Molecular characterization of Pseudomyxoma peritonei with single-cell and bulk RNA sequencing

Abstract

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.

Fig. 1

Diverse cell types identified via integrative single-cell transcriptomic analysis in pseudomyxoma peritonei (PMP) and healthy. (a) The uniform manifold approximation and projection plot shows the distinct cell types identified in all samples. (b) The dot map shows the expression levels of specific markers in each cell type. (c) The feature and violin plots display the expression patterns of epithelial-specific (upper panel) and mesenchymal-specific (lower panel) markers in the single-cell transcriptomic data of PMP and healthy sample (d) The feature plots present scatter plots depicting the distribution of epithelial-specific (left panel) and mesenchymal-specific (right panel) markers, highlighting the distinctions between PMP and healthy. P-values were calculated using the Wilcoxon rank-sum test with Bonferroni adjustment; ***P < 0.001.

Fig. 2

Comparison of the expressions between pseudomyxoma peritonei (PMP) and healthy control tissues. (a) Unsupervised hierarchical cluster analysis of expressions in PMP and healthy control tissues. In this analysis, 4,737 genes showing expression changes with standard deviation of 0.8 or more were used. (b) Function enrichment analyses of 1,171 differentially expressed genes between PMP and healthy control tissues. The analysis was conducted using the Gene Ontology biological process and KEGG pathway. (c) Heatmap depicting the expression patterns of 1,171 genes in fresh frozen and formalin-fixed paraffin-embedded samples. LCPM, log-transformed counts per million.