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Glypican Edit Wikipedia article
C-terminally truncated human glypican-1. PDB
Glypicans constitute one of the two major families of heparin sulfate proteoglycans, with the other major family being syndecans. Six glypicans have been identified in mammals, and are referred to as GPC1 through GPC6. In Drosophila two glypicans have been identified, and these are referred to as dally (division abnormally delayed) and dally-like. One additional glypican has been identified in C. elegans. Glypicans seem to play a vital role in developmental morphogenesis, and have been suggested as regulators for the Wnt and Hedgehog cell signaling pathways. They have additionally been suggested as regulators for fibroblast growth factor and bone morphogenic protein signaling.
While six glypicans have been identified in mammals, several characteristics remain consistent between these different proteins. First, the core protein of all glypicans is similar in size, approximately ranging between 60 and 70 kDa. Additionally, in terms of amino acid sequence, the location of fourteen cysteine residues is conserved; however, researchers describe glypicans as having moderate similarity in amino acid sequence overall. Nevertheless, it is thought that the fourteen conserved cysteine residues play a vital role in determining three-dimensional shape, thus suggesting the existence of a highly similar three-dimensional structure. Overall, GPC3 and GPC5 have very similar primary structures with 43% sequence similarity. On the other hand, GPC1, GPC2, GPC4, and GPC6 have between 35% and 63% sequence similarity. Thus, GPC3 and GPC5 are often referred to as one subfamily of glypicans, with GPC1, GPC2, GPC4, and GPC6 constituting the other group. Between the subfamilies of glypicans, there is about 25% sequence similarity. Furthermore, the amino acid sequence and structure of each glypican is well-conserved between species; it has been reported that all vertebrate glypicans are more than 90% similar regardless of the species.
For all members of the glypican family, the C-terminus of the protein is attached to the cell membrane covalently via a glycosylphosphatidylinositol (GPI) anchor. To allow for the addition of the GPI anchor, glypicans have a hydrophobic domain at the C-terminus of the protein. Within 50 amino acids of this GPI anchor, the heparan sulfate chains attach to the protein core. Therefore, unlike syndecans the heparan sulfate glycosaminoglycan chains attached to glypicans are located rather close to the cell-membrane. The glypicans found in vertebrates, Drosophila, and C. elegans all have an N-terminal signal sequence.
Glypicans are critically involved in developmental morphogenesis, and have been implicated as regulators in several cell signaling pathways. These include the Wnt and Hedgehog signaling pathways, as well as signaling of fibroblast growth factors and bone morphogenic proteins. The regulating processes performed by glypicans can either stimulate or inhibit specific cellular processes. The mechanisms by which glypicans regulate cellular pathways are not entirely elucidated. One commonly proposed mechanism suggests that glypicans behave as co-receptors which bind both the ligand and the receptor. Glypicans are expressed in various different amounts depending on the tissue, and they also are expressed to different degrees during the different stages of development. Drosophila studies have shown that dally mutants have irregular wing, antenna, genitalia, and brain development.
GPC5 and GPC6 are next to one another on chromosome 13q32 (in humans). GPC3 and GPC4 are also found next to one another, and are located on the human chromosome Xq26. Some suggest that this implies that these glypicans arose because of a gene duplication event. The gene for GPC1 is found on chromosome 2q36. Nearby genes include ZIC2, ZIC3, COL4A1/2, and COL4A3/4.
Since 1996, it has been known that patients with Simpson-Golabi-Behmel Syndrome (SGBS) have mutations in GPC3. Because this is an X-linked syndrome, it appears to affect males more significantly than females. While the phenotype associated with this condition can vary from mild to lethal, common symptoms include macroglossia, cleft palate, syndactyly, polydactyly, cystic and dysplastic kidneys, congenital heart defects, and a distinct facial appearance. Additional symptoms/characteristics have also been noted. Overall, these symptoms/characteristics are distinguished by prenatal and post-natal overgrowth. Typically, patients identified with SGBS have point mutations or microdeletions in the gene encoding GPC3, and the mutations can occur in multiple different locations of the gene. No correlation has been noticed between the location of the GPC3 mutation and the phenotypic manifestation of this disease. therefore, it is inferred that SGBS results due to a nonfunctional GPC3 protein. Researchers currently speculate that GPC3 is a negative regulator of cell proliferation, and this would explain why patients with SGBS experience overgrowth. Studies on mice support this speculation.
Glypican Implications in Cancer
Abnormal expression of glypicans has been noted in multiple types of cancer, including ovarian cancer, mesothelioma, pancreatic cancer, glioma, breast cancer and recently GCP2 in neuroblastoma. Most research involving the relationship between glypicans and cancer has focused on GPC1 and GPC3
GPC3 Implications in Cancer
Several studies have demonstrated a correlation between GPC3 expression levels and various types of cancer. To summarize these findings, it can be generally said that tissues which normally express GPC3 exhibit down-regulation of GPC3 expression during tumor progression. Similarly, the corresponding cancers of tissues which normally do not exhibit GPC3 expression often express GPC3. Furthermore, oftentimes GPC3 expression occurs during embryonic development in these tissues, and is subsequently re-expressed during tumor progression. Various studies have been conducted which support these general trends. For example, GPC3 expression can be detected in normal ovarian cells; however, several ovarian cancer cell lines do not express GPC3. Another study produced similar results for mesothelial cells and mesothelioma cell lines. This study by Murthy et al. showed down-regulation of GPC3 expression in rat mesothelioma and human mesothelioma cell lines. On the other hand, GPC3 expression is undetectable in healthy adult liver cells, while GPC3 expression occurs in the majority of human hepatocellular carcinomas. A similar correlation has been found in studies involving colorectal tumors. These results led researchers to label GPC3 as an oncofetal protein in both liver and intestine, as GPC3 is typically only expressed during embryonic development but also found in cancerous tumors. Interestingly enough, the studies by Lin et al. and Murthy et al. showed that GPC3 mutations do not occur in the coding sequence of this protein. Rather, Lin et al. reported that ovarian cancer cell lines do not express GPC3 due to hypermethylation of the GPC3 promoter. After removing these methyl groups, the authors restored expression of GPC3. In terms of the study published by Murthy et al., they found that mesothelioma cell lines contain a GPC3 promoter which is incorrectly methylated. In both of these studies, reestablishing expression of GPC3 prevented colony-forming by cancerous cells.
GPC1 Implications in Cancer
In addition to GPC3, GPC1 has also been implicated in tumor progression, and has been especially studied in pancreatic cancer, glioma, and breast cancer. Studies show that GPC1 expression is severely high in pancreatic ductal adenocarcinoma cells, and results indicate that GPC1 expression is linked to cancer progression, including tumor growth, angiogenesis and metastasis. In addition to overexpression of GPC1 on the plasma membrane of pancreatic ductal adenocarcinoma cells, studies have also shown that GPC1 is released into the tumor microenvironment by these cells. Because glypicans play a role in growth factor binding, researchers have speculated that increased levels of GPC1 in the tumor microenvironment may function to store growth factors for cancerous cells. Whipple et al. studied the effects of GCP1 on pancreatic adenocarcinoma cells in detail. These researchers reported from in vitro studies that by reducing the level of GCP1 in cancer cells, they were able to hinder the growth of these cells. Additionally, they introduced cancer cells with reduced levels of GCP1 into immunocompromised mice, and they found slow-growing tumors with reduced size, angiogenesis and metastases when compared with control GCP1 mice. Qiao et al. also reported that GPC1 is highly expressed in human glioma blood vessel endothelial cells. Furthermore, they also reported that increasing the level of GPC1 in mouse brain endothelial cells results in cell growth and stimulates mitosis in response to the angiogenic factor, FGF2. This suggests that GPC1 acts as a regulator for cell cycle progression. Matsuda et al. reported that GPC1 expression is well-above normal in human breast cancers, while expression of GPC1 is low in healthy breast tissue. Furthermore, it was noted that expression was not significantly increased for any other glypican. The data suggests that GPC1 plays a role in heparin-binding and cell cycle progression in the breast tissue.
Glypicans can modify cell signaling pathways and contribute to cellular proliferation and tissue growth. In Drosophila, the glypican dally assists diffusion of the BMP-family growth-promoting morphogen Decapentaplegic in the developing wing, while the developing haltere lacks dally and remains small. Extracellular localization of the other glypican in Drosophila, dally-like, is also required for the proper level of Hedgehog signaling in the developing wing.
- De Cat B, David G (2001). "Developmental roles of the glypicans". Semin. Cell Dev. Biol. 12 (2): 117–25. PMID 11292377. doi:10.1006/scdb.2000.0240.
- Filmus J, Capurro M, Rast J (2008). "Glypicans". Genome Biol. 9 (5): 224. PMC . PMID 18505598. doi:10.1186/gb-2008-9-5-224.
- Filmus, J.; Selleck, S.B. Glypicans: proteoglycans with a surprise. The Journal of Clinical Investigation. 2001, 108, 497-501.
- Filmus J (2001). "Glypicans in growth control and cancer". Glycobiology. 11 (3): 19R–23R. PMID 11320054.
- Lin H, Huber R, Schlessinger D, Morin PJ (1999). "Frequent silencing of the GPC3 gene in ovarian cancer cell lines". Cancer Res. 59 (4): 807–10. PMID 10029067.
- Murthy SS, Shen T, De Rienzo A, Lee WC, Ferriola PC, Jhanwar SC, Mossman BT, Filmus J, Testa JR (2000). "Expression of GPC3, an X-linked recessive overgrowth gene, is silenced in malignant mesothelioma". Oncogene. 19 (3): 410–6. PMID 10656689. doi:10.1038/sj.onc.1203322.
- Qiao D, Yang X, Meyer K, Friedl A (2008). "Glypican-1 regulates anaphase promoting complex/cyclosome substrates and cell cycle progression in endothelial cells". Mol. Biol. Cell. 19 (7): 2789–801. PMC . PMID 18417614. doi:10.1091/mbc.E07-10-1025.
- Matsuda K, Maruyama H, Guo F, Kleeff J, Itakura J, Matsumoto Y, Lander AD, Korc M (July 2001). "Glypican-1 is overexpressed in human breast cancer and modulates the mitogenic effects of multiple heparin-binding growth factors in breast cancer cells". Cancer Res. 61 (14): 5562–9. PMID 11454708.
- Crickmore MA, Mann RS (January 2007). "Hox control of morphogen mobility and organ development through regulation of glypican expression". Development. 134 (2): 327–34. PMID 17166918. doi:10.1242/dev.02737.
- Gallet A, Staccini-Lavenant L, Thérond PP (May 2008). "Cellular trafficking of the glypican Dally-like is required for full-strength Hedgehog signaling and wingless transcytosis". Dev. Cell. 14 (5): 712–25. PMID 18477454. doi:10.1016/j.devcel.2008.03.001.
- Su G, Meyer K, Nandini CD, Qiao D, Salamat S, Friedl A (June 2006). "Glypican-1 is frequently overexpressed in human gliomas and enhances FGF-2 signaling in glioma cells". Am. J. Pathol. 168 (6): 2014–26. PMC . PMID 16723715. doi:10.2353/ajpath.2006.050800.
- Pang RW, Joh JW, Johnson PJ, Monden M, Pawlik TM, Poon RT (April 2008). "Biology of hepatocellular carcinoma". Ann. Surg. Oncol. 15 (4): 962–71. PMID 18236113. doi:10.1245/s10434-007-9730-z.
- Cui S, Leyva-Vega M, Tsai EA, EauClaire SF, Glessner JT, Hakonarson H, Devoto M, Haber BA, Spinner NB, Matthews RP (2013). "Evidence from human and zebrafish that GPC1 is a biliary atresia susceptibility gene". Gastroenterology. 144 (5): 1107–1115.e3. PMC . PMID 23336978. doi:10.1053/j.gastro.2013.01.022.
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001863
Glypicans [PUBMED:8589707, PUBMED:7657705] are a family of heparan sulphate proteoglycans which are anchored to cell membranes by a glycosylphosphatidylinositol (GPI) linkage. Six members (GPC1-6) are known in vertebrates [PUBMED:11474185]. Structurally, these proteins consist of three separate domains:
- A signal sequence;
- An extracellular domain of about 500 residues that contains 12 conserved cysteines probably involved in disulphide bonds and which also contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains;
- A C-terminal hydrophobic region which is post-translationally removed after formation of the GPI-anchor.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|proteinaceous extracellular matrix (GO:0005578)|
|Molecular function||heparan sulfate proteoglycan binding (GO:0043395)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Author:||Finn RD, Bateman A|
|Number in seed:||16|
|Number in full:||1115|
|Average length of the domain:||345.80 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||85.86 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
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If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Glypican domain has been found. There are 18 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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