Deciphering the senescence-based tumoral heterogeneity and characteristics in pancreatic cancer: Results from parallel bulk and single-cell transcriptome data

Abstract

The prevalent intra- and intertumoral heterogeneity results in undesirable prognosis and therapy failure of pancreatic cancer, potentially resulting from cellular senescence. Herein, integrated analysis of bulk and single-cell RNA-seq profiling was conducted to characterize senescence-based heterogeneity in pancreatic cancer. Publicly available bulk and single-cell RNA sequencing from pancreatic cancer patients were gathered from TCGA-PAAD, PACA-AU, PACA-CA, and GSE154778 datasets. The activity of three senescence-related pathways (cell cycle, DNA repair, and inflammation) was scored utilizing ssGSEA algorithm. A series of functional verifications of crucial genes were accomplished in patient tissue and pancreatic cancer cells. Based upon them, unsupervised clustering analysis was executed to classify pancreatic cancer samples into distinct senescence-based clusters at the bulk and single-cell levels. For single-cell transcriptome profiling, cell clustering and annotation were implemented, and malignant cells were recognized utilizing infercnv algorithm. Two senescence-based clusters were established and highly reproducible at the bulk level, with the heterogeneity in prognosis, clinicopathological features, genomic CNVs, oncogenic pathway activity, immune microenvironment and immune checkpoints. Senescence-relevant gene CHGA, UBE2C and MCM10 were proved to correlate with the migration and prognosis of pancreatic cancer. At the single-cell level, seven cell types were annotated, comprising ductal cells 1, ductal cells 2, fibroblasts, macrophages, T cells, stellate cells, and endothelial cells. The senescence-based classification was also proven at the single-cell level. Ductal cells were classified as malignant cells and non-malignant cells. In the tumor microenvironment of malignant cells, hypoxia and angiogenesis affected senescent phenotype. The heterogeneity in senescence was also observed between and within cell types. Altogether, our findings unveil that cellular senescence contributes to intra- and intertumoral heterogeneity in pancreatic cancer, which might facilitate the development of therapeutics and precision therapy in pancreatic cancer.