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S100A2 (S100 calcium binding protein A2)

Written2011-11Christopher J Scarlett, Andrew V Biankin
Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St Darlinghurst, NSW 2010, Australia

(Note : for Links provided by Atlas : click)

Identity

Alias_namesS100L
S100 calcium-binding protein A2
Alias_symbol (synonym)CAN19
Other aliasMGC111539
HGNC (Hugo) S100A2
LocusID (NCBI) 6273
Atlas_Id 42191
Location 1q21.3  [Link to chromosome band 1q21]
Location_base_pair Starts at 153561109 and ends at 153565830 bp from pter ( according to hg19-Feb_2009)  [Mapping S100A2.png]
Fusion genes
(updated 2016)
EIF3D (22q12.3) / S100A2 (1q21.3)MID1 (Xp22.2) / S100A2 (1q21.3)RPRD2 (1q21.3) / S100A2 (1q21.3)
S100A2 (1q21.3) / EIF3D (22q12.3)S100A2 (1q21.3) / SGK223 (8p23.1)

DNA/RNA

 
  The S100A2 gene spans a total region of 4723 bp (NM_005978.3) consisting of three exons. Exon 1 is untranslated, exon 2 codes for the N-terminal 47 amino acids and exon 3 codes for the C-terminal 50 amino acids.
Description The nucleotide sequence and genomic organization of the S100A2 gene was originally described by Wicki et al. (1997), using a normal and a tumorigenic breast epithelial cell line. The structure of S100A2 was originally deduced by the analysis of cDNA from a positive genomic clone from an EMBL-3 SP6/T7 human female peripheral blood leukocyte genomic library (Clontech, no. HL 1111j). The human S100A2 gene is located next to the S100A4 locus on chromosome 1q21.3 within a cluster of S100 genes (Wolf et al., 2011), and part of the epidermal differentiation complex (Wolf et al., 2011). The S100A2 gene spans a total region of 4723 bp (NM_005978.3) consisting of three exons. The three-exon-structure contains the coding sequence within exons two and three, reflecting the common composition of S100 genes. Exon 1 is untranslated, exon 2 codes for the N-terminal 47 amino acids and exon 3 codes for the C-terminal 50 amino acids.
The S100A2 gene has a total length of 4723 bp and seven splice variants, which can be categorized into five variants with protein product and two transcripts without an open-reading frame. Four of the variants contain the three-exon structure with the coding sequences in exon 2 and exon 3, while also sharing identical protein sequences only differing in their untranslated 5' region (Wolf et al., 2011).
Transcription The S100A2 mRNA product length, including the poly-adenylate stretch, is 970 bp (NM_005978.3). The S100A2 gene has an open-reading frame of 294 nucleotides encoding for a protein of 97 amino acid residues with a molecular mass of 11,117 kDa (NM_005969.1; see below).
Wicki et al. (1997) identified an enhancer element in the promoter region necessary for the transcription of the S100A2 gene. This enhancer element is active in both orientations and either upstream or downstream of the reporter gene, and is both necessary and sufficient for transcription of the gene (Wicki et al., 1997).

Protein

Note The S100A2 gene encodes for a protein of 97 amino acid residues, with a molecular mass of 11,117 kDa (P29034; UniProtKB).
 
  The protein structure and amino acid sequence of S100A2 (human). Modified from Wolf et al., Amino Acids, 2011.
Description S100A2 is a member of the S100 family of calcium-binding proteins. The S100A2 gene encodes for a protein of 98 amino acid residues, with a molecular mass of 11,117 kDa (P29034; UniProtKB). S100 proteins are a family of low-molecular weight (9-12 kD), calcium-binding proteins that initiate a number of cellular processes such as cell division, motility, secretion, protein synthesis, and membrane permeability through both calcium dependent and independent mechanism. Greater than twenty five different S100 proteins have so far been identified with many mapping closely together on chromosome 1q21.
S100A2 calcium-binding protein is characterized by four helices, two distinct calcium-binding EF-hand motifs, a central hinge region and C- and N-terminal variable domains. S100 proteins are found in the cytoplasm as preassembled dimers. A potential role for S100 proteins in cancer originated from observations that the evolutionarily conserved gene cluster containing S100 genes on human chromosome 1q21 underwent several rearrangements during tumour development.
Expression S100A2 appears to be tissue specific as it is expressed in many normal and tumour tissues. Expression of S100A2 occurs in normal breast, lung, kidney, prostate, skin and oral squamous cell tissue, with loss of expression observed in associated carcinomas suggesting a putative tumour suppressor role; while in some malignant tissues, such as pancreatic, esophageal, gastric, papillary and follicular thyroid, some subsets of lung cancer and non-small cell lung cancer high expression of S100A2 is associated with poor prognosis and increased metastases. Clearly, expression of S100A2 is not ubiquitous for all tissues and there is evidently an element of tissue-specific expression.
Localisation S100A2 is primarily localised in the nucleus with translocation to the cytoplasm evident in a number of tissue types.
Function Little is known about S100A2 function and its potential contribution as either a tumour suppressor or contributor to tumorigenesis and metastases. Upon calcium binding a conformational change occurs exposing a target protein recognition site. Once in the calcium-activated state each monomer can interact with one target protein. In this state the S100 proteins act as calcium sensors and play a role in protein phosphorylation, enzyme activation via phosphorylation, inflammation, cellular contraction and relaxation by regulating cytoskeletal constituents including actin and myosin, and nuclear transcription promoting cell proliferation and differentiation.
Homology Close relation to S100A4 has been confirmed by sequence analysis. Both proteins share over 60% amino acid sequence identity (Glenney et al., 1989).

Mutations

Note Mutations have not been reported.

Implicated in

Note
  
Entity Pancreatic cancer
Note For pancreatic cancer high S100A2 expression co-segregated with a poor response to pancreatectomy. Patients with tumours that demonstrated high S100A2 expression did not have a significant survival benefit from pancreatectomy compared to biopsy alone, whereas S100A2 negative tumours did. In the subgroup of patients who had resections with clear surgical margins, those whose tumours demonstrated high, or mod/high expression of S100A2 co-segregated with a poor outcome suggesting that occult distant metastatic disease may have been present in patients with tumours that had high S100A2 expression at the time of pancreatectomy. In a supportive study, invasive pancreatic ductal carcinoma cells were shown to express higher levels of S100A2 than did intraductal papillary mucinous neoplasms (IPMN), pancreatitis affected epithelia or normal cells, while cell lines derived from metastatic sites expressed higher levels of S100A2 than those from primary sites. This study also demonstrated that patients with high S100A2 expression had poorer overall survival. Together, these data demonstrate that S100A2 expression is a good predictor of response to pancreatectomy for pancreatic cancer and suggests that high S100A2 expression may be a marker of a metastatic phenotype (Ohuchida et al., 2007; Biankin et al., 2009; Pinese et al., 2009).
  
  
Entity Esophageal squamous cell carcinoma (ESCC)
Note S100A2 was initially reported to be downregulated in a cohort of ESCC patients as measured by RT-PCR, with node-negative ESCC patients without S100A2 expression considered to be a high-risk group with poor survival. More recently, however, S100A2-overexpressing cancers showed a trend toward preferentially developing lymph node metastases and distant metastases, suggesting that S100A2 might be related to the progression of esophageal SCC (Kyriazanos et al., 2002; Ji et al., 2004; Imazawa et al., 2005; Cao et al., 2009).
  
  
Entity Barrett's adenocarcinomas
Note Expression of S100A2 mRNA and protein in Barrett's adenocarcinoma samples were performed by RT-PCR, and immunohistochemistry respectively. Frequent overexpression of S100A2 mRNA was observed in Barrett's adenocarcinomas, while overexpression of S100A2 protein was more frequently seen in well-differentiated tumours than in others. Contrary to the nuclear expression of S100A2 in normal esophageal mucosa, two thirds of Barrett's dysplasia and Barrett's adenocarcinomas that overexpressed S100A2 demonstrated stronger cytosolic staining than nuclear staining (Lee et al., 2006).
  
  
Entity Non-small cell lung cancer (NSCLC)
Note Many studies have been performed invetigating S100A2 expression in non-small cell lung cancer (NSCLC). Increased expression of S100A2 has been demonstrated in tumour cells, with S100A2 providing valuable prognostic parameters. Patients whose tumours had positive S100A2 expression had a significantly lower overall survival and disease-specific survival rate at 5 years after surgery than did patients with negative S100A2 expression. S100A2 was overexpressed in tumours that metastasized during the course of the disease. Overexpression of S100A2 in NSCLC cell cultures has been shown to increase transendothelial migration, corroborating the role of S100A2 in the metastatic process. High expression of S100A2 is associated with metastasis and predicts survival in early stages of NSCLC. These findings are supported by studies in a mouse model of non-small cell lung cancer (NSCLC) where NOD/SCID mice xenografted with NSCLC cells overexpressing S100A2 demonstrated significantly more metastases than vector alone transfected cells (Heighway et al., 2002; Diederichs et al., 2004; Smith et al., 2004; Wang et al., 2005; Zech et al., 2006; Bartling et al., 2007; Bulk et al., 2009; Strazisar et al., 2009a; Strazisar et al., 2009b).
  
  
Entity Gastric cancer
Note Early assessment of S100A2 expression in gastric cancer using serial analysis of gene expression (SAGE) revealed that over 90% of gastric tumours overexpressed S100A2 when compared to normal gastric mucosa. More recently, however, S100A2 protein expression in normal and benign gastric tissues has been reported with a loss of S100A2 expression in 52% of gastric adenocarcinomas. Loss of S100A2 expression was associated with histological differentiation, depth of invasion, lymphatic vessel invasion and lymph node metastasis. These conflicting data demonstrate the need for further studies into S100A2 expression and gastric adenocarcinomas to further elucidate the tumorigenic mechanisms underpinning gastric carcinogenesis (El-Rifai et al., 2002; Liu et al., 2008; Luo et al., 2011).
  
  
Entity Thyroid carcinomas
Note For thyroid carcinomas, S100A2 has been demonstrated to contribute to carcinogenic events in papillary carcinoma progression (90% positive), with S100A2 expression being one of the biological characteristics of anaplastic carcinoma (Ito et al., 2005).
  
  
Entity Ovarian carcinomas (various subtypes) / ovarian serous papillary tumours
Note S100A2 is highly overexpressed in the majority of ovarian carcinomas irrespective of the subtype, in particular S100A2 is overexpressed in ovarian serous papillary carcinomas compared to normal ovarian cell lines (Hough et al., 2001; Santin et al., 2004).
  
  
Entity Breast cancer
Note S100A2 expression in normal mammary epithelium is usually high, with loss of S100A2 associated with the development of malignant breast carcinoma. Studies have revealed that loss of S100A2 expression is not associated with early carcinogenesis from normal mammary epithelium to benign hyperplasia. These experiments provided early evidence that S100A2 repression in tumour cells may be mediated by site-specific methylation. Interestingly, recent investigations have demonstrated that the highly invasive basal breast cancers express significantly higher levels of S100A2 than non-basal breast malignancies (Wicki et al., 1997; Liu et al., 2000; McKiernan et al., 2011).
  
  
Entity Oral squamous cell carcinoma (OSCC) / laryngeal squamous cell carcinoma (LSCC)
Note Recent data has emerged surrounding the potential antitumour role of S100A2 in squamous cell carcinomas, partly via reduced expression of COX-2. For oral squamous cell carcinomas (OSCC) a higher rate of late cervical metastasis has been shown in patients with S100A2-negative tumours than those with S100A2-positive tumours, indicating that patients with stage I or II invasive OSCC without S100A2 expression should be considered a high-risk group for late cervical metastasis (poor overall survival). Loss of nuclear S100A2 may also serve as an independent prognostic marker for early-stage oral cancer patients at high risk of recurrence. A more aggressive treatment modality and intensive follow-up may be recommended for the patients with reduced expression of S100A2 in tumour cell nuclei. In laryngeal squamous cell carcinoma, a correlation was found between S100A2 tumour positivity and longer relapse-free and overall survival (Lauriola et al., 2000; Suzuki et al., 2005; Tsai et al., 2005; Tsai et al., 2006; Almadori et al., 2009).
  
  
Entity Bladder cancer
Note Conflicting data has emerged concerning S100A2 expression in bladder cancers. Overexpression of S100A2 mRNA has been demonstrated in bladder cancers using RT-PCR, however a study investigating S100A2 expression at the protein level demonstrated that S100A2 expression was significantly decreased in the bladder cancer specimens compared with the controls. The loss of expression of S100A2 and increased expression of another calcium binding protein, S100A4, were associated with muscle invasion with alterations in expression also associated with a greater risk of disease progression and a decreased chance of cancer-specific survival (Matsumoto et al., 2007; Yao et al., 2007).
  
  
Entity Squamous cell carcinoma of the head and neck (SCCHN)
Note In oral cancer cells the Ca2+ and cell cycle-dependent p53-S100A2 interaction might modulate proliferation, while for squamous cell carcinomas of the head and neck (SCCHN) it has been postulated that S100A2 may play a role in the metastasis of SCCHN, however most tumours expressed S100A2 but lymph node metastases showed a pattern of reduced staining for S100A2 compared with primary tumours (Mueller et al., 2005; Zhang et al., 2007).
  
  
Entity Lung adenocarcinoma / lung squamous cell carcinoma (LSCC)
Note Expression of S100A2 is reportedly downregulated in some lung squamous cell carcinomas, with S100A2 positivity being a favourable prognostic indicator in patients with p53-negative tumours (Feng et al., 2001; Shen et al., 2002; Matsubara et al., 2005).
  
  
Entity Prostate cancer
Note S100A2 expression was observed in the basal cells of non-malignant epithelium, while absent S100A2 expression was demonstrated in a cohort of 41 prostate cancer specimens, potentially due to promoter hypermethylation. In benign conditions such as benign prostate hyperplasia and prostatitis, high levels of S100A2 are observed with a progressive loss of S100A2 expression occurring with increasing tumour grade and metastases indicating that loss of S100A2 may be an important event during progression of prostate cancer. More recently, high S100A2 protein expression was observed in a cohort of benign prostatic hyperplasia, with little or no expression in prostate cancer cells, while a concomitant increase of S100A4 expression was observed in prostate cancer cells. These data suggest that the analysis of both S100A2 and S100A4 expression in prostatic tissues may be a useful prognostic indicator for prostate cancer (Gupta et al., 2003; Rehman et al., 2005; Kwon et al., 2010).
  
  
Entity Malignant melanoma
Note For malignant melanoma, loss of S100A2 gene expression may be an early event in the development of melanoma. All nevi showed moderate to high expression levels of S100A2, while the expression levels were low in cell lines established from primary melanomas and metastases did not express S100A2 mRNA (Maelandsmo et al., 1997).
  

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Citation

This paper should be referenced as such :
Scarlett, CJ ; Biankin, AV
S100A2 (S100 calcium binding protein A2)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(4):280-285.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/S100A2ID42191ch1q21.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Head and Neck: Laryngeal tumors: an overview


External links

Nomenclature
HGNC (Hugo)S100A2   10492
Cards
AtlasS100A2ID42191ch1q21
Entrez_Gene (NCBI)S100A2  6273  S100 calcium binding protein A2
AliasesCAN19; S100L
GeneCards (Weizmann)S100A2
Ensembl hg19 (Hinxton)ENSG00000196754 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000196754 [Gene_View]  chr1:153561109-153565830 [Contig_View]  S100A2 [Vega]
ICGC DataPortalENSG00000196754
TCGA cBioPortalS100A2
AceView (NCBI)S100A2
Genatlas (Paris)S100A2
WikiGenes6273
SOURCE (Princeton)S100A2
Genetics Home Reference (NIH)S100A2
Genomic and cartography
GoldenPath hg38 (UCSC)S100A2  -     chr1:153561109-153565830 -  1q21.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)S100A2  -     1q21.3   [Description]    (hg19-Feb_2009)
EnsemblS100A2 - 1q21.3 [CytoView hg19]  S100A2 - 1q21.3 [CytoView hg38]
Mapping of homologs : NCBIS100A2 [Mapview hg19]  S100A2 [Mapview hg38]
OMIM176993   
Gene and transcription
Genbank (Entrez)AF086003 AW195797 BC002829 BC105787 BQ953250
RefSeq transcript (Entrez)NM_005978
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)S100A2
Cluster EST : UnigeneHs.516484 [ NCBI ]
CGAP (NCI)Hs.516484
Alternative Splicing GalleryENSG00000196754
Gene ExpressionS100A2 [ NCBI-GEO ]   S100A2 [ EBI - ARRAY_EXPRESS ]   S100A2 [ SEEK ]   S100A2 [ MEM ]
Gene Expression Viewer (FireBrowse)S100A2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6273
GTEX Portal (Tissue expression)S100A2
Protein : pattern, domain, 3D structure
UniProt/SwissProtP29034   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP29034  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP29034
Splice isoforms : SwissVarP29034
PhosPhoSitePlusP29034
Domaine pattern : Prosite (Expaxy)EF_HAND_1 (PS00018)    EF_HAND_2 (PS50222)    S100_CABP (PS00303)   
Domains : Interpro (EBI)EF-hand-dom_pair    EF_Hand_1_Ca_BS    EF_hand_dom    S-100_dom    S100/CaBP-9k_CS    S100_Ca-bd_sub   
Domain families : Pfam (Sanger)S_100 (PF01023)   
Domain families : Pfam (NCBI)pfam01023   
Domain families : Smart (EMBL)S_100 (SM01394)  
Conserved Domain (NCBI)S100A2
DMDM Disease mutations6273
Blocks (Seattle)S100A2
PDB (SRS)2RGI    4DUQ   
PDB (PDBSum)2RGI    4DUQ   
PDB (IMB)2RGI    4DUQ   
PDB (RSDB)2RGI    4DUQ   
Structural Biology KnowledgeBase2RGI    4DUQ   
SCOP (Structural Classification of Proteins)2RGI    4DUQ   
CATH (Classification of proteins structures)2RGI    4DUQ   
SuperfamilyP29034
Human Protein AtlasENSG00000196754
Peptide AtlasP29034
HPRD01508
IPIIPI00019869   IPI00514806   
Protein Interaction databases
DIP (DOE-UCLA)P29034
IntAct (EBI)P29034
FunCoupENSG00000196754
BioGRIDS100A2
STRING (EMBL)S100A2
ZODIACS100A2
Ontologies - Pathways
QuickGOP29034
Ontology : AmiGOcalcium ion binding  protein binding  cellular_component  identical protein binding  endothelial cell migration  transition metal ion binding  
Ontology : EGO-EBIcalcium ion binding  protein binding  cellular_component  identical protein binding  endothelial cell migration  transition metal ion binding  
NDEx NetworkS100A2
Atlas of Cancer Signalling NetworkS100A2
Wikipedia pathwaysS100A2
Orthology - Evolution
OrthoDB6273
GeneTree (enSembl)ENSG00000196754
Phylogenetic Trees/Animal Genes : TreeFamS100A2
HOVERGENP29034
HOGENOMP29034
Homologs : HomoloGeneS100A2
Homology/Alignments : Family Browser (UCSC)S100A2
Gene fusions - Rearrangements
Fusion : MitelmanMID1/S100A2 [Xp22.2/1q21.3]  [t(X;1)(p22;q21)]  
Fusion : MitelmanRPRD2/S100A2 [1q21.3/1q21.3]  [t(1;1)(q21;q21)]  
Fusion: TCGAMID1 Xp22.2 S100A2 1q21.3 LUAD
Fusion: TCGARPRD2 1q21.3 S100A2 1q21.3 LGG
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerS100A2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)S100A2
dbVarS100A2
ClinVarS100A2
1000_GenomesS100A2 
Exome Variant ServerS100A2
ExAC (Exome Aggregation Consortium)S100A2 (select the gene name)
Genetic variants : HAPMAP6273
Genomic Variants (DGV)S100A2 [DGVbeta]
DECIPHERS100A2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisS100A2 
Mutations
ICGC Data PortalS100A2 
TCGA Data PortalS100A2 
Broad Tumor PortalS100A2
OASIS PortalS100A2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICS100A2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDS100A2
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 S100A2
DgiDB (Drug Gene Interaction Database)S100A2
DoCM (Curated mutations)S100A2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)S100A2 (select a term)
intoGenS100A2
NCG5 (London)S100A2
Cancer3DS100A2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM176993   
Orphanet
MedgenS100A2
Genetic Testing Registry S100A2
NextProtP29034 [Medical]
TSGene6273
GENETestsS100A2
Target ValidationS100A2
Huge Navigator S100A2 [HugePedia]
snp3D : Map Gene to Disease6273
BioCentury BCIQS100A2
ClinGenS100A2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6273
Chemical/Pharm GKB GenePA34904
Clinical trialS100A2
Miscellaneous
canSAR (ICR)S100A2 (select the gene name)
Probes
Litterature
PubMed75 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineS100A2
EVEXS100A2
GoPubMedS100A2
iHOPS100A2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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