scholarly journals Comprehensive Profiling of Cartilage Extracellular Matrix Formation and Maturation Using Sequential Extraction and Label-free Quantitative Proteomics

2010 ◽  
Vol 9 (6) ◽  
pp. 1296-1313 ◽  
Author(s):  
Richard Wilson ◽  
Anders F. Diseberg ◽  
Lavinia Gordon ◽  
Snezana Zivkovic ◽  
Liliana Tatarczuch ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Sequential Extraction ◽  
Quantitative Proteomics ◽  
Label Free ◽  
Cartilage Extracellular Matrix

scholarly journals Potential mechanisms of action of celastrol against rheumatoid arthritis: transcriptomic and proteomic analysis

2020 ◽  
Author(s):  
Xinqiang Song ◽  
SONG Xinqiang ◽  
DAI Erqin ◽  
ZHANG Yu ◽  
DU Hongtao ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Oxidative Stress ◽  
Extracellular Matrix ◽  
Quantitative Proteomics ◽  
Inflammatory Diseases ◽  
Mechanisms Of Action ◽  
Label Free ◽  
Expression Of Genes ◽  
Differential Expression Of Genes ◽  
Fibroblast Like Synoviocytes

Abstract Background: The natural triterpene celastrol exhibits potential anti-inflammatory activity in inflammatory diseases such as rheumatoid arthritis (RA). Methods: Here we explored through what proteins and processes celastrol may act in activated fibroblast-like synoviocytes (FLS) from RA patients. Differential expression of genes and proteins after celastrol treatment of FLS was examined using RNA sequencing, label-free relatively quantitative proteomics and molecular docking. Results: Expression of 26,565 genes and 3,372 proteins was analyzed. Celastrol was associated with significant changes in genes that respond to oxidative stress and oxygen levels, as well as genes that stabilize or synthesize components of the extracellular matrix. Conclusions: These results identify several potential mechanisms through which celastrol may inhibit inflammation in RA.

scholarly journals Potential mechanisms of action of celastrol against rheumatoid arthritis: transcriptomic and proteomic analysis

2020 ◽  
Author(s):  
Xinqiang Song ◽  
Erqin Dai ◽  
Yu Zhang ◽  
Hongtao Du ◽  
Lei Wang ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Oxidative Stress ◽  
Extracellular Matrix ◽  
Quantitative Proteomics ◽  
Inflammatory Diseases ◽  
Mechanisms Of Action ◽  
Label Free ◽  
Expression Of Genes ◽  
Differential Expression Of Genes ◽  
Fibroblast Like Synoviocytes

AbstractBackgroundThe natural triterpene celastrol exhibits potential anti-inflammatory activity in inflammatory diseases such as rheumatoid arthritis (RA).MethodsHere we explored through what proteins and processes celastrol may act in activated fibroblast-like synoviocytes (FLS) from RA patients. Differential expression of genes and proteins after celastrol treatment of FLS was examined using RNA sequencing, label-free relatively quantitative proteomics and molecular docking.ResultsExpression of 26,565 genes and 3,372 proteins was analyzed. Celastrol was associated with significant changes in genes that respond to oxidative stress and oxygen levels, as well as genes that stabilize or synthesize components of the extracellular matrix.ConclusionsThese results identify several potential mechanisms through which celastrol may inhibit inflammation in RA.

scholarly journals Sox9 Determines Translational Capacity During Early Chondrogenic Differentiation of ATDC5 Cells by Regulating Expression of Ribosome Biogenesis Factors and Ribosomal Proteins

2021 ◽  
Vol 9 ◽  
Author(s):  
Marjolein M. J. Caron ◽  
Maxime Eveque ◽  
Berta Cillero-Pastor ◽  
Ron M. A. Heeren ◽  
Bas Housmans ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Early Phase ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Chondrogenic Differentiation ◽  
Immediate Early ◽  
Label Free ◽  
Sox9 Expression ◽  
Network Analyses ◽  
Cartilage Extracellular Matrix

IntroductionIn addition to the well-known cartilage extracellular matrix-related expression of Sox9, we demonstrated that chondrogenic differentiation of progenitor cells is driven by a sharply defined bi-phasic expression of Sox9: an immediate early and a late (extracellular matrix associated) phase expression. In this study, we aimed to determine what biological processes are driven by Sox9 during this early phase of chondrogenic differentiation.MaterialsSox9 expression in ATDC5 cells was knocked down by siRNA transfection at the day before chondrogenic differentiation or at day 6 of differentiation. Samples were harvested at 2 h and 7 days of differentiation. The transcriptomes (RNA-seq approach) and proteomes (Label-free proteomics approach) were compared using pathway and network analyses. Total protein translational capacity was evaluated with the SuNSET assay, active ribosomes were evaluated with polysome profiling, and ribosome modus was evaluated with bicistronic reporter assays.ResultsEarly Sox9 knockdown severely inhibited chondrogenic differentiation weeks later. Sox9 expression during the immediate early phase of ATDC5 chondrogenic differentiation regulated the expression of ribosome biogenesis factors and ribosomal protein subunits. This was accompanied by decreased translational capacity following Sox9 knockdown, and this correlated to lower amounts of active mono- and polysomes. Moreover, cap- versus IRES-mediated translation was altered by Sox9 knockdown. Sox9 overexpression was able to induce reciprocal effects to the Sox9 knockdown.ConclusionHere, we identified an essential new function for Sox9 during early chondrogenic differentiation. A role for Sox9 in regulation of ribosome amount, activity, and/or composition may be crucial in preparation for the demanding proliferative phase and subsequent cartilage extracellular matrix production of chondroprogenitors in the growth plate in vivo.

Development of Algorithms for Mass Spectrometry-based Label-free Quantitative Proteomics*

2011 ◽  
Vol 38 (6) ◽  
pp. 506-518 ◽  
Author(s):  
Wei ZHANG ◽  
Ji-Yang ZHANG ◽  
Hui LIU ◽  
Han-Chang SUN ◽  
Chang-Ming XU ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Label Free

scholarly journals A Label-Free Cellular Proteomics Approach to Decipher the Antifungal Action of DiMIQ, a Potent Indolo[2,3-b]Quinoline Agent, against Candida albicans Biofilms

2020 ◽  
Vol 22 (1) ◽  
pp. 108
Author(s):  
Robert Zarnowski ◽  
Anna Jaromin ◽  
Agnieszka Zagórska ◽  
Eddie G. Dominguez ◽  
Katarzyna Sidoryk ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Candida Albicans ◽  
Ribosomal Proteins ◽  
Nucleotide Metabolism ◽  
Antibiofilm Activity ◽  
Label Free ◽  
Xtt Assay ◽  
Fungal Cell ◽  
Select Amino Acid ◽  
Cellular Oxidation

Candida albicans forms extremely drug-resistant biofilms, which present a serious threat to public health globally. Biofilm-based infections are difficult to treat due to the lack of efficient antifungal therapeutics, resulting in an urgent demand for the development of novel antibiofilm strategies. In this study, the antibiofilm activity of DiMIQ (5,11-dimethyl-5H-indolo[2,3-b]quinoline) was evaluated against C. albicans biofilms. DiMIQ is a synthetic derivative of indoquinoline alkaloid neocryptolepine isolated from a medicinal African plant, Cryptolepis sanguinolenta. Antifungal activity of DiMIQ was determined using the XTT assay, followed by cell wall and extracellular matrix profiling and cellular proteomes. Here, we demonstrated that DiMIQ inhibited C. albicans biofilm formation and altered fungal cell walls and the extracellular matrix. Cellular proteomics revealed inhibitory action against numerous translation-involved ribosomal proteins, enzymes involved in general energy producing processes and select amino acid metabolic pathways including alanine, aspartate, glutamate, valine, leucine and isoleucine. DiMIQ also stimulated pathways of cellular oxidation, metabolism of carbohydrates, amino acids (glycine, serine, threonine, arginine, phenylalanine, tyrosine, tryptophan) and nucleic acids (aminoacyl-tRNA biosynthesis, RNA transport, nucleotide metabolism). Our findings suggest that DiMIQ inhibits C. albicans biofilms by arresting translation and multidirectional pathway reshaping of cellular metabolism. Overall, this agent may provide a potent alternative to treating biofilm-associated Candida infections.

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