Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumour microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7,581 malignant cells and 40,285 immune cells from 15 primary NPC tumours and one normal sample. We revealed malignant signatures capturing intratumoural transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as CLEC9A+ dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell-cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs), CLEC9A+ DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for the precision therapies in NPC. Fifteen patients who were pathologically diagnosed with non-keratinizing or keratinizing NPC were enrolled in this study; normal nasopharyngeal epithelial tissue from one patient with chronic nasopharyngitis was also collected as a control. The samples were all fresh-processed for 10x genomics V2 3' single cell RNA sequencing. Raw data access provided at: NGB Nucleotide Sequence Archive (accession code: CNP0000428)