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Ince, D.

Publications and source records attributed to Ince, D..

3 recordsLinked to original sources

Adipocyte Expression of O-Glycoprotein Procollagen C-Endopeptidase Enhancer Protein 2 (PCPE2): Mechanisms Linking Fibrosis and Beiging of White Adipose Tissue

BackgroundProcollagen C-endopeptidase enhancer protein 2 (Pcpe2) has been primarily investigated in collagen processing during wound healing and is assumed to function similarly to Pcpe1 in the extracellular matrix (ECM). Our studies suggest that Pcpe2 has unique structural and functional features not shared with Pcpe1. MethodsTo study the role of Pcpe2 in adipose tissue remodeling, we created adipose tissue-specific knockout of Pcpe2 (TgAd+Pcpe2KO) and adipose tissue-specific Pcpe2 overexpressing (TgAd+Pcpe2Ox) mice and performed in vivo and ex vivo experiments. ResultsWe show that TgAd+Pcpe2KO mice are resistant to WD-induced obesity and exhibit reductions in body and fat pad mass. Promethion cage studies showed no significant differences in lean mass or food intake, yet WD-fed TgAd+Pcpe2KO mice exhibited significantly higher energy expenditure than negative Cre littermate controls. WD-fed TgAd+Pcpe2KO mice also showed reduced plasma glucose and lipoprotein lipid concentrations compared to controls. While markers of adipose tissue inflammation were reduced in WD-fed TgAd+Pcpe2KO mice. Examination of mature adipocytes from white adipose tissue showed that WD consumption greatly stimulated Pcpe2 expression, while no change in Pcpe2 expression in the stromal vascular cells was noted. However, in VAT precursor cells (PCs), the CD140b+ population showed a shift from fibroadipogenic precursors towards adipocyte PCs in TgAd+Pcpe2KO mice. This shift in PCs may account for the attenuation of local inflammation and fibrosis in the absence of Pcpe2. Ex vivo differentiation of adipose PCs showed that loss of Pcpe2 enhanced adipocyte differentiation, reducing TGF{beta}-like signaling via pSmad2/3, and increasing mitochondrial function. Furthermore, unlike Pcpe1, Pcpe2 contains a mucin-like linker domain with nine sites of O-linked glycosylation which may regulate receptor signaling at the plasma membrane. ConclusionsOur results show the ECM O-glycoprotein Pcpe2 is a robust marker of unhealthy adipose tissue expansion in humans and mice and contributes to inflammation and fibrosis associated with WD-induced obesity.

cell biology↗

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in terms of glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamics (MD) simulations of TIM-3 and -4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.

cancer biology↗

A systematic comparison of current bioinformatic tools for glycoproteomics data

Glycosylation is one of the most common post-translational modifications and generates an enormous amount of proteomic diversity; changes in glycosylation are associated with nearly all disease states. Intact glycoproteomics seeks to determine the site-localization and composition of glycans along a protein backbone via mass spectrometry. Following data acquisition, raw files are analyzed using search algorithms to define peptide sequence, glycan composition, and site localization. Glycoproteomics is rapidly expanding, creating the pressing need to establish bioinformatic community standards. Recently, several new search algorithms were released, many of which vary in terms of search strategy, localization system, score cutoffs, and glycan databases, thus warranting a comprehensive comparison of these new programs along with existing programs. Here, we analyzed three common samples: an enriched cell lysate, a mixture of 6 glycoproteins, and a mucin-domain glycoprotein. All raw files were searched with comparable parameters among software and the results were extensively manually validated to compare accuracy and completion of the output. Our results highlight the continued need for manual validation of glycopeptide spectral matches, especially for O-glycopeptides. Despite this, O-Pair outperformed all other programs in correct identification of O-glycopeptides and its localization system proved to be useful. On the other hand, Byonic and pGlyco performed best for N-glycoproteomics; the former was best for proteome-wide searches, but the latter identified more N-glycosites in less complex samples. Overall, we summarize the strengths, weaknesses, and potential improvements for these search algorithms. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC="FIGDIR/small/484528v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@17c371forg.highwire.dtl.DTLVardef@70532org.highwire.dtl.DTLVardef@e640b7org.highwire.dtl.DTLVardef@a2bb26_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗