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Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

ABSTRACT: Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

PROVIDER: PRJNA949595 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23994090.fastq.gz	Fastqsanger.gz
	SRR23994091.fastq.gz	Fastqsanger.gz
	SRR23994092.fastq.gz	Fastqsanger.gz
	SRR23994093.fastq.gz	Fastqsanger.gz
	SRR23994094.fastq.gz	Fastqsanger.gz

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Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

Project description:Through single-cell transcriptomic profiling of five samples with Pseudomyxoma Peritonei (PMP) , we identified ten distinct cell type-specific clusters, including an epithelial cell community with significantly increased expression of canonical epithelial molecules, and a mesenchymal cell community with notably higher expression of established mesenchymal molecules, supporting the presence of both epithelial and mesenchymal molecular characteristics in PMP disease.

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N-glycan profiling of Pseudomyxoma peritonei

Project description:Pseudomyxoma peritonei (PMP) is a subtype of mucinous adenocarcinoma of the appendix, We compared N-linked glycan profiles of PMP tissues to those of normal appendix. N-glycosidase F liberated N-glycan profiles of eight normal appendix samples and eight low-grade and eight high-grade PMP specimens were analyzed by MALDI-TOF mass spectrometry. The most prominent alteration was increased and complex fucosylation in high-grade carcinoma. Authors: Lilli Saarinen, Pirjo Nummela, Hannele Leinonen, Annamari Heiskanen, Alexandra Thiel, Caj Haglund, Anna Lepistö, Tero Satomaa, Sampsa Hautaniemi, and Ari Ristimäki; from Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki; Glykos Finland Ltd, Helsinki; Department of Surgery, University of Helsinki and Helsinki University Hospital; Translational Cancer Biology, Research Programs Unit, University of Helsinki; and Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, Finland.

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Gene expression profiling study to identify molecular markers exhibiting distinct characteristics of Pseudomyxoma Peritonei [Fresh Frozen]

Project description:The purpose of this study is to evaluate gene expression changes and identify characteristics in patients with Pseudomyxoma Peritonei (PMP). We analyzed RNA-seq data to identify gene signatures associated with PMP development using 19 fresh frozen tissue samples including 12 PMPs (discovery cohort). Through analyzing the differences in gene expression between normal tissues and PMP, we identified statistically significant gene groups, and confirmed the biological functions and pathways associated with these gene groups.

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A gene expression profiling study to identify distinct molecular markers in formalin-fixed, paraffin-embedded samples of Pseudomyxoma Peritonei [FFPE]

Project description:The purpose of this study is to evaluate gene expression changes and identify characteristics in patients with Pseudomyxoma Peritonei (PMP). We analyzed RNA-seq data from 34 formalin-fixed paraffin-embedded (FFPE) samples, including 25 PMPs (validation cohort), to identify gene signatures associated with the development of PMP. We confirmed protein expression levels using a tissue microarray (TMA) cohort of PMP patients. Through analyzing the differences in gene expression between normal tissues and PMP, we identified statistically significant gene groups, and confirmed the biological functions and pathways associated with these gene groups.

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Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix

Project description:Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix

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Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix

Project description:Pseudomyxoma peritonei (PMP) is a rare disease caused by mucin-producing tumors developed most frequently from the appendix. This disease shows distinct clinical features by the cancerous cells producing mucin in the abdominal cavity. Although frequent mutations in the KRAS and GNAS genes have been reported in PMP, gene expression profiles of the tumors remain to be fully clarified because of its rarity and the difficulties in collecting pure cancerous cells scattered with a large volume of mucins. To disclose the molecular features of PMP cells, we performed RNA-seq analysis of ten PMPs and their matched non-tumorous colonic epithelium in combination with laser-microdissection. As a result, we identified a total of 5,747 differently expressed genes (DEGs) between the tumors and non-tumorous colonic epithelium. A cell-of-origin subtype analysis with nearest template prediction algorithm corroborated that PMP tumor cells belonged to the goblet cell subtype, suggesting that tumorous cells of PMP have a feature of differentiation to goblet cells. Interestingly, gene set enrichment analysis (GSEA) uncovered that the tumors were significantly associated with three ontology terms, namely epithelial mesenchymal transition (EMT), tumor necrosis factor-alpha (TNF-α), and angiogenesis. Comparison of gene expression profiles between disseminated peritoneal adenomucinosis (DPAM) and peritoneal mucinous adenocarcinomas (PMCA) identified a total of 687 DEGs. Additional GSEA revealed that ontology terms “G2M checkpoint” and “E2F targets” were significantly enriched in PMCA supporting the view that PMCA has more aggressive properties than DPAM. These data may be useful for the understanding of molecular characteristics of PMP.

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Project description:Pseudomyxoma peritonei (PMP), a rare condition characterized by mucinous ascites in the peritoneal cavity, often leads to a poor prognosis. However, omics profiling of this disease remains significantly underexplored. Here, we present single-cell transcriptomic profiling of five PMP cases to identify cell type-specific gene features associated with PMP pathogenesis. Additionally, we provide bulk RNA-seq datasets from two independent cohorts: 19 fresh frozen tissue samples (12 PMPs) and 34 formalin-fixed paraffin-embedded (FFPE) samples (25 PMPs). We also offer protein expression data from a tissue microarray (TMA) analysis of 90 samples (45 PMPs). Our single-cell and bulk transcriptomic profiles, along with TMA verifications, reveal the cellular diversity of PMP, highlighting the coexistence of epithelial and mesenchymal characteristics within PMP cells. These datasets enhance our understanding of PMP pathogenesis and provide a valuable resource for uncovering the intricate molecular landscape of PMP, with the potential to improve clinical utility through further research.

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Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal cancer

Project description:Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal cancer

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