Exploring the acting mechanism of patient-derived organoids-pancreatic cancer primary tumor-derived immune cells based on single-cell RNA sequencing

XU Yingcui; LU Heming; CAO Tingting

doi:10.3969/j.issn.1674-3806.2024.12.15

Abstract：Objective To explore the acting mechanism of patient-derived organoids(PDO)-pancreatic cancer primary tumor-derived immune cells based on single-cell ribonucleic acid(RNA)sequencing.Methods Single-cell RNA sequencing datasets of pancreatic cancer was obtained from the Genome Expression Omnibus(GEO)database,and the relevant clinical data of 185 cases of pancreatic cancer patients were downloaded from the Cancer Genome Atlas(TCGA)database.After quality control,dimensionality reduction,clustering and cellular annotation,the differences in the composition and distribution of immune cells on pancreatic cancer primary tumors and PDO were analyzed,and the differentially expressed genes(DEGs)of immune cells were screened.Molecular interactions between immune cells were analyzed using CellChat,and the immune cell communication patterns were recognized.Subsequently,Gene Ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed for neutrophils DEGs.Finally,the effects of expression levels of FFAR2 and RASGEF1C genes on survival prognosis of the patients were analyzed.Results In this study,22 cell populations were successfully identified and further categorized into 11 types of different cells,among which there were 4 types of immune cells,including neutrophils.The single-cell RNA sequencing data of immune cells were extracted to obtain 30 141 cells,including 2 282 cells from PDO model and 7 319 cells from primary tumors.There were significant differences in the composition and number of immune cells in the samples from different sources.The molecular interactions between immune cells and the communication patterns of immune cells were analyzed through CellChat,and the transforming growth factor-beta(TGF-β)signaling pathway and neutrophils were identified as playing an important role in the development of pancreatic cancer.In addition,the study found that neutrophils could activate TGF-β and other signaling patterns and pathways at the same time.DEGs of neutrophils were mainly involved in biological processes such as regulation of immunoreaction,activation of immune response transport,activation of innate immune response,and were enriched in signaling pathways such as primary immune deficiency and asthma.The less studied FFAR2 and RASGEF1C genes in neutrophil DEGs were selected for survival analysis,and the results suggested that the high expressions of FFAR2 and RASGEF1C were helpful to improve the survival prognosis of the pancreatic cancer patients.Conclusion This study confirms the difference of immune cells between primary tumors and PDO in pancreatic cancer,and lays the foundation for studies on organoid in pancreatic cancer.