76   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8IV76  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8IV76
Splice isoforms : SwissVarQ8IV76
PhosPhoSitePlusQ8IV76
Domaine pattern : Prosite (Expaxy)PAS (PS50112)   
Domains : Interpro (EBI)PAS   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)PAS (SM00091)  
Conserved Domain (NCBI)PASD1
DMDM Disease mutations139135
Blocks (Seattle)PASD1
SuperfamilyQ8IV76
Human Protein AtlasENSG00000166049
Peptide AtlasQ8IV76
HPRD06613
IPIIPI00167383   IPI00855915   
Protein Interaction databases
DIP (DOE-UCLA)Q8IV76
IntAct (EBI)Q8IV76
FunCoupENSG00000166049
BioGRIDPASD1
STRING (EMBL)PASD1
ZODIACPASD1
Ontologies - Pathways
QuickGOQ8IV76
Ontology : AmiGOtranscription coactivator binding  nucleus  nucleoplasm  negative regulation of circadian rhythm  negative regulation of transcription, DNA-templated  rhythmic process  Cry-Per complex  
Ontology : EGO-EBItranscription coactivator binding  nucleus  nucleoplasm  negative regulation of circadian rhythm  negative regulation of transcription, DNA-templated  rhythmic process  Cry-Per complex  
NDEx NetworkPASD1
Atlas of Cancer Signalling NetworkPASD1
Wikipedia pathwaysPASD1
Orthology - Evolution
OrthoDB139135
GeneTree (enSembl)ENSG00000166049
Phylogenetic Trees/Animal Genes : TreeFamPASD1
HOVERGENQ8IV76
HOGENOMQ8IV76
Homologs : HomoloGenePASD1
Homology/Alignments : Family Browser (UCSC)PASD1
Gene fusions - Rearrangements
Fusion: TCGADCX Xq23 PASD1 Xq28 KIRC
Fusion: TCGATEC - PASD1 Xq28 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPASD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PASD1
dbVarPASD1
ClinVarPASD1
1000_GenomesPASD1 
Exome Variant ServerPASD1
ExAC (Exome Aggregation Consortium)PASD1 (select the gene name)
Genetic variants : HAPMAP139135
Genomic Variants (DGV)PASD1 [DGVbeta]
DECIPHER (Syndromes)X:150732007-150845211  ENSG00000166049
CONAN: Copy Number AnalysisPASD1 
Mutations
ICGC Data PortalPASD1 
TCGA Data PortalPASD1 
Broad Tumor PortalPASD1
OASIS PortalPASD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPASD1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPASD1
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)X-chromosome gene database
BioMutasearch PASD1
DgiDB (Drug Gene Interaction Database)PASD1
DoCM (Curated mutations)PASD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PASD1 (select a term)
intoGenPASD1
NCG5 (London)PASD1
Cancer3DPASD1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
MedgenPASD1
Genetic Testing Registry PASD1
NextProtQ8IV76 [Medical]
TSGene139135
GENETestsPASD1
Huge Navigator PASD1 [HugePedia]
snp3D : Map Gene to Disease139135
BioCentury BCIQPASD1
ClinGenPASD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD139135
Chemical/Pharm GKB GenePA134909788
Clinical trialPASD1
Miscellaneous
canSAR (ICR)PASD1 (select the gene name)
Probes
Litterature
PubMed18 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePASD1
EVEXPASD1
GoPubMedPASD1
iHOPPASD1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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