New SDC function prediction based on protein-protein interaction using bioinformatics tools

Zandonadi, Flávia S.; Cruz, Elisa Castañeda Santa; Korvala, Johanna

doi:10.1016/j.compbiolchem.2019.107087

Cited by 7 publications

(3 citation statements)

References 122 publications

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“…In two recent studies, syndecan-2 interaction partners were extracted from various interactome databases and previous highthroughput AP-MS experiments (Huttlin et al, 2015;Gondelaud and Ricard-Blum, 2019;Zandonadi et al, 2019). These did not overlap with the novel MS partners identified in our study and is probably a consequence of the different AP methods, tissues and cell models used.…”

Section: Discussionmentioning

confidence: 63%

The Cardiac Syndecan-2 Interactome

Mathiesen

Lunde

Stensland

et al. 2020

Front. Cell Dev. Biol.

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The extracellular matrix (ECM) is important in cardiac remodeling and syndecans have gained increased interest in this process due to their ability to convert changes in the ECM to cell signaling. In particular, syndecan-4 has been shown to be important for cardiac remodeling, whereas the role of its close relative syndecan-2 is largely unknown in the heart. To get more insight into the role of syndecan-2, we here sought to identify interaction partners of syndecan-2 in rat left ventricle. By using three different affinity purification methods combined with mass spectrometry (MS) analysis, we identified 30 novel partners and 9 partners previously described in the literature, which together make up the first cardiac syndecan-2 interactome. Eleven of the novel partners were also verified in HEK293 cells (i.e., AP2A2, CAVIN2, DDX19A, EIF4E, JPH2, MYL12A, NSF, PFDN2, PSMC5, PSMD11, and RRAD). The cardiac syndecan-2 interactome partners formed connections to each other and grouped into clusters mainly involved in cytoskeletal remodeling and protein metabolism, but also into a cluster consisting of a family of novel syndecan-2 interaction partners, the CAVINs. MS analyses revealed that although syndecan-2 was significantly enriched in fibroblast fractions, most of its partners were present in both cardiomyocytes and fibroblasts. Finally, a comparison of the cardiac syndecan-2 and-4 interactomes revealed surprisingly few protein partners in common.

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Section: Discussionmentioning

confidence: 63%

The Cardiac Syndecan-2 Interactome

Mathiesen

Lunde

Stensland

et al. 2020

Front. Cell Dev. Biol.

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“…71% of syndecan-4-specific binding proteins are implicated in integrin signalling, the rest are extracellular or associated with exosomes with roles in cell communication [58]. Another review from 2019 uses bioinformatics tools to predict binding partners of syndecans [63].…”

Section: Syndecan Core Protein Signallingmentioning

confidence: 99%

Syndecan receptors: pericellular regulators in development and inflammatory disease

et al. 2021

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The syndecans are the major family of transmembrane proteoglycans, usually bearing multiple heparan sulfate chains. They are present on virtually all nucleated cells of vertebrates and are also present in invertebrates, indicative of a long evolutionary history. Genetic models in both vertebrates and invertebrates have shown that syndecans link to the actin cytoskeleton and can fine-tune cell adhesion, migration, junction formation, polarity and differentiation. Although often associated as co-receptors with other classes of receptors (e.g. integrins, growth factor and morphogen receptors), syndecans can nonetheless signal to the cytoplasm in discrete ways. Syndecan expression levels are upregulated in development, tissue repair and an array of human diseases, which has led to the increased appreciation that they may be important in pathogenesis not only as diagnostic or prognostic agents, but also as potential targets. Here, their functions in development and inflammatory diseases are summarized, including their potential roles as conduits for viral pathogen entry into cells.

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“…Sci. 2021, 22, 9395 2 of 26 such as regulating cell viability and maintaining the integrity of tissue structure [8][9][10][11]. They have been widely used for medical and health purposes, such as the treatment of osteoarthritis, cardiovascular diseases and tissue regeneration.…”

Section: Introductionmentioning

confidence: 99%

The Regulatory Network of Sturgeon Chondroitin Sulfate on Colorectal Cancer Inhibition by Transcriptomic and Proteomic Analysis

Shen

et al. 2021

IJMS

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Chondroitin sulfate (CS) is a food-derived bioactive substance with multiple biological functions, which exists in animal cartilage and/or bone. Sturgeon, a type of cartilaginous fish, is rich in CS. Our recent study demonstrated the effect of sturgeon chondroitin sulfate (SCS) on reducing colorectal cancer cell proliferation and tumor formation. However, the molecular mechanisms of its anticancer activity remain unknown. In this study, the cell proliferation assay and flow cytometric analysis were used to examine the cell viability and apoptosis of colon cancer cell HT-29 cells and normal colonic epithelial cell NCM460 cells. Transcriptomic and proteomic studies were used to identify the main targets of SCS. SCS showed little effect on the genes/proteins expression profile of NCM460 cells but more sensitive to HT-29, in which 188 genes and 10 proteins were differentially expressed after SCS treatment. Enrichment analysis of those genes/proteins showed that the majority of them are involved in DNA replication, cell cycle progression and apoptosis. Quantitative RT-PCR and Western blot were used to determine essential genes/proteins and networks targeted by SCS to exert inhibiting the development of colorectal cancer function. This study provided great insights into developing food-derived novel therapeutics for colorectal cancer treatment.

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New SDC function prediction based on protein-protein interaction using bioinformatics tools

Cited by 7 publications

References 122 publications

The Cardiac Syndecan-2 Interactome

The Cardiac Syndecan-2 Interactome

Syndecan receptors: pericellular regulators in development and inflammatory disease

The Regulatory Network of Sturgeon Chondroitin Sulfate on Colorectal Cancer Inhibition by Transcriptomic and Proteomic Analysis

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