Revealing Tumor Environment Complexity in Pancreatic Cancer via Single-Cell Analysis
Summary
The scientists characterized the distinct tumor microenvironment of five patients using single cell transcriptome sequencing (scRNA-seq). Three of the patients had pancreatic ductal adenocarcinoma (PDAC), while two of the patients had undifferentiated carcinoma with osteoclast-like large cells (UCOGCP). They also found that CD74 has a major influence on the way the UCOGCP microenvironment evolves. In conclusion, the findings of their study gave an understanding of the production and activity of OGCs as well as the tumor microenvironment of UCOGCP, which shed light on the prognosis and course of the treatment plan for this unique form of pancreatic cancer.
Research Criteria
They performed scRNA-seq to examine the various tumor microenvironments of one patient with UCOGCP and three patients with PDAC. The results of the data analysis were supported by immunohistochemistry (IHC) staining. 18,376 cells from the four samples were collected after the raw data had undergone quality control.
Fig.1 Experimental design. (Wang, 2022)
Sample Type
Fresh tumor tissues of PDAC patients with or without UCOGC.
Result—scRNA-Seq Cellular Contribution
They were able to acquire 18,376 cells from these samples after passing quality screening, and the preliminary group was organized into ten groups after being clustered. The next step was to get 19 subpopulations at a resolution of 0.6. Of these, pca_0714 primarily comprised Ductal type I, T cells, and myeloid cells, whereas the other samples contained all subpopulations. They analyzed the expression levels of epithelial markers EPCAM and KRT19 as well as the OGC marker CD68 in UCOGC samples (pca ai1) and two duct type I cell populations in clusters 13 and 15. This was done because it is possible that OGCs originate from a combination of mesenchymal and epithelial cells. According to the findings, cluster 15 exhibited expression of KRT19 but not EPCAM. Additionally, the genes KRT81, PAEP, and LINC01615 were also found to be expressed in cluster 15. IHC staining of KRT81 revealed that OGC was positive for KRT81, which suggests that OGC most likely originated from mesenchymal-epithelial cells rather than bone marrow cells.
Fig.2 The scRNA-seq summarized the differences in tumor microenvironment between UCOGCP and other PDAC. (Wang, 2022)
Result—The Trajectory Analysis of the Ductal Cells in UCOGCP
Following the application of the Seurat process for clustering, a total of 8 distinct clusters were discovered. The trajectory analysis produced a total of three branches, and clusters 13 and 15 were found to be placed in branches that were distinct from one another. The results of the mapping study showed that state 1 is predominantly composed of epithelial clusters that are devoid of EPCAM. After this, the expression patterns that were found to be characteristic of these two separate clades were quantified and organized into four unique clusters. The highly expressed pre-branch genes are predominantly enriched in the "membrane-tethered organelle localization," "membrane docking," and "vesicle organization" GOBP pathways, and the genes that are highly expressed in cell destiny 2 are enriched in the "nuclear fission" related pathways. High levels of gene expression were found in cell fate 1 for those genes that were enriched in 'SRP-dependent co-translational proteins,' 'organization of the cell-cell junction,' 'epidermal development,' and 'cornification'.
Fig.3 Heterogeneity of epithelial cells in UCOGCP sample. (Wang, 2022)
Creative Biolabs' Service
Single Cell RNA Sequencing Service
Rarely are cell populations uniform and coordinated in their traits. The goal of single-cell RNA sequencing is to reveal the diversity of the transcriptome in diverse samples. To maximize your project's flexibility, speed, and data quality, Creative Biolabs offers end-to-end workflows that include sample preparation, library development, and data analysis.
Learn moreCreative Biolabs offers single cell RNA sequencing (scRNA-seq) services to researchers by leveraging cutting-edge sequencing technology and bioinformatics tools to generate high-quality data and perform downstream analysis. Researchers can acquire a better knowledge of the molecular pathways underpinning cellular activities and diseases by using our scRNA-seq service.
To learn more details, please contact us.
Reference
- Wang, X.; et al. Single-cell RNA-seq reveals the genesis and heterogeneity of tumor microenvironment in pancreatic undifferentiated carcinoma with osteoclast-like giant-cells. Molecular Cancer. 2022, 21(1): 133.
