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Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma

ABSTRACT: Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma

PROVIDER: PRJNA835448 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19097905.fastq.gz	Fastqsanger.gz
	SRR19097905_1.fastq.gz	Fastqsanger.gz
	SRR19097905_2.fastq.gz	Fastqsanger.gz
	SRR19097906.fastq.gz	Fastqsanger.gz
	SRR19097906_1.fastq.gz	Fastqsanger.gz

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Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma

Project description:Fibrolamellar carcinoma (FLC) is an aggressive liver cancer that predominantly afflicts adolescents and young adults. Patients with FLC are characterized by a heterozygous deletion on chromosome 19 that creates an oncogenic gene fusion, DNAJB1-PRKACA. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer progression, metastasis, and/or drug resistance. To bridge this knowledge gap, we propose to assess pathways relevant to proteoglycans, a major component of the extracellular matrix. We leveraged single-cell ATAC-seq to analyze the diversity of VCAN accessibility across different cell types.

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Chemical, Molecular, and Single-nucleus Analysis Reveal Chondroitin Sulfate Proteoglycan Aberrancy in Fibrolamellar Carcinoma.

Project description:Fibrolamellar carcinoma (FLC) is an aggressive liver cancer with no effective therapeutic options. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer growth and/or metastasis. To bridge this knowledge gap, we assessed pathways relevant to proteoglycans, a major component of the extracellular matrix. We first analyzed gene expression data from FLC and nonmalignant liver tissue (n = 27) to identify changes in glycosaminoglycan (GAG) biosynthesis pathways and found that genes associated with production of chondroitin sulfate, but not other GAGs, are significantly increased by 8-fold. We then implemented a novel LC/MS-MS based method to quantify the abundance of different types of GAGs in patient tumors (n = 16) and found that chondroitin sulfate is significantly more abundant in FLC tumors by 6-fold. Upon further analysis of GAG-associated proteins, we found that versican (VCAN) expression is significantly upregulated at the mRNA and protein levels, the latter of which was validated by IHC. Finally, we performed single-cell assay for transposase-accessible chromatin sequencing on FLC tumors (n = 3), which revealed for the first time the different cell types in FLC tumors and also showed that VCAN is likely produced not only from FLC tumor epithelial cells but also activated stellate cells. Our results reveal a pathologic aberrancy in chondroitin (but not heparan) sulfate proteoglycans in FLC and highlight a potential role for activated stellate cells.SignificanceThis study leverages a multi-disciplinary approach, including state-of-the-art chemical analyses and cutting-edge single-cell genomic technologies, to identify for the first time a marked chondroitin sulfate aberrancy in FLC that could open novel therapeutic avenues in the future.

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Analysis of Cellular Resistance to Clostridioides difficile TcdB2 Reveals Regulators of Chondroitin Sulfate Proteoglycan 4

Project description:Analysis of Cellular Resistance to Clostridioides difficile TcdB2 Reveals Regulators of Chondroitin Sulfate Proteoglycan 4

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Identification of a chondroitin sulfate linkage region trisaccharide

Project description:Here, using LC-MS/MS, we describe for the first time a linkage region trisaccharide comprising [-GlcUA-Gal-Xyl-O-] as an alternative point of entry for glycosaminoglycan (GAG) biosynthesis. The trisaccharide was identified in the proteoglycan bikunin from urine of human healthy donors present as a disulfated pentasaccharide, [deltaHexUA-GalNAc(S)-GlcUA-Gal(S)-Xyl-O-] after chondroitinase ABC degradation. Furthermore, it was identified in chondroitin sulfate primed on xylosides isolated from human cell lines, present as the corresponding disulfated pentasaccharide after chondroitinase ABC degradation.

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Project description:Chondroitin sulfate proteoglycans are integral components of the extracellular matrix. These are composed of repeating disaccharide units of glucuronic acid and N-acetylgalactosamine linked to a serine residue on the core protein through an oligosaccharide linker. The functions of chondroitin sulfate proteoglycans are regulated by the disaccharide heteropolymers attached to the core protein. The degree of sulfation and modifications on the oligosaccharide linker differs in different tissues depending upon its function. Here, we characterized the chondroitin sulfate-linked peptides using mass spectrometric-based glycoproteomics approach. We analyzed plasma, urine and fibroblasts from apparently healthy individuals by mass spectrometry. We identified 230 glycopeptides belonging to 25 chondroitin sulfate-linked proteoglycans.

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PREDICTIVE MODELING OF THERAPEUTIC RESPONSE TO CHONDROITIN SULFATE/GLUCOSAMINE HYDROCHLORIDE IN KNEE OSTEOARTHRITIS

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