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SPINT1 (serine peptidase inhibitor, Kunitz type 1)

Written2009-02Hiroaki Kataoka
Section of Oncopathology, Regenerative Biology, Faculty of Medicine, University of Miyazaki 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan

(Note : for Links provided by Atlas : click)

Identity

Other namesHAI
HAI-1
HAI1
MANSC2
HGNC (Hugo) SPINT1
LocusID (NCBI) 6692
Atlas_Id 44384
Location 15q15.1  [Link to chromosome band 15q15]
Location_base_pair Starts at 41136643 and ends at 41149853 bp from pter ( according to hg19-Feb_2009)  [Mapping SPINT1.png]
Fusion genes
(updated 2016)
KRT19 (17q21.2) / SPINT1 (15q15.1)NCOA3 (20q13.12) / SPINT1 (15q15.1)PHB2 (12p13.31) / SPINT1 (15q15.1)
SPINT1 (15q15.1) / C7orf49 (7q33)SPINT1 (15q15.1) / CALM3 (19q13.32)SPINT1 (15q15.1) / DTWD2 (5q23.1)
SPINT1 (15q15.1) / HIF1A (14q23.2)SPINT1 (15q15.1) / SPINT2 (19q13.2)TIMM17B (Xp11.23) / SPINT1 (15q15.1)

DNA/RNA

 
  Structure of the human SPINT1 gene.
Description The human SPINT1 gene spans approximately 13.6 kb in length and consists of 11 exons separated by 10 introns. The size of the exons ranges from 26 bp (exon 6) to about 0.8kb (exon 11). The size of introns ranges from 83 bp to about 7 kb. The first exon encodes only a part of 5'-untranslated region (UTR) of the SPINT1 transcript. Exon 2 contains the remaining 5'-UTR and the putative signal sequence. Two Kunitz-type inhibitor domains (KD-1 and KD-2) are encoded by exons 5 and 9, respectively.
Transcription There are two major transcripts, isoform 1 (also known as HAI-1B) and isoform 2 (also known as HAI-1 or HAI-1A) produced by alternative splicing. Isoform 1 and isoform 2 mRNAs encode for 529 and 513 amino acids, respectively.

Protein

 
  Structures of SPINT1 protein isoform 1 (HAI-1B) and isoform 2 (HAI-1A). SP, signal peptide; MANSC, motif at N terminus with seven cysteines; KD-1, Kunitz domain-1; LDLa, low-density lipoprotein receptor domain class A; KD-2, Kunitz domain-2; TM, transmembrane domain. Isoform 1 (HAI-1B) contains an extra 16 amino acids adjacent to the C terminus of KD-1.
Description The protein encoded by this gene is a member of the Kunitz family of serine proteinase inhibitors. Shimomura et al. (1997) purified this protein from a conditioned medium of a gastric carcinoma cell line MKN45 as a potent inhibitor specific for hepatocyte growth factor activator (HGFAC), a serum serine proteinase that is thought to be involved in the proteolytic activation of hepatocyte growth factor (HGF) in injured tissues. For this reason, SPINT1 was initially designated as HGFAC inhibitor type 1 (HAI-1). The initially cloned cDNA of SPINT1 encoded a 513 amino acids protein (478-amino acid mature protein with a calculated molecular mass of 53.3 kD). SPINT1 is a transmembrane protein expressed on the cell surface. It is composed of an extracellular domain containing an N-terminal Kunitz domain (KD1), a low-density lipoprotein (LDL) receptor-like domain and a C-terminal Kunitz domain (KD2), followed by a transmembrane region and a short cytoplasmic domain. Later, a major transcript variant, also known as HAI-1B, was reported by Kirchhofer et al. (2003). This variant encodes the longer isoform consisting of an extra 16 amino acids adjacent to the C terminus of Kunitz domain-1 (KD1); however, there is no functional difference between HAI-1 (HAI-1A) and HAI-1B.
Previous studies demonstrated that SPINT1 potently inhibits the action of a variety of trypsin-like serine proteinases, some of which may be involved in carcinogenesis, invasion and metastasis. These proteinases include HGFAC, matriptase/ST14, hepsin/TMPRSS1 and human kallikrein 1-related peptidases such as KLK4 and KLK5. Among them, matriptase/ST14 and hepsin/TMPRSS1 belong to the type II transmembrane serine protease superfamily. Other possible target proteinases include prostasin/PRSS8 and trypsin. Evidence suggests that matriptase/ST14 is the most important cognate proteinase of SPINT1 on epithelial surface. KD-1 is responsible for the inhibition of two major target proteinases, matriptase/ST14 and HGFAC.
Expression SPINT1 protein is strongly expressed in the surface epithelium of gastrointestinal tracts, endocervical epithelium, ductal epithelia of biliary tracts and pancreas, prostatic glandular epithelium and renal tubular epithelium. It is also strongly expressed in hair cortex and cuticle cells, and to a lesser degree in epidermal keratinocytes. Mesothelial cells on the serous surface also express SPINT1. Weaker expression has been detected in the endothelial cells of capillaries, venules and lymphatics. Placental tissue shows very high level of SPINT1 mRNA, and villous cytotrophoblasts are mainly responsible for this expression.
Localisation SPINT1 is mainly located on the basolateral membrane of polarized epithelial cells.
Function To date, several proposed functions of SPINT1 have been reported.
  • Inhibition of serine proteinases: SPINT1 strongly inhibits HGFAC, trypsin, KLK4, KLK5, matriptase/ST14, prostasin/PRSS8 and hepsin/TMPRSS1.
  • Optimal regulation of pericellular proteinase activity: Evidence has suggested that SPINT1 is required for the trafficking of proforms of matriptase/ST14 to the cell surface and also for the activation of pro-matriptase/ST14 even though it can inhibit matriptase/ST14 activity. Therefore, without SPINT1, activation and proper localization of matriptase/ST14 appear to be significantly impaired. Such paradoxical effects of SPINT1 are also observed in the interaction with HGFAC. SPINT1 inhibits HGFAC, but paradoxically, serves as a reservoir of active HGFAC on the cell surface.
  • Regulation of pericellular HGF activation: Among target proteinases of SPINT1, HGFAC, matriptase/ST14 and hepsin/TMPRSS1 are known to activate precursor form of HGF (proHGF). Thus, SPINT1 is thought to regulate pericellular proHGF activation.
  • Function in the placenta development: SPINT1 is essential in the placental development, as SPINT1-deficient mouse embryos die during mid-gestation due to impaired formation of the placental labyrinth layer.
  • Function in the skin development: Rescue of the placental function results in successful delivery of SPINT-1-deficient neonates. However, they die within 16 days after delivery with significant skin abnormalities such as abnormal keratinization and impaired formation of hair cuticle. Therefore, SPINT1 is critical in the regulated keratinization of epidermis and formation of hair cuticle.
  • Tumor suppressor activity: Transgenic overexpression of matriptase/ST14 resulted in skin carcinogenesis. However, the development of skin cancer (squamous cell carcinoma) was suppressed when SPINT1 was co-expressed.
  • Homology SPINT-2 (also known as HAI-2 or placental bikunin) is also a membrane-bound Kunitz-type serine proteinase inhibitor consisting of two extracellular Kunitz domain. The amino acids identity between SPINT1 KD-1 and SPINT2 KD-1 is 54%, and between SPINT1 KD-2 and SPINT2 KD-2 is 36 %. However, SPINT2 lacks MANSC domain and LDL receptor-like domain.

    Implicated in

    Note
    Entity Various cancers
    Oncogenesis A possible tumor suppressor activity of SPINT1 has been reported in matriptase/ST14-induced skin carcinogenesis. Immunohistochemical studies suggest that the balance between SPINT1 and its target proteinase such as matriptase/ST14 may be important in the progression of breast cancer and prostate cancer. Downregulation of SPINT1 is also reported in part of the colon, renal cell and ovarian carcinoma cases. In vitro knockdown of SPINT1 results in an invasive phenotype of certain epithelial and carcinoma cells.
      

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    Citation

    This paper should be referenced as such :
    Kataoka, H
    SPINT1 (serine peptidase inhibitor, Kunitz type 1)
    Atlas Genet Cytogenet Oncol Haematol. 2010;14(1):58-61.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/SPINT1ID44384ch15q15.html


    External links

    Nomenclature
    HGNC (Hugo)SPINT1   11246
    Cards
    AtlasSPINT1ID44384ch15q15
    Entrez_Gene (NCBI)SPINT1  6692  serine peptidase inhibitor, Kunitz type 1
    AliasesHAI; HAI1; MANSC2
    GeneCards (Weizmann)SPINT1
    Ensembl hg19 (Hinxton)ENSG00000166145 [Gene_View]  chr15:41136643-41149853 [Contig_View]  SPINT1 [Vega]
    Ensembl hg38 (Hinxton)ENSG00000166145 [Gene_View]  chr15:41136643-41149853 [Contig_View]  SPINT1 [Vega]
    ICGC DataPortalENSG00000166145
    TCGA cBioPortalSPINT1
    AceView (NCBI)SPINT1
    Genatlas (Paris)SPINT1
    WikiGenes6692
    SOURCE (Princeton)SPINT1
    Genomic and cartography
    GoldenPath hg19 (UCSC)SPINT1  -     chr15:41136643-41149853 +  15q13.3   [Description]    (hg19-Feb_2009)
    GoldenPath hg38 (UCSC)SPINT1  -     15q13.3   [Description]    (hg38-Dec_2013)
    EnsemblSPINT1 - 15q13.3 [CytoView hg19]  SPINT1 - 15q13.3 [CytoView hg38]
    Mapping of homologs : NCBISPINT1 [Mapview hg19]  SPINT1 [Mapview hg38]
    OMIM605123   
    Gene and transcription
    Genbank (Entrez)AB000095 AI684245 AK300195 AK303899 AK314825
    RefSeq transcript (Entrez)NM_001032367 NM_003710 NM_181642
    RefSeq genomic (Entrez)NC_000015 NC_018926 NG_029239 NT_010194 NW_004929398
    Consensus coding sequences : CCDS (NCBI)SPINT1
    Cluster EST : UnigeneHs.233950 [ NCBI ]
    CGAP (NCI)Hs.233950
    Alternative Splicing GalleryENSG00000166145
    Gene ExpressionSPINT1 [ NCBI-GEO ]   SPINT1 [ EBI - ARRAY_EXPRESS ]   SPINT1 [ SEEK ]   SPINT1 [ MEM ]
    Gene Expression Viewer (FireBrowse)SPINT1 [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)6692
    GTEX Portal (Tissue expression)SPINT1
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtO43278 (Uniprot)
    NextProtO43278  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProO43278
    Splice isoforms : SwissVarO43278 (Swissvar)
    PhosPhoSitePlusO43278
    Domaine pattern : Prosite (Expaxy)BPTI_KUNITZ_1 (PS00280)    BPTI_KUNITZ_2 (PS50279)    LDLRA_1 (PS01209)    LDLRA_2 (PS50068)    MANSC (PS50986)   
    Domains : Interpro (EBI)Kunitz_BPTI    LDLR_class-A_CS    LDrepeatLR_classA_rpt    MANSC_dom    MANSC_N    Prtase_inh_Kunz-CS   
    Domain families : Pfam (Sanger)Kunitz_BPTI (PF00014)    Ldl_recept_a (PF00057)    MANEC (PF07502)   
    Domain families : Pfam (NCBI)pfam00014    pfam00057    pfam07502   
    Domain families : Smart (EMBL)KU (SM00131)  LDLa (SM00192)  MANEC (SM00765)  
    DMDM Disease mutations6692
    Blocks (Seattle)SPINT1
    PDB (SRS)1YC0    2MSX    4ISL    4ISN    4ISO   
    PDB (PDBSum)1YC0    2MSX    4ISL    4ISN    4ISO   
    PDB (IMB)1YC0    2MSX    4ISL    4ISN    4ISO   
    PDB (RSDB)1YC0    2MSX    4ISL    4ISN    4ISO   
    Structural Biology KnowledgeBase1YC0    2MSX    4ISL    4ISN    4ISO   
    SCOP (Structural Classification of Proteins)1YC0    2MSX    4ISL    4ISN    4ISO   
    CATH (Classification of proteins structures)1YC0    2MSX    4ISL    4ISN    4ISO   
    SuperfamilyO43278
    Human Protein AtlasENSG00000166145
    Peptide AtlasO43278
    HPRD05494
    IPIIPI00376403   IPI00011643   IPI01009996   
    Protein Interaction databases
    DIP (DOE-UCLA)O43278
    IntAct (EBI)O43278
    FunCoupENSG00000166145
    BioGRIDSPINT1
    STRING (EMBL)SPINT1
    ZODIACSPINT1
    Ontologies - Pathways
    QuickGOO43278
    Ontology : AmiGOneural tube closure  serine-type endopeptidase inhibitor activity  extracellular region  extracellular space  plasma membrane  negative regulation of endopeptidase activity  membrane  extracellular matrix organization  positive regulation of glial cell differentiation  branching involved in labyrinthine layer morphogenesis  placenta blood vessel development  extracellular exosome  cellular response to BMP stimulus  negative regulation of neural precursor cell proliferation  
    Ontology : EGO-EBIneural tube closure  serine-type endopeptidase inhibitor activity  extracellular region  extracellular space  plasma membrane  negative regulation of endopeptidase activity  membrane  extracellular matrix organization  positive regulation of glial cell differentiation  branching involved in labyrinthine layer morphogenesis  placenta blood vessel development  extracellular exosome  cellular response to BMP stimulus  negative regulation of neural precursor cell proliferation  
    Pathways : KEGGTranscriptional misregulation in cancer   
    NDEx NetworkSPINT1
    Atlas of Cancer Signalling NetworkSPINT1
    Wikipedia pathwaysSPINT1
    Orthology - Evolution
    OrthoDB6692
    GeneTree (enSembl)ENSG00000166145
    Phylogenetic Trees/Animal Genes : TreeFamSPINT1
    Homologs : HomoloGeneSPINT1
    Homology/Alignments : Family Browser (UCSC)SPINT1
    Gene fusions - Rearrangements
    Fusion : MitelmanNCOA3/SPINT1 [20q13.12/15q15.1]  [t(15;20)(q15;q13)]  
    Polymorphisms : SNP, variants
    NCBI Variation ViewerSPINT1 [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)SPINT1
    dbVarSPINT1
    ClinVarSPINT1
    1000_GenomesSPINT1 
    Exome Variant ServerSPINT1
    ExAC (Exome Aggregation Consortium)SPINT1 (select the gene name)
    Genetic variants : HAPMAP6692
    Genomic Variants (DGV)SPINT1 [DGVbeta]
    Mutations
    ICGC Data PortalSPINT1 
    TCGA Data PortalSPINT1 
    Broad Tumor PortalSPINT1
    OASIS PortalSPINT1 [ Somatic mutations - Copy number]
    Somatic Mutations in Cancer : COSMICSPINT1 
    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 SPINT1
    DgiDB (Drug Gene Interaction Database)SPINT1
    DoCM (Curated mutations)SPINT1 (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)SPINT1 (select a term)
    intoGenSPINT1
    Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
    Diseases
    DECIPHER (Syndromes)15:41136643-41149853  ENSG00000166145
    CONAN: Copy Number AnalysisSPINT1 
    Mutations and Diseases : HGMDSPINT1
    OMIM605123   
    MedgenSPINT1
    Genetic Testing Registry SPINT1
    NextProtO43278 [Medical]
    TSGene6692
    GENETestsSPINT1
    Huge Navigator SPINT1 [HugePedia]
    snp3D : Map Gene to Disease6692
    BioCentury BCIQSPINT1
    ClinGenSPINT1
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD6692
    Chemical/Pharm GKB GenePA36076
    Clinical trialSPINT1
    Miscellaneous
    canSAR (ICR)SPINT1 (select the gene name)
    Probes
    Litterature
    PubMed61 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineSPINT1
    EVEXSPINT1
    GoPubMedSPINT1
    iHOPSPINT1
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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