Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Lines and Cell Culture Conditions
2.2. Fluorescence Activated Cell Sorting (FACS)
2.3. Immunoprecipitation and Western Blot Analysis
2.4. Proteomic Analysis
2.5. Immunofluorescense
2.6. Bioinformatic Analysis
2.6.1. Subcellular Localization and Functional Annotation
2.6.2. Protein Interaction Network
2.7. RT-qPCR Analysis
2.8. Statistical Analysis
3. Results
3.1. Identification of SDC1-Interacting Proteins
3.2. Sub-Cellular Localization of Interacting Proteins and Related Pathways
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Saunders, S.; Jalkanen, M.; O’Farrell, S.; Bernfield, M. Molecular cloning of syndecan, an integral membrane proteoglycan. J. Cell Biol. 1989, 108, 1547–1556. [Google Scholar] [CrossRef]
- Bernfield, M.; Götte, M.; Park, P.W.; Reizes, O.; Fitzgerald, M.L.; Lincecum, J. Functions of cell surface heparan sulfate proteoglycans. Annu. Rev. Biochem. 1999, 68, 729–777. [Google Scholar] [CrossRef]
- Alexopoulou, A.N.; Multhaupt, H.A.B.; Couchman, J.R. Syndecans in wound healing, inflammation and vascular biology. Int. J. Biochem. Cell Biol. 2007, 39, 505–528. [Google Scholar] [CrossRef]
- Zimmermann, P.; Zhang, Z.; Degeest, G.; Mortier, E.; Leenaerts, I.; Coomans, C.; Schulz, J.; N’Kuli, F.; Courtoy, P.J.; David, G. Syndecan recyling is controlled by syntenin-PIP2 interaction and Arf6. Dev. Cell 2005, 9, 377–388. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Beauvais, D.M.; Burbach, B.J.; Rapraeger, A.C. The syndecan-1 ectodomain regulates αvβ3 integrin activily in human mammary carcinoma cells. J. Cell Biol. 2004, 167, 171–181. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, W.; Litwack, E.D.; Stanley, M.J.; Langford, J.K.; Lander, A.D.; Sanderson, R.D. Heparan Sulfate Proteoglycans as Adhesive and Anti-invasive Molecules. J. Biol. Chem. 2002, 273, 22825–22832. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Brockstedt, U.; Dobra, K.; Nurminen, M.; Hjerpe, A. Immunoreactivity to cell surface syndecans in cytoplasm and nucleus: Tubulin-dependent rearrangements. Exp. Cell Res. 2002, 274, 235–245. [Google Scholar] [CrossRef]
- Chen, L.; Sanderson, R.D. Heparanase regulates levels of syndecan-1 in the nucleus. PLoS ONE 2009, 4, e4947. [Google Scholar] [CrossRef] [Green Version]
- Purushothaman, A.; Hurst, D.R.; Pisano, C.; Mizumoto, S.; Sugahara, K.; Sanderson, R.D. Heparanase-mediated loss of nuclear syndecan-1 enhances Histone Acetyltransferase (HAT) activity to promote expression of genes that drive an aggressive tumor phenotype. J. Biol. Chem. 2011, 286, 30377–30383. [Google Scholar] [CrossRef] [Green Version]
- Zong, F.; Fthenou, E.; Wolmer, N.; Hollósi, P.; Kovalszky, I.; Szilák, L.; Mogler, C.; Nilsonne, G.; Tzanakakis, G.; Dobra, K. Syndecan-1 and FGF-2, but not FGF receptor-1, share a common transport route and co-localize with heparanase in the nuclei of mesenchymal tumor cells. PLoS ONE 2009, 4, e7346. [Google Scholar] [CrossRef] [Green Version]
- Chen, K.; Williams, K.J. Molecular mediators for raft-dependent endocytosis of syndecan-1, a highly conserved, multifunctional receptor. J. Biol. Chem. 2013, 288, 13988–13999. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zong, F.; Fthenou, E.; Castro, J.; Péterfia, B.; Kovalszky, I.; Szilák, L.; Tzanakakis, G.; Dobra, K. Effect of syndecan-1 overexpression on mesenchymal tumour cell proliferation with focus on different functional domains. Cell Prolif. 2010, 43, 29–40. [Google Scholar] [CrossRef]
- Zong, F.; Fthenou, E.; Mundt, F.; Szatmári, T.; Kovalszky, I.; Szilák, L.; Brodin, D.; Tzanakakis, G.; Hjerpe, A.; Dobra, K. Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration. PLoS ONE 2011, 6, e14816. [Google Scholar] [CrossRef] [PubMed]
- Szatmári, T.; Mundt, F.; Heidari-Hamedani, G.; Zong, F.; Ferolla, E.; Alexeyenko, A.; Hjerpe, A.; Dobra, K. Novel Genes and Pathways Modulated by Syndecan-1: Implications for the Proliferation and Cell-Cycle Regulation of Malignant Mesothelioma Cells. PLoS ONE 2012, 7, e48091. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Moggridge, S.; Sorensen, P.H.; Morin, G.B.; Hughes, C.S. Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics. J. Proteome Res. 2018, 17, 1730–1740. [Google Scholar] [CrossRef] [PubMed]
- Uhlen, M.; Oksvold, P.; Fagerberg, L.; Lundberg, E.; Jonasson, K.; Forsberg, M.; Zwahlen, M.; Kampf, C.; Wester, K.; Hober, S. Towards a knowledge-based human protein atlas. Nat. Biotechnol. 2010, 28, 1248–1250. [Google Scholar] [CrossRef]
- Pontén, F.; Jirström, K.; Uhlen, M. The Human Protein Atlas—A tool for pathology. J. Pathol. A J. Pathol. Soc. Great Br. Irel. 2008, 216, 387–393. [Google Scholar] [CrossRef]
- Uhlén, M.; Björling, E.; Agaton, C.; Szigyarto, C.A.-K.; Amini, B.; Andersen, E.; Andersson, A.-C.; Angelidou, P.; Asplund, A.; Asplund, C. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteom. 2005, 4, 1920–1932. [Google Scholar] [CrossRef] [Green Version]
- Berglund, L.; Björling, E.; Oksvold, P.; Fagerberg, L.; Asplund, A.; Szigyarto, C.A.-K.; Persson, A.; Ottosson, J.; Wernérus, H.; Nilsson, P. A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol. Cell. Proteom. 2008, 7, 2019–2027. [Google Scholar] [CrossRef] [Green Version]
- Uhlén, M.; Fagerberg, L.; Hallström, B.M.; Lindskog, C.; Oksvold, P.; Mardinoglu, A.; Sivertsson, Å.; Kampf, C.; Sjöstedt, E.; Asplund, A. Tissue-based map of the human proteome. Science 2015, 347, 1260419. [Google Scholar] [CrossRef]
- Thul, P.J.; Åkesson, L.; Wiking, M.; Mahdessian, D.; Geladaki, A.; Blal, H.A.; Alm, T.; Asplund, A.; Björk, L.; Breckels, L.M. A subcellular map of the human proteome. Science 2017, 356, eaal3321. [Google Scholar] [CrossRef] [PubMed]
- Uhlen, M.; Zhang, C.; Lee, S.; Sjöstedt, E.; Fagerberg, L.; Bidkhori, G.; Benfeitas, R.; Arif, M.; Liu, Z.; Edfors, F. A pathology atlas of the human cancer transcriptome. Science 2017, 357, eaan2507. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Orre, L.M.; Vesterlund, M.; Pan, Y.; Arslan, T.; Zhu, Y.; Woodbridge, A.F.; Frings, O.; Fredlund, E.; Lehtiö, J. SubCellBarCode: Proteome-wide mapping of protein localization and relocalization. Mol. Cell 2019, 73, 166–182.e7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Almagro Armenteros, J.J.; Sønderby, C.K.; Sønderby, S.K.; Nielsen, H.; Winther, O. DeepLoc: Prediction of protein subcellular localization using deep learning. Bioinformatics 2017, 33, 3387–3395. [Google Scholar] [CrossRef] [PubMed]
- Zhang, B.; Kirov, S.; Snoddy, J. WebGestalt: An integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005, 33, W741–W748. [Google Scholar] [CrossRef] [PubMed]
- Mering, C.v.; Huynen, M.; Jaeggi, D.; Schmidt, S.; Bork, P.; Snel, B. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 2003, 31, 258–261. [Google Scholar] [CrossRef]
- Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498–2504. [Google Scholar] [CrossRef]
- Ishihara, M.; Fedarko, N.S.; Conrad, H. Transport of heparan sulfate into the nuclei of hepatocytes. J. Biol. Chem. 1986, 261, 13575–13580. [Google Scholar]
- Fedarko, N.S.; Ishihara, M.; Conrad, H.E. Control of cell division in hepatoma cells by exogenous heparan sulfate proteoglycan. J. Cell. Physiol. 1989, 139, 287–294. [Google Scholar] [CrossRef]
- Cheng, F.; Petersson, P.; Arroyo-Yanguas, Y.; Westergren-Thorsson, G. Differences in the uptake and nuclear localization of anti-proliferative heparan sulfate between human lung fibroblasts and human lung carcinoma cells. J. Cell. Biochem. 2001, 83, 597–606. [Google Scholar] [CrossRef]
- Richardson, T.P.; Trinkaus-Randall, V.; Nugent, M.A. Regulation of heparan sulfate proteoglycan nuclear localization by fibronectin. J. Cell Sci. 2001, 114, 1613–1623. [Google Scholar] [PubMed]
- Busch, S.J.; Martin, G.A.; Barnhart, R.L.; Mano, M.; Cardin, A.D.; Jackson, R.L. Trans-repressor activity of nuclear glycosaminoglycans on Fos and Jun/AP-1 oncoprotein-mediated transcription. J. Cell Biol. 1992, 116, 31–42. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kovalszky, I.; Dudás, J.; Oláh-Nagy, J.; Pogány, G.; Töváry, J.; Timár, J.; Kopper, L.; Jeney, A.; Iozzo, R.V. Inhibition of DNA topoisomerase I activity by heparin sulfate and modulation by basic fibroblast growth factor. Mol. Cell. Biochem. 1998, 183, 11–23. [Google Scholar] [CrossRef] [PubMed]
- Stewart, M.D.; Ramani, V.C.; Sanderson, R.D. Shed Syndecan-1 Translocates to the Nucleus of Cells Delivering Growth Factors and Inhibiting Histone Acetylation A novel mechanism of tumor-host cross-talk. J. Biol. Chem. 2015, 290, 941–949. [Google Scholar] [CrossRef] [Green Version]
- Stewart, M.D.; Sanderson, R.D. Heparan sulfate in the nucleus and its control of cellular functions. Matrix Biol. 2014, 35, 56–59. [Google Scholar] [CrossRef]
- Szatmári, T.; Mundt, F.; Kumar-Singh, A.; Möbus, L.; Ötvös, R.; Hjerpe, A.; Dobra, K. Molecular targets and signaling pathways regulated by nuclear translocation of syndecan-1. BMC Cell Biol. 2017, 18. [Google Scholar] [CrossRef] [Green Version]
- Tange, T.Ø.; Nott, A.; Moore, M.J. The ever-increasing complexities of the exon junction complex. Curr. Opin. Cell Biol. 2004, 16, 279–284. [Google Scholar] [CrossRef]
- Bono, F.; Ebert, J.; Lorentzen, E.; Conti, E. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 2006, 126, 713–725. [Google Scholar] [CrossRef] [Green Version]
- Le Hir, H.; Gatfield, D.; Braun, I.C.; Forler, D.; Izaurralde, E. The protein Mago provides a link between splicing and mRNA localization. EMBO Rep. 2001, 2, 1119–1124. [Google Scholar] [CrossRef] [Green Version]
- McCracken, S.; Lambermon, M.; Blencowe, B.J. SRm160 splicing coactivator promotes transcript 3′-end cleavage. Mol. Cell. Biol. 2002, 22, 148–160. [Google Scholar] [CrossRef] [Green Version]
- Gehring, N.H.; Kunz, J.B.; Neu-Yilik, G.; Breit, S.; Viegas, M.H.; Hentze, M.W.; Kulozik, A.E. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 2005, 20, 65–75. [Google Scholar] [CrossRef]
- Kshirsagar, M.; Parker, R. Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. Genetics 2004, 166, 729–739. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hernández, G.; Ramírez, M.J.; Minguillón, J.; Quiles, P.; de Garibay, G.R.; Aza-Carmona, M.; Bogliolo, M.; Pujol, R.; Prados-Carvajal, R.; Fernández, J. Decapping protein EDC4 regulates DNA repair and phenocopies BRCA1. Nat. Commun. 2018, 9, 1–11. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fromm, S.A.; Truffault, V.; Kamenz, J.; Braun, J.E.; Hoffmann, N.A.; Izaurralde, E.; Sprangers, R. The structural basis of Edc3-and Scd6-mediated activation of the Dcp1: Dcp2 mRNA decapping complex. EMBO J. 2012, 31, 279–290. [Google Scholar] [CrossRef] [PubMed]
- Chang, C.-T.; Bercovich, N.; Loh, B.; Jonas, S.; Izaurralde, E. The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1. Nucleic Acids Res. 2014, 42, 5217–5233. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Desmeules, P.; Joubert, P.; Zhang, L.; Al-Ahmadie, H.A.; Fletcher, C.D.; Vakiani, E.; Delair, D.F.; Rekhtman, N.; Ladanyi, M.; Travis, W.D. A subset of malignant mesotheliomas in young adults are associated with recurrent EWSR1/FUS-ATF1 fusions. Am. J. Surg. Pathol. 2017, 41, 980. [Google Scholar] [CrossRef] [PubMed]
KEGG_ID | Pathways | p-value |
---|---|---|
hsa03040 | Spliceosome | <0.001 |
hsa03010 | Ribosome | <0.001 |
hsa03013 | RNA transport | <0.001 |
hsa03015 | mRNA surveillance pathway | <0.001 |
hsa05168 | Herpes simplex infection | 0.001 |
hsa03450 | Non-homologous end-joining | 0.002 |
hsa04110 | Cell cycle | 0.036 |
hsa04114 | Oocyte meiosis | 0.036 |
Protein | Function | Average Peak Area |
---|---|---|
EWSR1 | Ewing sarcoma RNA Binding Protein, gene expression, cell signaling, RNA processing and transport. | 1017854433 |
FUS | DNA/RNA-binding protein, transcription regulation, RNA splicing, RNA transport, DNA repair and damage response | 605530108 |
SRSF3 | Serine and Arginine Rich Splicing Factor 3 | 385181348 |
HNRPNK | Heterogeneous nuclear ribonucleoprotein K, pre-mRNA processing and mRNA metabolism and transport. | 295093486 |
HNRH1 | Heterogeneous nuclear ribonucleoprotein H isoform X2 | 187344787 |
DDX5 | DEAD box protein 5 or RNA helicase p68, translation initiation and ribosome and spliceosome assembly. | 170687719 |
NONO | Non-POU domain-containing octamer-binding protein, many nuclear processes and binds to both DNA and RNA | 160241747 |
SRSF1 | Serine/arginine-rich splicing factor 1 (SRSF1) | 147735561 |
EDC4 | Enhancer of mRNA-decapping protein 4. | 140588443 |
RENT1 | UPF1 RNA Helicase and ATPase, mRNA nuclear export and mRNA surveillance | 132528140 |
TAF15 | TATA-binding protein-associated factor 2N, basal transcription | 128505347 |
MYO1C | Myosin-Ic, the nuclear isoform associates with RNA polymerase I and II and functions in transcription initiation. | 113213904 |
DDX17 | DEAD box protein 17, RNA helicases | 111436913 |
SRSF7 | Serine/arginine-rich splicing factor 7 (SRSF7) | 99271832 |
EIF3C | Eukaryotic Translation Initiation Factor 3 Subunit C | 85388787 |
EIF3L | Eukaryotic Translation Initiation Factor 3 Subunit L | 78620983 |
HNRPM | Heterogeneous nuclear ribonucleoprotein M, mRNA splicing via spliceosome | 77690416 |
ILF3 | Interleukin enhancer-binding factor 3, RNA-binding protein, biogenesis of circular RNAs (circRNAs) | 77171065 |
SRSF4 | Splicing factor, arginine/serine-rich 4 | 44588287 |
THOC4 | THO complex subunit 4, nuclear export of spliced and unspliced mRNA. | 41230482 |
DHX15 | Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 | 35497317 |
XRCC5 | Ku80 protein, DNA repair | 35470341 |
ABCF1 | ATP-binding cassette sub-family F member 1, plays a role in enhancement of protein synthesis and inflammation | 15304939 |
EIF5B | Eukaryotic translation initiation factor 5B | 10174063 |
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Kumar-Singh, A.; Shrinet, J.; Parniewska, M.M.; Fuxe, J.; Dobra, K.; Hjerpe, A. Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells. Biomolecules 2020, 10, 1034. https://doi.org/10.3390/biom10071034
Kumar-Singh A, Shrinet J, Parniewska MM, Fuxe J, Dobra K, Hjerpe A. Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells. Biomolecules. 2020; 10(7):1034. https://doi.org/10.3390/biom10071034
Chicago/Turabian StyleKumar-Singh, Ashish, Jatin Shrinet, Malgorzata Maria Parniewska, Jonas Fuxe, Katalin Dobra, and Anders Hjerpe. 2020. "Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells" Biomolecules 10, no. 7: 1034. https://doi.org/10.3390/biom10071034