Combining bulk and scRNA‐seq to explore the molecular mechanisms governing the distinct efferocytosis activities of a macrophage subpopulation in PDAC

作者：Shaoliang Zhu, Quan Cheng, Mengjie Zou, Chunxing Li, Yi Tang, Longjie Xia, Yanming Jiang, Zheng Gong, Zhenyong Tang, Yuntian Tang, Honglin Luo, Ningfu Peng, Xiaojing Wang, Xiao-Feng Dong · 发表于：Journal of Cellular and Molecular Medicine · 年份：2024 · DOI：10.1111/jcmm.18266 · 被引用次数：11 · 研究领域：Phagocytosis and Immune Regulation、Pancreatic and Hepatic Oncology Research、Immune cells in cancer

Pancreatic ductal adenocarcinoma (PDAC), a very aggressive tumour, is currently the third leading cause of cancer-related deaths. Unfortunately, many patients face the issue of inoperability at the diagnostic phase leading to a quite dismal prognosis. The onset of metastatic processes has a crucial role in the elevated mortality rates linked to PDAC. Individuals with metastatic advances receive only palliative therapy and have a grim prognosis. It is essential to carefully analyse the intricacies of the metastatic process to enhance the prognosis for individuals with PDAC. Malignancy development is greatly impacted by the process of macrophage efferocytosis. Our current knowledge about the complete range of macrophage efferocytosis activities in PDAC and their intricate interactions with tumour cells is still restricted. This work aims to resolve communication gaps and pinpoint the essential transcription factor that is vital in the immunological response of macrophage populations. We analysed eight PDAC tissue samples sourced from the gene expression omnibus. We utilized several software packages such as Seurat, DoubletFinder, Harmony, Pi, GSVA, CellChat and Monocle from R software together with pySCENIC from Python, to analyse the single-cell RNA sequencing (scRNA-seq) data collected from the PDAC samples. This study involved the analysis of a comprehensive sample of 22,124 cells, which were classified into distinct cell types. These cell types encompassed endothelial and e...