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ECM1 (extracellular matrix protein 1)

Written2014-09Piedad C Gomez-Contreras, Geeta Lal
Department of Surgery, Section of Surgical Oncology, Endocrine Surgery, University of Iowa, Iowa City, IA. 52242, USA
This article is an update of :
2009-10Joseph Merregaert, Wim Van Hul
Laboratory of Molecular Biotechnology, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk/Antwerp, Belgium

(Note : for Links provided by Atlas : click)


HGNC (Hugo) ECM1
LocusID (NCBI) 1893
Atlas_Id 40398
Location 1q21.3  [Link to chromosome band 1q21]
Location_base_pair Starts at 150508109 and ends at 150513789 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping ECM1.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
PFKFB3 (10p15.1)::ECM1 (1q21.3)


  A. ECM1 DNA. B. ECM1 transcripts.
Description The gene was initially described as having 10 exons. Afterwards an alternative spliced exon 5a was detected (Johnson et al., 1997).
Transcription Four transcripts are described of which three transcripts have been identified by Northern blot analysis and 1 by PCR (Smits et al., 2000).
ECM1a (lacks exon 5a, 1.8 kb); ECM1b (exon 5a and exon 7 are missing, 1.4 kb); ECM1c (contains exon 5a, 1.85 kb); ECM1d (splice variant in which 71 bp of the 3' end of intron 1 are transcribed, resulting in a truncated 57 aa protein, only detected by PCR, DQ010946).


  Schematic representation of ECM1 and its four splice variants. ECM1 protein is divided in a signal sequence (19 aa) (black box) and four different domains based on the presence or absence of cysteines: an N-terminal cysteine-free domain (white box), two tandem repeats (green and gray box), and a C-terminal region (blue box). ECM1c differs from ECM1a containing 19 aa encoded by exon 5a, ECM1b results from an alternative trancript caused by splicing out exon 7 (shaded black). ECM1d encodes a truncated protein composed of 57 aa containing exon 1, exon 2 and a part of exon 3.
Expression ECM1a is widely expressed in liver, small intestines, lung, ovary, prostate, testis, skeletal muscle, pancreas, kidney, placenta, heart, basal keratinocytes, dermal blood vessels, and adnexal epithelia including hair follicles and sweat glands (Smits et al., 1997). ECM1 overexpression has also been identified in corneal epithelium (Turner et al., 2007) and epididymal tissue. In the latter, it has been proposed as a potential biomarker to distinguish obstructive from non-obstructive azoospermia based on the analysis of levels of the protein in seminal fluid (Drabovich et al., 2013).
ECM1b is detectable in tonsils and the spinous and granular layers of the epidermis.
ECM1c is expressed in the basal layer of the epidermis. ECM1 expression in human skin is regulated by age and ultraviolet light exposure and as such, may be a cutaneous stress response (Sander et al., 2006).
Important remark: ECM1 antibodies available to detect ECM1 protein are not able to discriminate between ECM1a and ECM1c.
ECM1d: expression pattern is not known yet.
Localisation Ultrastructurally, ECM1a/c is a basement membrane protein in human skin and is part of network-like suprastructures containing perlecan (Mongiat et al., 2003), collagen type IV and laminin 332 as constituents.
Function The exact biological function of ECM1 is not elucidated yet, but evidence for its involvement in important biophysiological processes, like skin differentiation, endochondral bone formation and angiogenesis have now emerged. ECM1 inhibits the hypertrophy of chondrocytes as well as mineralization of the matrix and endochondral bone formation. In the broader context of skin biology, ECM1 appears to have many functions and particular a 'biological super-glue' action has been hypothesized. ECM1 also appears to have a role in regulating migration of type 2 helper T cells (Li et al., 2011).
Homology Homology and protein-protein interactions: a computationally predicted three-dimensional structure of ECM1a is depicted below.
Based on the third serum albumin domain ECM1a protein can be divided into four domains. The first domain containing alpha-helices (alphaD1) and three serum albumin subdomain-like domains (SASDL 2-4), each of three sequences comparable with a complete subdomain of the third serum albumin domain. AlphaD1 exits only of Alpha-helices, whereas SASDL2 and -3 are capable of binding most of the extracellular matrix proteins identified so far (collagen type IV, laminin 332, fibronectin, perlecan, fibulin 1C/D, fibulin-3 and MMP-9) (Sercu et al., 2009; Sercu et al., 2008; Fujimoto et al., 2005). Other cDNA clones known to react with ECM1 fragments in (yeast two-hybrid asays) include legumain, human insulin-like growth factor, epidermal growth factor, human chorionic somatomammotropin, human alpha 2 hemoglobin, NADH dehydrogenase and ubiquinone (Fujimoto et al., 2006).
ECM1 also binds COMP (cartilage oligometric matrix protein) both in vitro and in vivo via the COMP EGF domain (Kong et al., 2010). In addition, ECM1 also binds the type II transmembrane protein PLSCR1 (phospholipid scramblase 1) via its tandem repeat region (Merregaert et al., 2010).


Note Mutations were described in lipoid proteinosis (LiP; OMIN#247100), also known as hyalinosis cutis et mucosae or Urbach-Wiethe disease. This is a rare, autosomal recessive disorder characterized by generalized thickening of skin, mucosae, and certain viscera. Histologically, there is widespread deposition of hyaline (glycoprotein) material and disruption/reduplication of basement membrane. Classic features include beaded eyelid papules and laryngeal infiltration leading to hoarseness. More than 40 distinct missense, nonsense, splice site, small and large deletions and insertions have been reported, as summarized in Table 1. Approximately 50% of the mutations cluster to exon 6 and 7 of the gene. Examining the immunostaining pattern of skin biopsies using anti-ECM1 antibody can be used for the rapid diagnosis of LiP (Chan et al., 2004c).
  Table 1. Summary of ECM1 mutations in lipoid proteinosis.

Implicated in

Entity Various cancers
Note A survey of ECM1 expression in different tumors indicated that ECM1, although not tumor specific, is significantly elevated in many malignant epithelial tumors that gave rise to metastases (Wang et al., 2003). ECM1 overexpression has been described in cancers of the breast, thyroid (Lal et al., 2008; Kebebew et al., 2005; Pauws et al., 2004) and head and neck squamous cell carcinomas (HNSCC), specifically, laryngeal carcinomas. Other carcinomas with increased ECM1 expression include hepatocellular carcinoma, cholangiocarcinomas, cutaneous melanoma cell lines (Lal et al., 2013) and gastric carcinomas (Wu et al., 2014).
In addition, ECM1 upregulation has been associated with poor prognosis and metastases in breast (Lal et al., 2009), laryngeal (Gu et al., 2013; Han et al., 2006), hepatocellular (Chen et al., 2011), gastric and cholangiocarcinomas (Xiong et al., 2012). ECM1 expression also appears to be a predictor of primary uveal melanoma metastasis in a study using microarray expression (Onken et al., 2010).
Together with the observation that human recombinant ECM1 stimulates proliferation of cultured endothelial cells and promotes blood vessel formation in the chorioallantoic membrane of chicken embryos suggest that ECM1 is a possible trigger for angiogenesis, tumor progression and malignancies (Han et al., 2001). ECM1 has been correlated with elevated lymphatic and microvessel density in laryngeal (Han et al., 2006) and gastric tumors (Wu et al., 2014) and also correlated with estrogen responsiveness in breast cancer. In the latter ECM1 expression also correlates with VEGF-C suggesting that they may have a synergistic effect on lymphangiogenesis and facilitation of lymphatic metastases (Wu et al., 2012). In cholangiocarcinomas, ECM1 expression is also correlated with expression the tumor marker CA19-9, MMP-9 and the estrogen receptor (Xiong et al., 2012).
ECM1 also appears to play a role in the migration, invasion and attachment properties of cancer cells, as seen in studies of cholangiocarcinoma and melanoma cell lines (Xiong et al., 2012; Lal et al., 2013).
Overexpression of ECM1 in cancer cells appears to be mediated by the Akt/NF-κB signaling axis (Xiong et al., 2012). ECM1 expression is also partly regulated by transcription factor AP2C (TFAP2C) in melanoma cells, and its effect is mediated by direct interaction with the ECM1 promoter (Lal et al., 2013).
Entity Lipoid proteinosis
Disease Lipoid proteinosis, also known as hyalinosis cutis et mucosae or Urbach-Wiethe disease.
Lipoid proteinosis is a rare autosomal recessive genodermatosis characterized by the deposition of an amorphous hyaline material in the skin, mucosa, and viscera. Papular infiltration of the margin of the lids producing 'itchy eyes', and infiltration in the tongue and its frenulum, in the larynx leading to hoarseness, and in the skin (e.g., elbows and axilla) are characteristic (Hamada et al., 2003; Hamada et al., 2002).
Entity Lichen sclerosus et atrophicus
Disease Lichen sclerosus (LS) is a chronic inflammatory skin disorder of unknown etiology that results in white plaques with epidermal atrophy. It has both genital and extragenital presentations. HLA-subtype susceptibility and high rates of other autoimmune disorders suggest that autoantibodies to specific mucocutaneous antigens may be involved in the etiology of lichen sclerosus. The similarities with lipoid proteinosis, which results from mutations in the ECM1 gene, suggested that this protein may be an autoantigen in lichen sclerosus. Indeed, circulating auto-antibodies to ECM1 were found in the sera of 67% of lichen sclerosus patients (Oyama et al., 2003; Oyama et al., 2004).
In conclusion lipoid proteinosis and lichen sclerosus are immunogenetic counterparts targeting ECM1.
Entity Ulcerative colitis
Note A nonsynonymous SNP (rs11205387) has been associated with ulcerative colitis (Fisher et al., 2008). ECM1 variation was not associated with Crohn's disease (Anderson et al., 2009). Incorporation of the analysis of ECM1 genetic variants into a diagnostic algorithm including serological and inflammatory markers resulted in improved accuracy in identifying inflammatory bowel disease and in particular, differentiating between ulcerative colitis and Crohn's disease (Plevy et al., 2013).


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A Chinese family with lipoid proteinosis resulting from a homozygous missense mutation in the extracellular matrix protein 1 gene.
Wang XP, Huo J, Liu Y, Wang WJ, Xu QQ, Ma JH, An JG, Wang JM, Xiao SX.
J Eur Acad Dermatol Venereol. 2009 Nov;23(11):1336-8. doi: 10.1111/j.1468-3083.2009.03207.x. Epub 2009 Apr 2.
PMID 19368610
Extracellular matrix protein 1 is correlated to carcinogenesis and lymphatic metastasis of human gastric cancer.
Wu Q, Li X, Yang H, Lu C, You J, Zhang Z.
World J Surg Oncol. 2014 Apr 29;12:132. doi: 10.1186/1477-7819-12-132.
PMID 24779890
Expression and clinical significance of extracellular matrix protein 1 and vascular endothelial growth factor-C in lymphatic metastasis of human breast cancer.
Wu QW, She HQ, Liang J, Huang YF, Yang QM, Yang QL, Zhang ZM.
BMC Cancer. 2012 Jan 27;12:47. doi: 10.1186/1471-2407-12-47.
PMID 22284579
Overexpression of ECM1 contributes to migration and invasion in cholangiocarcinoma cell.
Xiong GP, Zhang JX, Gu SP, Wu YB, Liu JF.
Neoplasma. 2012;59(4):409-15. doi: 10.4149/neo_2012_053.
PMID 22489696
Treatment of lipoid proteinosis due to the p.C220G mutation in ECM1, a major allele in Chinese patients.
Zhang R, Liu Y, Xue Y, Wang Y, Wang X, Shi S, Cai T, Wang Q.
J Transl Med. 2014 Apr 4;12:85. doi: 10.1186/1479-5876-12-85.
PMID 24708644


This paper should be referenced as such :
Piedad C Gomez-Contreras, Geeta Lal
ECM1 (extracellular matrix protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2015;19(7):445-452.
Free journal version : [ pdf ]   [ DOI ]
History of this paper:
Merregaert, J ; Van, Hul W. ECM1 (Extracellular matrix protein 1). Atlas Genet Cytogenet Oncol Haematol. 2010;14(8):749-752.

External links


HGNC (Hugo)ECM1   3153
Atlas Explorer : (Salamanque)ECM1
Entrez_Gene (NCBI)ECM1    extracellular matrix protein 1
GeneCards (Weizmann)ECM1
Ensembl hg19 (Hinxton)ENSG00000143369 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000143369 [Gene_View]  ENSG00000143369 [Sequence]  chr1:150508109-150513789 [Contig_View]  ECM1 [Vega]
ICGC DataPortalENSG00000143369
TCGA cBioPortalECM1
AceView (NCBI)ECM1
Genatlas (Paris)ECM1
SOURCE (Princeton)ECM1
Genetics Home Reference (NIH)ECM1
Genomic and cartography
GoldenPath hg38 (UCSC)ECM1  -     chr1:150508109-150513789 +  1q21.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)ECM1  -     1q21.2   [Description]    (hg19-Feb_2009)
GoldenPathECM1 - 1q21.2 [CytoView hg19]  ECM1 - 1q21.2 [CytoView hg38]
Genome Data Viewer NCBIECM1 [Mapview hg19]  
OMIM247100   602201   
Gene and transcription
Genbank (Entrez)AK097046 AK097205 AK292435 AK301369 AK302279
RefSeq transcript (Entrez)NM_001202858 NM_004425 NM_022664
Consensus coding sequences : CCDS (NCBI)ECM1
Gene ExpressionECM1 [ NCBI-GEO ]   ECM1 [ EBI - ARRAY_EXPRESS ]   ECM1 [ SEEK ]   ECM1 [ MEM ]
Gene Expression Viewer (FireBrowse)ECM1 [ Firebrowse - Broad ]
GenevisibleExpression of ECM1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1893
GTEX Portal (Tissue expression)ECM1
Human Protein AtlasENSG00000143369-ECM1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ16610   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ16610  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ16610
Domains : Interpro (EBI)ECM1    Serum_albumin-like   
Domain families : Pfam (Sanger)ECM1 (PF05782)   
Domain families : Pfam (NCBI)pfam05782   
Conserved Domain (NCBI)ECM1
AlphaFold pdb e-kbQ16610   
Human Protein Atlas [tissue]ENSG00000143369-ECM1 [tissue]
Protein Interaction databases
IntAct (EBI)Q16610
Ontologies - Pathways
Ontology : AmiGOossification  angiogenesis  positive regulation of endothelial cell proliferation  negative regulation of cytokine-mediated signaling pathway  protease binding  chondrocyte development  regulation of type 2 immune response  endochondral bone growth  interleukin-2 receptor binding  extracellular matrix structural constituent  protein binding  extracellular region  extracellular space  regulation of transcription by RNA polymerase II  inflammatory response  signal transduction  protein C-terminus binding  negative regulation of peptidase activity  enzyme binding  regulation of bone mineralization  negative regulation of bone mineralization  extracellular matrix  platelet dense granule lumen  biomineral tissue development  positive regulation of I-kappaB kinase/NF-kappaB signaling  laminin binding  positive regulation of angiogenesis  collagen-containing extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  extracellular exosome  regulation of T cell migration  
Ontology : EGO-EBIossification  angiogenesis  positive regulation of endothelial cell proliferation  negative regulation of cytokine-mediated signaling pathway  protease binding  chondrocyte development  regulation of type 2 immune response  endochondral bone growth  interleukin-2 receptor binding  extracellular matrix structural constituent  protein binding  extracellular region  extracellular space  regulation of transcription by RNA polymerase II  inflammatory response  signal transduction  protein C-terminus binding  negative regulation of peptidase activity  enzyme binding  regulation of bone mineralization  negative regulation of bone mineralization  extracellular matrix  platelet dense granule lumen  biomineral tissue development  positive regulation of I-kappaB kinase/NF-kappaB signaling  laminin binding  positive regulation of angiogenesis  collagen-containing extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  extracellular exosome  regulation of T cell migration  
REACTOMEQ16610 [protein]
REACTOME PathwaysR-HSA-114608 [pathway]   
NDEx NetworkECM1
Atlas of Cancer Signalling NetworkECM1
Wikipedia pathwaysECM1
Orthology - Evolution
GeneTree (enSembl)ENSG00000143369
Phylogenetic Trees/Animal Genes : TreeFamECM1
Homologs : HomoloGeneECM1
Homology/Alignments : Family Browser (UCSC)ECM1
Gene fusions - Rearrangements
Fusion : FusionHubCSNK1E--ECM1    ECM1--HSA-MIR-6723    ECM1--KRT13    ECM1--LPIN1    ECM1--SNAPC4    KRT13--ECM1    MUC21--ECM1    PFKFB3--ECM1    RHCG--ECM1    SNRNP70--ECM1   
Fusion : QuiverECM1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerECM1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ECM1
Exome Variant ServerECM1
GNOMAD BrowserENSG00000143369
Varsome BrowserECM1
ACMGECM1 variants
Genomic Variants (DGV)ECM1 [DGVbeta]
DECIPHERECM1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisECM1 
ICGC Data PortalECM1 
TCGA Data PortalECM1 
Broad Tumor PortalECM1
OASIS PortalECM1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICECM1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DECM1
Mutations and Diseases : HGMDECM1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
DgiDB (Drug Gene Interaction Database)ECM1
DoCM (Curated mutations)ECM1
CIViC (Clinical Interpretations of Variants in Cancer)ECM1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
OMIM247100    602201   
Genetic Testing Registry ECM1
NextProtQ16610 [Medical]
Target ValidationECM1
Huge Navigator ECM1 [HugePedia]
Clinical trials, drugs, therapy
Protein Interactions : CTDECM1
Pharm GKB GenePA27598
Clinical trialECM1
DataMed IndexECM1
PubMed103 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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