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ABSTRACT: Bacteria associated with peritoneal metastasis of Pseudomyxoma Peritonei

PROVIDER: PRJEB67895 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12161400.fastq.gz	Fastqsanger.gz
	ERR12165600.fastq.gz	Fastqsanger.gz
	ERR12161401.fastq.gz	Fastqsanger.gz
	ERR12165601.fastq.gz	Fastqsanger.gz
	ERR12165602.fastq.gz	Fastqsanger.gz

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Chitinophagaceae bacterium PMP191F isolate:PMP191F

Project description:Bacterial species associated with 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.

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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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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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Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

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

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

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

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Project description:WES of PDX, PDXO and patient samples from Pseudomyxoma Peritonei (PMP)

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A Novel Assessment of Metabolic Pathways in Peritoneal Metastases from Low-Grade Appendiceal Mucinous Neoplasms

Project description:Background: There is a paucity of targeted therapies for patients with pseudomyxoma peritonei (PMP) secondary to low-grade appendiceal mucinous neoplasms (LAMNs). Dysregulated metabolism has emerged as a hallmark of cancer, and the relationship of metabolomics and cancer is an area of active scientific exploration. We sought to characterize phenotypic differences found in peritoneal metastases (PM) derived from LAMN versus adenocarcinoma. Methods: Tumors were washed with phosphate-buffered saline (PBS), microdissected, then dissociated in ice-cold methanol dried and reconstituted in pyridine. Samples were derivatized in tert-butyldimethylsilyl (TBDMS) and subjected to gas chromatography-coupled mass spectrometry. Metabolites were assessed based on a standard library. RNA sequencing was performed, with pathway and network analyses on differentially expressed genes.Results: Eight peritoneal tumor samples were obtained and analyzed: LAMNs (4), and moderate to poorly differentiated adenocarcinoma (colon [1], appendix [3]). Decreases in pyroglutamate, fumarate, and cysteine in PM from LAMNs were found compared with adenocarcinoma. Analyses showed the differential gene expression was dominated by the prevalence of metabolic pathways, particularly lipid metabolism. The gene retinol saturase (RETSAT), downregulated by LAMN, was involved in the multiple metabolic pathways that involve lipids. Using network mapping, we found IL1B signaling to be a potential top-level modulation candidate. Conclusions: Distinct metabolic signatures may exist for PM from LAMN versus adenocarcinoma. A multitude of genes are differentially regulated, many of which are involved in metabolic pathways. Additional research is needed to identify the significance and applicability of targeting metabolic pathways in the potential development of novel therapeutics for these challenging tumors.

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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.

2018-08-03 | PXD010086 | Pride

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