EXT1 (exostosin glycosyltransferase 1)

2021-01-01 Jean Loup Huret Affiliation

jean-loup.huret@atlasgeneticsoncology.org

Identity

HGNC

EXT1

LOCATION

8q24.11

IMAGE

LEGEND

Figure 1. Probe(s) - Courtesy Mariano Rocchi

LOCUSID

2131

ALIAS

EXT,LGCR,LGS,TRPS2,TTV

FUSION GENES

Show Gene Fusions

Abstract

EXT1 is an endoplasmic reticulum-resident type II transmembrane protein with glycosyltransferase activity, involved in chain elongation of heparan sulfate. Heparan sulfate proteoglycans bind a large number of extracellular proteins, regulating membrane signaling, consequently playing a critical role in cell determination, differentiation, and migration. Germline mutations in EXT1 are responsible for hereditary multiple exostoses (osteochondromas), and EXT1 deletion is also found in tricho-rhino-phalangeal syndrome type II (also called Langer-Giedion syndrome), a contiguous gene deletion syndrome. We also review EXT1 alterations in various cancers.

DNA/RNA

Description

Genomic size: 312,457 bp; 11 exons.

Transcription

Transcript (hg38) including UTRs: chr8:117,794,490 - 118,111,853, size: 317,364 bp on minus strand; coding region: chr8:117,799,712 - 118,111,046, size: 311,335 bp, according to UCSC. Another transcript has 5 exons.

Proteins

Note

EXT1 is a type II transmembrane protein endoplasmic reticulum-resident glycosyl transferase.

Figure 2. EXT1 gene and protein domains

Description

EXT1 is a 746 amino acids (aa) protein (canonical form) involved in the chain elongation of heparan sulfate biosynthesis, adding saccharides to proteoglycans. EXT1 contains from N-term to C-term a cytoplasmic domain (aa 1-7), a transmembrane region (aa 8-28), and a lumenal domain (aa 29-746) with two glycosyl transferase domains: the exostosin domain and the glycosyl-transferase domain (Figures 2, 3 and 4).
Other sites according to Prosite
- Protein kinase C phosphorylation sites: aa 35, 41, 81, 297, 344, 392, 547, 609, 641, 673, 686
- Casein kinase II phosphorylation site: aa 35, 102,1 99, 244, 310, 317, 417, 425, 563, 571, 573, 584
- conserved cysteine between EXT genes: C: aa 98, 103, 109, 298, 312, 334, 652, 704 and disulfide bond between aa 652 and aa 704
- DXD motifs: DRD aa 162-164, 313-315; DED aa 565-567; DPD aa 694-696 (The DXD motif is a short conserved motif found in many families of glycosyltransferases, that requires divalent cations (InterPro); note manganese binding site at aa 567. The GlcNAc transferase shows a preference for Mn2+ over Ca2+ or Mg2+. The GlcNAc transferase reaction (see below) proceeds across a pH range of 5-8, whereas the GlcA transferase reaction showed an optimum at pH 5.5-6.5 (Wei et al., 2000).
- N-myristoylation sites (role in membrane targeting): aa 14-19, 245-250
- N-glycosylation sites: aa 89, 330
- Amidation site XGRK (protects from proteolysis): GKK: aa 94-97, GKR: aa 267-270, GRR: aa 338-341
Exostosins family members contain:
- a glucuronyl-transferase domain ("Exostosin" domain (aa 110-396 in the case of EXT1), and therefore EXT1 belongs to the "GT47" glucuronyl (GlcA) family of GT (glycosyltransferases) (corresponding to EC 2.4.1.225), and
- an acetylglucosaminyl-transferase domain ("Glycosyl transferase" domain (aa 480-729 in the case of EXT1)), and therefore EXT1 also belongs to the "GT64" glucosaminyl (GlcNAc: glucosamine (GlcN), acetylated) family of glycosyltransferases (corresponding to EC 2.4.1.224) (see below Figures 5, 6 and 7).

Figure 3. EXT1 amino acids sequence

Expression

EXT1 mRNA is expressed ubiquitously, with a low cell type specificity.
Ext1^-/- embryonic stem cells failed to commit to lineage differentiation in mice (Kraushaar et al., 2010). EXT1 is expressed during early embryogenesis (embryonic portion of the ectoderm, parietal and visceral endoderm, and the trophoblastic cells) and can be detected in all tissues in adult mice. EXT1 homozygous mutants mice fail to gastrulate (Lin et al., 2000), and knockdown of Ext1 causes gastrulation defects in Xenopus (Shieh et al., 2014). EXT1 mutant embryos fail to form mesoderm. Indian hedgehog, an important regulator of developmental processes, is expressed during gastrulation, and hedgehog and downstream BMPs (bone morphogenetic proteins), also markers for mesoderm differentiation, were reduced.
Ext1 and Ext2 were concomitantly expressed in hypertrophic chondrocytes of forelimb bones from 1-day-old neonatal mouse, but down-regulated in maturing chondrocytes of developing cartilage from 21-day-old mouse (Kobayashi et al., 2000). In developing foetal tooth, staining was detected in ameloblasts and in the basal lamina. In mature tooth, EXT1 was expressed in odontoblasts and the predentin but not in the dentin (Pääkkönen et al., 2017).
Proper expression of Ext1 is required for cardiogenesis in the mouse. FGF signaling is altered upon Ext1 deletion. FGF signaling controls cell proliferation of cardiac progenitors Ext1 is crucial for outflow tract formation in distinct progenitor cells, and heparan sulfate (HS) modulates FGF signaling during early heart development (Zhang et al., 2015).
Ext1^-/- causes severe axon guidance errors, indicating that heparan sulfate proteoglycans (see below) are important regulators of axon guidance. This resulted in defective brain morphogenesis in the embryonic mouse (Inatani and Yamaguchi, 2003). Development of the central nervous system proceeds through patterning of the neural tube, generation of neurons and their migration, extension of axons and dendrites and formation of synapses. Heparan sulfate is functionally involved in various aspects of neural development (Yamaguchi et al., 2010). Genetic alteration of heparan sulfate proteoglycans synthesis results in abnormal brain phenotypes in mice. Knockdown of Ext1 in nestin-positive (nestin: neuroectodermal stem cell marker) neural stem cells resulted in defects in neural patterning and cortical neurogenesis. Ext1-deficient neural stem cells exhibited reduced proliferation in response to FGF2 and FGF8 (Wade et al., 2014).
Ext1^-/- mice exhibited altered dendritic cell homing (Bao et al., 2010).

Figure 4. EXT1 crystal structure according to ModBase. "ModBase 1-429" correspond grossly to the exostosin domain, and "ModBase 475-730" to the glycosyl transferase domain.

Localisation

Both EXT1 and EXT2 localize and accumulate in the Golgi apparatus. Mutated EXT1 and EXT2, as is found in hereditary multiple exostoses (HME), also localize in the Golgi (Kobayashi et al., 2000; McCormick et al., 2000), the site where heparan sulfate polymerization occurs.

Function

EXT1 is an endoplasmic reticulum-resident type II transmembrane glycosyltransferase. EXT1 and EXT2 are involved in the chain elongation step (polymerisation) of heparan sulfate and heparin biosyntheses (see KEGG pathway https://www.genome.jp/kegg-bin/show_pathway?map00534+2.4.1.224) (Okada et al., 2010). Heparan sulfate and heparin are glycosaminoglycans (long polysaccharides chains made of repeating disaccharides (these disaccharides consist of one beta-D-glucuronic acid (GlcA) and one alpha-D-glucosamine (GlcN)) (Figure 5). Glycosaminoglycans are highly polar and attract water; see for review on heparan sulfate proteoglycans Sarrazin et al., 2011.
EXT1 and EXT2 form a hetero-oligomeric complex in vivo. The enzyme complex encoded by the EXT1 and EXT2 acts as bifunctional glycosyltransferases (Lind et al., 1998):
1- N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (EC 2.4.1.225) and
2- glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (EC 2.4.1.224), see Figure 6 and 7) (see Lind et al., 1998).
In EXT1, the N-terminal domain with GT47 activity adds GlcA residues, and the C-terminal domain with GT64 activity adds GlcNAc residues to the long glycosaminoglycans chains (proteoglycans=protein+glycosaminoglycan).
Table 1: Enzyme Nomenclature, activity, and protein domains

IUBMB Entry	Enzyme	Saccharide involved	Protein domains	Enzymatic activity
EC 2.4.1.225	glucuronosyltransferase	glucuronic acid (GlcA)	N-terminal domain: GT47 family	GT47 adds GlcA residues
EC 2.4.1.224	glucosaminyltransferase	glucosamine (GlcN))	C-terminal domain: GT64 family	GT64 adds GlcNAc residues

IUBMB Enzyme Nomenclature: https://www.qmul.ac.uk/sbcs/iubmb/
Carbohydrate-Active enZYmes Database: http://www.cazy.org/GT47.html and http://www.cazy.org/GT64.html :
The long heparan synthases are made of two domains. The N-terminal domain, which adds b-1,4-GlcA residues, belongs to family GT47 while the C-terminal domain, which adds a-1,4-GlcNAc residues, belongs to family GT64.
Heparan sulfate proteoglycans (HSPGs) have a critical role in cell determination, differentiation, and migration by regulating membrane signalings and growth factors. Heparan sulfate proteoglycans have been implicated in regulating the distribution and receptor binding of several members of FGF, Wnt, transforming growth factor beta (TGFB), and Hedgehog families (Koziel et al., 2004).
Ext1 mutant mice die around embryonic day 14. The mutation mainly affected heparan sulfate chain length. Embryonic fibroblasts with homozygous Ext1 mutation produced shorter heparan sulfate chains (Yamada et al., 2004). Overexpression of EXT1 resulted in increased heparan sulfate chain length, which was even more pronounced in cells coexpressing EXT2, whereas overexpression of EXT2 alone had no detectable effect on heparan sulfate chain elongation (Busse et al., 2007).
The expression of heparanase ( HPSE), an endoglycosidase that cleaves heparan sulfate proteoglycans, was enhanced in Ext-1-knockdown cells (Wang et al., 2013).
Hedgehog proteins bind heparan sulfate and EXT1 is therefore required for Hedgehog signaling. BMP2 and BMP4 are also downstream targets of Hedgehog signaling (Lin et al., 2000). Decreased Ext1 was shown to reduce the level of Wnt and Bmp4 signaling in Xenopus. Ext1-dependent synthesis of heparan sulfate proteoglycans is critical for Wnt and BMP signaling (Shieh et al., 2014).
Cell surface heparin sulfate is also known to mediate the binding of FGFs and their FGFRs. Ext1^-/- results in impaired FGF signaling and aberrant differentiation commitment in embryonic stem cells (Kraushaar et al., 2010). TGFBR2 and EXT1 enhanced chemosensitivity to interferon-alpha/5-fluorouracil (IFN-α /5-FU) on advanced hepatocellular carcinoma by accelerating apoptosis. EXT1 overexpression enhanced endoplasmic reticulum stress response/signaling pathway leading to autophagy and apoptosis. Ext1 mutant fibroblasts displayed reduced ability to attach to collagen I and to contract collagen lattices, decreased phosphorylation of MAPK3 / MAPK1 (so called ERK1/2) in response to FGF2 stimulation. Cell proliferation induced by FGF2 and FGF10 is reduced in Ext1 mutant fibroblasts. (Osterholm et al., 2009).
NREP (also called P311 or C5ORF13) is down regulated in EXT1-mutated fibroblasts. The Ext1 mutation leads to a heparan sulfate defect resulting in low efficiency of the interaction between TGFB1 and its receptor, which results in disturbed Smad phosphorylation and less autoinduction of TGFB1 and less TGFB1 expression (Katta et al., 2018).
Calcitonin related polypeptides were significantly increased in patients with osteochondroma and EXT1 gene mutation. Calcitonin related polypeptides can arrest the cell cycle in G0/G1 phase, thereby inhibiting cell proliferation (Wu et al., 2018).
EXT1 was identified as a common interactor of NOTCH1 and FBXW7, regulating the NOTCH pathway in an FBXW7-dependend manner: depletion of EXT1 using small interfering RNA increased NOTCH transactivation activity; two important NOTCH1-target genes, HES1 and MYC had increased mRNA expression (Daakour et al., 2016). EXT1, down-regulated by MIR665, promotes cell apoptosis via MAPK3/MAPK1 (ERK1/2) signaling pathway in acute lymphoblastic leukemia (Liu et al., 2019). Overexpression of EXT2 enhanced the heparan sulfate sulfotransferase NDST1 expression, EXT1 had opposite effects (Prestoe et al., 2008).

Figure 5. Saccharides and proteoglycans

Homology

The other members of the EXT family proteins are EXT2, EXTL1, EXTL2 and EXTL3. Tout-velu (ttv) is the Drosophila homologue of EXT1 (Bellaiche and Perrimon, 1998).

Figure 6. Glucuronosyl transferase activity

Figure 7. Glucosaminyl transferase activity

Mutations

Germinal

Most hereditary multiple exostoses patients bear a heterozygous mutation in the genes encoding exostosin glycosyltransferase EXT1 or EXT2, leading to a systemic heparan sulfate deficiency of about 50%. About 10% of the patients have de novo mutations. The prevalence in western population is 1 to 2 out of 100,000. The penetrance is close to 100%. Mutations include nucleotide substitutions (54%), small deletions (27%) and small insertions (16%), of which the majority is predicted to result in a truncated or non-functional protein (review in Reijnders and Bovée, 2009; Cousminer et al., 2016; DArienzo et al., 2019).

Implicated in

Top note

High expression is an unfavorable prognostic marker in lung cancer, thyroid cancer, and cervical cancer, according to the Human Protein Atlas (TCGA studies).
Table 2: EXT1 alterations in various cancers Main data from TCGA PanCan studies, according to BioPortal (rounded numbers; too small data were discarded).
Renal (clear cell)1% of 511 cases Melanoma6% of 444 cases2%3% Uveal melanoma5% of 80 cases

Entity name

Bone development

Note

Ext1-dependent heparan sulfate regulates Indian hedgehog (Ihh) signaling during endochondral ossification. During bone development, wild-type embryos display well-organized zones of proliferating and hypertrophic chondrocytes. In contrast, Ext1^-/- mutants reveal joint fusions and a severe delay in hypertrophic differentiation. Ext1^-/- mice synthesize reduced amounts of heparan sulfate, which leads to enhanced Indian Hedgehog diffusion. Heparan sulfate restricts Ihh propagation in mice, negatively regulating Ihh signaling. Ext1^-/- mutants have an elevated range of Ihh signaling during embryonic chondrocyte differentiation (Koziel et al., 2004; Hilton et al., 2005). Bones: Ext1 expression and heparan sulfate production are needed to maintain the phenotype and function of joint-forming cells and coordinate local signaling by BMP, hedgehog and Wnt/β-catenin (CTNNB1) pathways, critical for skeletogenesis (Mundy et al., 2011). EXT1-synthesized glycosaminoglycans also interact with FGFs and their receptors and affect their regulatory functions in bone development (Lin et al., 2000). Ablation of Ext1 in limb bud mesenchyme causes severe skeletal defects (shortening and broadening) in mice, embryos. Loss of heparan sulfate expression altered spatial range of BMP signaling and localization of BMP2 protein. BMP signaling plays a major role in the development of mesenchymal condensation, compromised in the absence of heparan sulfate (Matsumoto et al., 2010). Loss of Ext1 combined with loss of cell cycle regulators Tp53 and Cdkn2a promotes peripheral chondrosarcomagenesis in the mouse (de Andrea et al., 2015).
Ext1 knock-down decreases canonical Wnt signaling activation during chondrogenesis in cultured chondrogenic mouse cells and Ext1 overexpression enhances canonical Wnt signaling activation. Activation of Wnt signaling using a GSK3 inhibitor resulted in a down-regulation of Ext1 expression. Conversely, a Wnt inhibitor up-regulated Ext1 expression. This suggest the existence of a regulatory loop between EXT1 and Wnt signaling during chondrogenesis (Wang et al., 2019).

Entity name

Hereditary multiple exostoses (HME) or Hereditary multiple osteochondromas.

Disease

HME is inherited in an autosomal dominant manner that affects about 1 in 50,000 children. Osteochondromas are the most common benign bone tumors, representing approximately 50% of all primary benign tumors of bone. They gradually develop and increase in size in the first decade of life (Reijnders and Bovée 2008).
EXT1 accounts for 45%-65% of HME-causing mutations, and EXT2 for 30%. Mutations in EXT1 are distributed over all the 11 exons. Inactivating mutations (nonsense, frame shift, and splice-site mutations) represent the majority of multiple osteochondromas causing mutations. Mutations and variants are reported in the online Multiple Osteochondromas Mutation Database at http://medgen.ua.ac.be/LOVD (Jennes et al., 2009). A germline mutation combined with loss of the remaining wild type allele support the Knudsons two hit model for tumor suppressor genes in osteochondroma development. These results indicate that in cartilaginous cells of the growth plate, inactivation of both copies of the EXT1-gene is required for osteochondroma formation in hereditary cases (Bovée 2002).
Compound heterozygous Ext1^+/-;Ext2^+/- mutant mice develop multiple osteochondromas (Zak et al., 2011).
EXT genes and heparan sulfate are needed to establish and maintain perichondriums phenotype and border function, restrain pro-chondrogenic signaling (hedgehog and BMP signaling) and restrict chondrogenesis. Normal EXT expression and heparan sulfate levels restrain BMP signaling and promote FGF signaling, a major anti-chondrogenic pathway expressed in various non-cartilaginous tissues including perichondrium. Loss of EXT expression and/or heparan sulfate level promote BMP signaling and impair FGF signaling, inducing osteochondroma development (Huegel et al., 2013; Pacifici 2018; note: see Figure 2 in Pacifici 2018).

Prognosis

Recurrent pain was found in 60 and 80% of children and adults respectively, with an impact on quality of life (Goud et al., 2012). Short stature, deformities, functional limitation, coxa valga and scoliosis are frequently observed with systemic consequences on the health, well-being, social interactions and personal perception in patients. Osteochondromas may be located in potentially dangerous and delicate locations: osteochondromas in the intracanal surface of the vertebrae can cause nerve damage and progressive impediment of motion (Pacifici 2017; Pacifici 2018).

Oncogenesis

Malignant transformation into chondrosarcoma, is low in solitary osteochondromas (

Entity name

Solitary osteochondromas

Note

85% of all osteochondromas are solitary (nonhereditary) lesions.
Osteochondromas originate in proliferating chondrocytes. Postnatal inactivation of Ext1 generates osteochondromas in mice and homozygous loss of ext1 is required for osteochondromagenesis (Jones et al., 2009). Loss of heterozygosity of EXT1 is common in solitary osteochondroma. Ext1 ^+/- or Ext2 ^+/- mutant mice were found to be largely normal. In multiple osteochondroma-related osteochondroma (see above), additional identified genetic changes include LOH and aneuploidy. LOH causes loss of the remaining wild-type allele, resulting in EXT1 or EXT2-null cells. Homozygous EXT1 deletions were present only in the cartilage cap of osteochondroma (Hameetman et al., 2007; Wilpshaar and Bovée, 2018).

Entity name

Breast cancer

Note

Estrogen receptor (ER)-negative tumors had increased expression of enzymes involved in the extension of heparan sulfate chains including EXT1. EXT1 was also overexpressed in tumors of patients who subsequently developed distant metastasis (Julien et al., 2011), whereas, in a study of 15 estrogen receptor-positive breast cancer patients with metastases, the expression of EXT1 was significantly decreased in the metastatic group compared to the control group (Taghavi et al., 2016). Knockdown of EXT1 repressed cancer cell stemness and downregulated epithelial mesenchymal transition (EMT) markers and migratory behavior in a human breast cancer cell line. Overexpression of EXT1 enhanced cell surface heparan sulfate, promoted EMT overexpression and transformed normal breast epithelial cells to the malignant form. This report implies a tissue-or cell-type specific role of EXT1 as a suppressor or promoter of cancer growth (Manandhar et al., 2017).

Entity name

Lung adenocarcinoma

Note

Lung adenocarcinoma cell lines/stromal fibroblasts composite spheroid with a mutation in Ext1 and thus a low heparan sulfate content showed impaired cell migration and a lower proliferation rate. Ext1-levels modulate tumor cell proliferation (&OUML;sterholm et al., 2012).
Among the 522 patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA) database, 6.4% had deletions in EXT1. However, a 9-gene signature ( HMMR, B4GALT1, SLC16A3, ANGPTL4, EXT1, GPC1, RBCK1, SOD1, and AGRN) has been identified as an independent prognostic factor and associated with metastasis (Zhang et al., 2019).

Entity name

Hepatocellular carcinoma

Note

EXT1 was identified as 5-FU-sensitizing gene, through activation of TGFB-enhancing chemosensitivity to 5-FU, in advanced hepatocellular carcinoma (Sakabe et al., 2013). In patients with high EXT1 expression, the median disease-free survival was 18 months. The 1-, 2-, and 5-year disease-free survival rates were 61%, 39%, and 0% respectively. In the low EXT1 expression group, the median disease-free survival was 50 months. The 1-, 2-, and 5-year disease-free survival rates were 78%, 64%, and 44%, respectively (Dong et al., 2018).

Entity name

Cholangiocarcinoma

Note

The EXT1 expression level in the plasma of human and hamster cholangiocarcinomas were significantly higher compared to healthy controls (Khoontawad et al. 2014).

Entity name

Brain tumors

Note

Heparan sulfate synthesized by EXT1 regulates receptor tyrosine kinase signaling and promotes resistance to EGFR inhibitors in glioblastoma multiforme. Signaling from receptor tyrosine kinases contributes to therapeutic resistance in glioblastoma multiforme. Heparan sulfate-null cells had decreased proliferation, invasion, and reduced activation of multiple receptor tyrosine kinases (Ohkawa et al., 2020).
Activity of the heparan sulfate biosynthetic system was decreased by 1.5-2-fold in gliomas Grade II-III and by 1.5-2-fold in glioblastoma multiforme compared with the para-tumorous brain tissue. The most significant contribution to the overall inhibition of the system was due to down-regulation of the expression of genes responsible for elongation of the heparan sulfate chains (exostosin glycosyltransferases EXT1 and EXT2) and its sulfation (Ushakov et al., 2017).

Entity name

Prostate carcinoma

Note

Heparan sulfate biosynthesis is impaired in benign prostate hyperplasia and prostate adenocarcinomas. Genes involved in both synthesis and modification/degradation of heparan sulfate were studied. Their expression was reduced, but EXT1 expression was relatively less reduced than others (EXT2, HPSE, sulfatases .) (Suhovskih et al., 2014).

Entity name

Acute lymphoblastic leukemia (ALL)

Note

EXT1 expression is downregulated in childhood and adult ALL. Low EXT1 and high MIR665 expression in adult ALL bone marrow are correlated with poor patient survival. Overexpression of EXT1 markedly inhibited cell proliferation. (Liu et al., 2019). EXT1 promoter CpG island hypermethylation leads to gene silencing in leukemia cell lines, whereas all normal tissues analyzed (lymphocytes, bone marrow, breast, colon and skin) were completely unmethylated at the EXT1 and EXT2 promoters. The epigenetic inactivation of EXT1 leads to the loss of heparan sulfate synthesis. The highest prevalence of EXT1 hypermethylation was found in acute lymphoblastic leukemia (32% of 37 cell lines) and acute promyelocytic leukemia (25% of 31 cell lines), followed at a more moderate rate by acute myeloblastic leukemia (7 % of 27 cell lines). Reactivation of EXT1 expression by a demethylating agent restores heparan sulfate synthesis and showed tumor-suppressor-like properties (Ropero et al., 2004).

Entity name

Multiple myeloma

Note

A high EXT1 expression was associated with a worse overall survival in multiple myeloma (Bret et al., 2009). EXT1 knockdown inhibited the in vivo multiple myeloma tumor growth, resulting in a significantly extended survival. Heparan sulfate proteoglycans act as multifunctional scaffolds regulating important biologic processes, including cell adhesion and migration, tissue morphogenesis, and angiogenesis. Heparan sulfate chains are crucial for the growth and survival of multiple myeloma cells (Reijmers et al., 2010).

Entity name

"Non-melanoma" skin cancers

Note

Hypermethylation of EXT1 promotor, leading to gene silencing, was found in 14% of 28 non-melanoma skin cancers cell lines (Ropero et al., 2004).

Entity name

Tricho-rhino-phalangeal syndrome type II (also called Langer-Giedion syndrome)

Disease

Tricho-rhino-phalangeal syndrome type II is a contiguous gene deletion syndrome caused by the deletion of both TRPS1 (8q23.3, 115408496-115668975 bp) and EXT1 (8q24.11, 117794490-118111826 bp) genes (see Figure 8). It combines signs of Tricho-rhino-phalangeal syndrome type I (sparse hair, bulbous tip of nose, long philtrum, thin upper vermilion border and large ears, brachydactyly, hip dysplasia, and short stature), due to the deletion of TRPS1, multiple osteochondromas (EXT1 deletion), and mild intellectual disability.

Figure 8. Location of TRPS1 and EXT1 (montage from UCSC pictures).

Entity name

Autism spectrum disorder

Note

Heparan sulfate was eliminated from postnatal neurons by conditionally inactivating Ext1 in mice. Mutant mice showed autistic symptoms, including impairments in social interaction, expression of stereotyped, repetitive behavior, and impairments in ultrasonic vocalization. The behavioral defects were accompanied by impaired glutamatergic transmission (Irie et al., 2012).
Two unrelated boys presented with hereditary multiple exostoses and autism associated with mental retardation. A deletion 1742delTGT-G in exon 9 of EXT1, causing a frameshift, was detected in one case, and a deletion 2093delTT in exon 11 of EXT1, causing transcription termination, was detected in the other case. The authors pointed that EXT1 is expressed in the brain, and that both EXT1 and EXT2 are required for the biosynthesis of heparan sulfate, which also has activity in the brain (Li et al., 2002).
A patient presented with Langer-Giedion syndrome and high-functioning autism. The karyotype found a microdeletion in mosaic 46,XY/46,XY,del(8)(q24.1q24.3) (Miyuru and Shehan 2018).
A meta-analysis of genome-wide association studies of over 16,000 individuals with autism spectrum disorder identified a significant association of ASD with EXT1 (Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium, 2017).

Entity name

Membranous nephropathy

Note

A subset of membranous nephropathy is associated with accumulation of EXT1 and EXT2 in the glomerular basement membrane. Autoimmune disease is common in this group of patients (Sethi et al., 2019).
A case of familial nephropathy in which a steroid-sensitive nephrotic syndrome and multiple exostoses due to mutation of EXT1 has been described. There was a glomerular basement membrane deposition of fibrillar collagen. (Roberts and Gleadle, 2008).

Breakpoints

Figure 9. EXT1 translocations/fusion partners

Note

Table 3: EXT1 and 13 translocations/fusion partners

EXT1 partner gene	Partner location (bp) EXT1 location: 117794490 -118111826	Translocation	Cancer type
TINAGL1		t(1:8)(p35;q24)	Breast carcinoma
RSF1		t(8;11)(q24;q14)	Breast carcinoma
FAM155A		t(8;13)(q24;q33)	Bladder urothelial carcinoma

SAMD12	118377988-118621945	(8q24)	Breast carcinoma Head and Neck squamous cell carcinoma Ovarian adenocarcinoma Stomach adenocarcinoma
WDYHV1	123416725-123442240	(8q24)	Bladder urothelial carcinoma
TMEM65	124310918-124372699	(8q24)	Lung squamous cell carcinoma
NSMCE2	125091860-125367120	(8q24)	Sarcoma
PVT1	127794533-128101253	(8q24)	Lung squamous cell carcinoma
OC90	132024216 -132059382	(8q24)	Lung adenocarcinoma
LRRC6	132570419-132675617	(8q24)	Breast carcinoma
PTK2	140657900-141001282	(8q24)	Ovarian serous cystadenocarcinoma
TSNARE1	142212080-142403182	(8q24)	Esophageal carcinoma
ADGRB1	142449649-142545007	(8q24)	Low grade glioma

References: Yoshihara et al., 2015; Gao et al., 2018; Calabrese et al., 2020.

Article Bibliography

Reference Number	Pubmed ID	Last Year	Title	Authors
1	28540026	2017	Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.
2	32025019	2020	Genomic basis for RNA alterations in cancer.	Calabrese C et al
3	22848466	2012	Fibroblast EXT1-levels influence tumor cell proliferation and migration in composite spheroids.	Österholm C et al
4	21093315	2010	Endothelial heparan sulfate controls chemokine presentation in recruitment of lymphocytes and dendritic cells to lymph nodes.	Bao X et al
5	9665133	1998	Tout-velu is a Drosophila homologue of the putative tumour suppressor EXT-1 and is needed for Hh diffusion.	Bellaiche Y et al
6	19298595	2009	Expression of genes encoding for proteins involved in heparan sulphate and chondroitin sulphate chain synthesis and modification in normal and malignant plasma cells.	Bret C et al
7	17761672	2007	Contribution of EXT1, EXT2, and EXTL3 to heparan sulfate chain elongation.	Busse M et al
8	29538090	2018	High-functioning autism in a Sri Lankan youth with Langer-Giedion syndrome.	Chandradasa M et al
9	27616605	2016	Assessing the general population frequency of rare coding variants in the EXT1 and EXT2 genes previously implicated in hereditary multiple exostoses.	Cousminer DL et al
10	31853203	2019	Hereditary Multiple Exostoses: Current Insights.	D'Arienzo A et al
11	27229929	2016	Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor.	Daakour S et al
12	30278583	2018	Increased EXT1 gene copy number correlates with increased mRNA level predicts short disease-free survival in hepatocellular carcinoma without vascular invasion.	Dong S et al
13	29617662	2018	Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.	Gao Q et al
14	22637207	2012	Pain, physical and social functioning, and quality of life in individuals with multiple hereditary exostoses in The Netherlands: a national cohort study.	Goud AL et al
15	17341731	2007	The role of EXT1 in nonhereditary osteochondroma: identification of homozygous deletions.	Hameetman L et al
16	15777636	2005	EXT1 regulates chondrocyte proliferation and differentiation during endochondral bone development.	Hilton MJ et al
17	23458899	2013	Perichondrium phenotype and border function are regulated by Ext1 and heparan sulfate in developing long bones: a mechanism likely deranged in Hereditary Multiple Exostoses.	Huegel J et al
18	14605369	2003	Mammalian brain morphogenesis and midline axon guidance require heparan sulfate.	Inatani M et al
19	22411800	2012	Autism-like socio-communicative deficits and stereotypies in mice lacking heparan sulfate.	Irie F et al
20	19810120	2009	Multiple osteochondromas: mutation update and description of the multiple osteochondromas mutation database (MOdb).	Jennes I et al
21	20080592	2010	A mouse model of osteochondromagenesis from clonal inactivation of Ext1 in chondrocytes.	Jones KB et al
22	22025563	2011	Selectin ligand sialyl-Lewis x antigen drives metastasis of hormone-dependent breast cancers.	Julien S et al
23	29580921	2018	Potential role for Ext1-dependent heparan sulfate in regulating P311 gene expression in A549 carcinoma cells.	Katta K et al
24	24018821	2014	Increase of exostosin 1 in plasma as a potential biomarker for opisthorchiasis-associated cholangiocarcinoma.	Khoontawad J et al
25	10679296	2000	Association of EXT1 and EXT2, hereditary multiple exostoses gene products, in Golgi apparatus.	Kobayashi S et al
26	15177029	2004	Ext1-dependent heparan sulfate regulates the range of Ihh signaling during endochondral ossification.	Koziel L et al
27	20022960	2010	Heparan sulfate is required for embryonic stem cells to exit from self-renewal.	Kraushaar DC et al
28	12032595	2002	Association of autism in two patients with hereditary multiple exostoses caused by novel deletion mutations of EXT1.	Li H et al
29	10926768	2000	Disruption of gastrulation and heparan sulfate biosynthesis in EXT1-deficient mice.	Lin X et al
30	9756849	1998	The putative tumor suppressors EXT1 and EXT2 are glycosyltransferases required for the biosynthesis of heparan sulfate.	Lind T et al
31	31465316	2019	EXT1, Regulated by MiR-665, Promotes Cell Apoptosis via ERK1/2 Signaling Pathway in Acute Lymphoblastic Leukemia.	Liu NW et al
32	29050299	2017	Exostosin 1 regulates cancer cell stemness in doxorubicin-resistant breast cancer cells.	Manandhar S et al
33	20404326	2010	Conditional ablation of the heparan sulfate-synthesizing enzyme Ext1 leads to dysregulation of bone morphogenic protein signaling and severe skeletal defects.	Matsumoto Y et al
34	10639137	2000	The putative tumor suppressors EXT1 and EXT2 form a stable complex that accumulates in the Golgi apparatus and catalyzes the synthesis of heparan sulfate.	McCormick C et al
35	21185280	2011	Synovial joint formation requires local Ext1 expression and heparan sulfate production in developing mouse embryo limbs and spine.	Mundy C et al
36	33028660	2021	Heparan Sulfate Synthesized by Ext1 Regulates Receptor Tyrosine Kinase Signaling and Promotes Resistance to EGFR Inhibitors in GBM.	Ohkawa Y et al
37	20377530	2010	Biosynthesis of heparan sulfate in EXT1-deficient cells.	Okada M et al
38	19850926	2009	Mutation in the heparan sulfate biosynthesis enzyme EXT1 influences growth factor signaling and fibroblast interactions with the extracellular matrix.	Osterholm C et al
39	28448806	2017	Exostosin 1 is expressed in human odontoblasts.	Pääkkönen V et al
40	29277722	2018	The pathogenic roles of heparan sulfate deficiency in hereditary multiple exostoses.	Pacifici M et al
41	18337501	2008	Heparan sulfate biosynthesis enzymes EXT1 and EXT2 affect NDST1 expression and heparan sulfate sulfation.	Presto J et al
42	19965677	2010	Targeting EXT1 reveals a crucial role for heparan sulfate in the growth of multiple myeloma.	Reijmers RM et al
43	18216313	2008	Familial nephropathy and multiple exostoses with exostosin-1 (EXT1) gene mutation.	Roberts IS et al
44	15385438	2004	Epigenetic loss of the familial tumor-suppressor gene exostosin-1 (EXT1) disrupts heparan sulfate synthesis in cancer cells.	Ropero S et al
45	23457527	2013	Identification of the genes chemosensitizing hepatocellular carcinoma cells to interferon-α/5-fluorouracil and their clinical significance.	Sakabe T et al
46	21690215	2011	Heparan sulfate proteoglycans.	Sarrazin S et al
47	31061139	2019	Exostosin 1/Exostosin 2-Associated Membranous Nephropathy.	Sethi S et al
48	24782989	2014	Transcriptional Activity of Heparan Sulfate Biosynthetic Machinery is Specifically Impaired in Benign Prostate Hyperplasia and Prostate Cancer.	Suhovskih AV et al
49	27895739	2016	Gene expression profiling of the 8q22-24 position in human breast cancer: TSPYL5, MTDH, ATAD2 and CCNE2 genes are implicated in oncogenesis, while WISP1 and EXT1 genes may predict a risk of metastasis.	Taghavi A et al
50	29104277	2017	Heparan Sulfate Biosynthetic System Is Inhibited in Human Glioma Due to EXT1/2 and HS6ST1/2 Down-Regulation.	Ushakov VS et al
51	24447567	2014	Matrix regulators in neural stem cell functions.	Wade A et al
52	31330188	2019	Exostosin-1 enhances canonical Wnt signaling activity during chondrogenic differentiation.	Wang X et al
53	23054193	2013	Involvement of Ext1 and heparanase in migration of mouse FBJ osteosarcoma cells.	Wang Y et al
54	10864928	2000	Location of the glucuronosyltransferase domain in the heparan sulfate copolymerase EXT1 by analysis of Chinese hamster ovary cell mutants.	Wei G et al
55	30262140	2018	The role of EXT1 gene mutation and its high expression of calcitonin gene-related peptide in the development of multiple exostosis.	Wu ZY et al
56	20807644	2010	Roles of heparan sulfate in mammalian brain development current views based on the findings from Ext1 conditional knockout studies.	Yamaguchi Y et al
57	25500544	2015	The landscape and therapeutic relevance of cancer-associated transcript fusions.	Yoshihara K et al
58	21310272	2011	Compound heterozygous loss of Ext1 and Ext2 is sufficient for formation of multiple exostoses in mouse ribs and long bones.	Zak BM et al
59	31847905	2019	Identification of a novel glycolysis-related gene signature for predicting metastasis and survival in patients with lung adenocarcinoma.	Zhang L et al
60	26295701	2015	Heparan Sulfate Biosynthesis Enzyme, Ext1, Contributes to Outflow Tract Development of Mouse Heart via Modulation of FGF Signaling.	Zhang R et al
61	25644707	2015	Cell cycle deregulation and mosaic loss of Ext1 drive peripheral chondrosarcomagenesis in the mouse and reveal an intrinsic cilia deficiency.	de Andrea CE et al

Other Information

Locus ID:

NCBI: 2131
MIM: 608177
HGNC: 3512
Ensembl: ENSG00000182197

Variants:

dbSNP: 2131
ClinVar: 2131
TCGA: ENSG00000182197
COSMIC: EXT1

RNA/Proteins

Gene ID	Transcript ID	Uniprot
ENSG00000182197	ENST00000378204	Q16394
ENSG00000182197	ENST00000436216	H7C1H6
ENSG00000182197	ENST00000437196	F8WF54

Expression (GTEx)

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

Pathways

Pathway	Source	External ID
Glycosaminoglycan biosynthesis - heparan sulfate / heparin	KEGG	ko00534
Glycosaminoglycan biosynthesis - heparan sulfate / heparin	KEGG	hsa00534
Metabolic pathways	KEGG	hsa01100
Glycosaminoglycan biosynthesis, heparan sulfate backbone	KEGG	hsa_M00059
Glycosaminoglycan biosynthesis, heparan sulfate backbone	KEGG	M00059
Metabolism	REACTOME	R-HSA-1430728
Metabolism of carbohydrates	REACTOME	R-HSA-71387
Glycosaminoglycan metabolism	REACTOME	R-HSA-1630316
Heparan sulfate/heparin (HS-GAG) metabolism	REACTOME	R-HSA-1638091
HS-GAG biosynthesis	REACTOME	R-HSA-2022928

Protein levels (Protein atlas)

Not detected

Low

Medium

High

References

Pubmed ID	Year	Title	Citations
38215181	2024	The exostosin glycosyltransferase 1/STAT3 axis is a driver of breast cancer aggressiveness.	1
38215181	2024	The exostosin glycosyltransferase 1/STAT3 axis is a driver of breast cancer aggressiveness.	1
36982528	2023	Exostosin 1 Knockdown Induces Chemoresistance in MV3 Melanoma Cells by Upregulating JNK and MEK/ERK Signaling.	1
38154829	2023	Clinical significance of exostosin 1 in confirmed and suspected lupus membranous nephropathy.	0
36982528	2023	Exostosin 1 Knockdown Induces Chemoresistance in MV3 Melanoma Cells by Upregulating JNK and MEK/ERK Signaling.	1
38154829	2023	Clinical significance of exostosin 1 in confirmed and suspected lupus membranous nephropathy.	0
35106951	2022	Genetic and functional analyses detect an EXT1 splicing pathogenic variant in a Chinese hereditary multiple exostosis (HME) family.	2
35194125	2022	Prevalence of neural epidermal growth factor-like 1- and exostosin 1/exostosin 2-associated membranous nephropathy: a single-center retrospective study in Japan.	14
36676722	2022	Haploinsufficiency of EXT1 and Heparan Sulphate Deficiency Associated with Hereditary Multiple Exostoses in a Pakistani Family.	0
35106951	2022	Genetic and functional analyses detect an EXT1 splicing pathogenic variant in a Chinese hereditary multiple exostosis (HME) family.	2
35194125	2022	Prevalence of neural epidermal growth factor-like 1- and exostosin 1/exostosin 2-associated membranous nephropathy: a single-center retrospective study in Japan.	14
36676722	2022	Haploinsufficiency of EXT1 and Heparan Sulphate Deficiency Associated with Hereditary Multiple Exostoses in a Pakistani Family.	0
33478971	2021	In Patients with Membranous Lupus Nephritis, Exostosin-Positivity and Exostosin-Negativity Represent Two Different Phenotypes.	34
33565239	2021	EXT1 methylation promotes proliferation and migration and predicts the clinical outcome of non-small cell lung carcinoma via WNT signalling pathway.	8
33596140	2021	Identification of Novel Mutations in the EXT1 and EXT2 Genes of Chinese Patients with Hereditary Multiple Osteochondromas.	0

Citation

Jean Loup Huret

EXT1 (exostosin glycosyltransferase 1)

Atlas Genet Cytogenet Oncol Haematol. 2021-01-01

Online version: http://atlasgeneticsoncology.org/gene/212/tumors-explorer/js/teaching-explorer/

Historical Card

2002-03-01 EXT1 (exostosin glycosyltransferase 1) by Judith VMG Bovée Affiliation

2000-01-01 EXT1 (exostosin glycosyltransferase 1) by Judith VMG Bovée Affiliation

Afdeling Pathologie, Leids Universitair Medisch Centrum, Postbus 9600, L1-Q, 2300 RC Leiden, the Netherlands