Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of wild-type, Gal-1 knockout, Gal-3 knockout and Gal-1/Gal-3 double knockout mouse embryonic stem cells (mESC) deprived of LIF for 7 days

ABSTRACT: Galectin-1 (Gal-1) and Galectin-3 (Gal-3) are conserved carbohydrate-binding proteins that also display RNA-binding activity. We generated mouse embryonic stem cells (mESC) constitutively depleted of Gal-1 and/or Gal-3 using CRISPR-Cas9, and assessed the transcriptomic effects of the individual or concomitant depletion of Gal-1 and Gal-3 in mESCs differentiated by deprivation of the leukaemia inhibitory factor (LIF) for 7 days. Wild-type cells were employed as control.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-9262 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Identification of interactors is a major attempt in cell biology. Not only protein-protein but also protein-carbohydrate interactions are of high relevance for signal transduction in biological systems. Here we aim to identify novel interacting binding partners for the β-galactoside-binding proteins Galectin-1 (Gal-1) and Galectin-3 (Gal-3) in context of the eye disease proliferative vitreoretinopathy (PVR). PVR is one of the most common failures after retinal detachment surgeries and is characterized by the migration, adhesion and epithelial-to-mesenchymal transition (EMT) of retinal pigment epithelial cells (RPE) and the subsequent formation of sub- and epiretinal fibrocellular membranes. Gal-1 and Gal-3 bind in a dose- and carbohydrate-dependent manner to mesenchymal RPE cells and inhibit cellular processes like attachment and spreading. Yet knowledge about glycan-dependent interactors of Gal-1 and Gal-3 on RPE cells is very limited, although this is a prerequisite to unravel the influence of galectins on distinct cellular processes in RPE cells. In this approach, we identified by galectin pull-down experiments and quantitative proteomic screening 131 Galectin-3 and 15 Galectin-1 interactors. They mainly play a role in multiple binding processes and are mostly membrane proteins. Here we focused on two novel identified interactors of Gal-1 and Gal-3 in the context of PVR: the low-density lipoprotein receptor LRP1 and the platelet-derived growth factor receptor beta PDGFRB. We observed crosslinking and lattice formation of exogenous Gal-1 and Gal-3 with LRP1/PDGFRB and ITGB1 on the cell surface of human RPE cells. Weaker binding of Gal-1 and Gal-3 on these interactors and no lattice formation on the cell surface was seen, when complex-type-N-glycosylation was inhibited by treatment of the cells with Kifunensine. In conclusion, the identified specific glycoprotein ligands for Gal-1 and Gal-3 give us new insights in the highly specific binding of galectins to dedifferentiated RPE cells and the resulting prevention of PVR-associated cellular events.

Dataset Information

RNA-seq of wild-type, Gal-1 knockout, Gal-3 knockout and Gal-1/Gal-3 double knockout mouse embryonic stem cells (mESC) deprived of LIF for 7 days

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