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

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

PROVIDER: PRJNA1106532 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28854300.fastq.gz	Fastqsanger.gz
	SRR28854301.fastq.gz	Fastqsanger.gz
	SRR28854302.fastq.gz	Fastqsanger.gz
	SRR28854303.fastq.gz	Fastqsanger.gz
	SRR28854304.fastq.gz	Fastqsanger.gz

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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.

2025-04-30 | GSE266302 | GEO

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.

2018-08-03 | PXD010086 | Pride

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.

2024-10-09 | GSE228377 | GEO

Exome sequencing of pseudomyxoma peritonei

Project description:Pseudomyxoma peritonei (PMP) is a subtype of mucinous adenocarcinoma mainly restricted to the peritoneal cavity and most commonly originating from the appendix. In this study, we sequenced whole coding genome of nine PMP tumors and paired normal tissues in order to identify commonly mutated genes and signaling pathways affected in PMP.

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Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

Project description:Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

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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.

2024-10-09 | GSE228376 | GEO

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.

2024-10-09 | GSE228375 | GEO

Prognosis conferred by molecular features of appendix-derived Pseudomyxoma Peritonei.

Project description:IntroductionPseudomyxoma Peritonei (PMP) is an extremely rare disease characterized by progressive accumulation of mucinous ascites and implants in the peritoneum. We investigated the prognostic value for response to cytoreductive surgery (CRS) or hyperthermic intraperitoneal chemotherapy (HIPEC) and dissected potential beneficial targeted therapy utilizing genomic characteristics.MethodsWhole-exome sequencing (WES) was performed on tissue specimens and matched white blood cells from 81 patients with PMP. The study investigated mutational signatures, profiling, and their correlation with progression-free survival (PFS) and overall survival (OS).ResultsSignature 3 (HRD) and signature 15 (dMMR) were dominant. NMF cluster 1, characterized by signature 4, exhibited a worse prognosis. The p53 and TGF-β signaling pathways may contribute as risk factors for worse OS and PFS, respectively. MUC16-mutated patients had worse PFS (P = 0.016) and OS (P = 0.004) compared to wild-type patients. Patients with tumor mutational burden (TMB) > 1(P = 0.026) or alterations in TP53 (P = 0.006) or SMAD4 (P = 0.013) had significantly worse OS compared to those with a TMB < 1 or normal genes. Patients with homologous recombination deficiency (HRD) positivity (P = 0.003) or alterations in TGFBR2 (P = 0.037) experienced worse PFS compared to their respective control groups. Furthermore, NMF cluster1 (P = 0.020), TP53 (P = 0.004), and MUC16 (P = 0.013) were identified as independent prognostic factors for OS, while HRD status (P = 0.003) was independent predictors for PFS in PMP.ConclusionsThe study reveals that genomic profiling can serve as a robust tool for identifying prognostic markers in PMP. The identified genomic mutations and signaling pathway offer new avenues for targeted therapies.

| S-EPMC11867523 | biostudies-literature

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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5349f7b2-36ff-420f-b917-b16e10af4a42 - samples

Project description:Mesothelioma of the peritoneum (n=21) and Pseudomyxoma peritonei/mucinous adenocarcinoma of the appendix (n=11)

| EGAD00001008826 | EGA