Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma

Abstract

Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignancy with a complex tumor ecosystem. How the interplay between tumor cells, EBV, and the microenvironment contributes to NPC progression and immune evasion remains unclear. Here we performed single-cell RNA sequencing on ~104,000 cells from 19 EBV + NPCs and 7 nonmalignant nasopharyngeal biopsies, simultaneously profiling the transcriptomes of malignant cells, EBV, stromal and immune cells. Overall, we identified global upregulation of interferon responses in the multicellular ecosystem of NPC. Notably, an epithelial-immune dual feature of malignant cells was discovered and associated with poor prognosis. Functional experiments revealed that tumor cells with this dual feature exhibited a higher capacity for tumorigenesis. Further characterization of the cellular components of the tumor microenvironment (TME) and their interactions with tumor cells revealed that the dual feature of tumor cells was positively correlated with the expression of co-inhibitory receptors on CD8 + tumor-infiltrating T cells. In addition, tumor cells with the dual feature were found to repress IFN-γ production by T cells, demonstrating their capacity for immune suppression. Our results provide new insights into the multicellular ecosystem of NPC and offer important clinical implications.

Single-Nucleus Transcriptomic Analysis Reveals Important Cell Cross-Talk in Diabetic Kidney Disease

“…Single-cell sequencing (scRNA-seq) is a technological evolution and provides unprecedented insight into cell communication (10)(11)(12). In experimental studies of renal diseases (13)(14)(15)(16), scRNA-seq technology furthers the understanding of the mechanisms and cell-to-cell interactions involved in disease pathogenesis.…”

The Role of EBV-Encoded LMP1 in the NPC Tumor Microenvironment: From Function to Therapy

“…NPC is characterized by the presence of an abundant lymphoid and stromal infiltrate. The anti-tumor function of the CTLs in NPC is believed to be suppressed by cytokines, immune checkpoint proteins, and cancer-derived exosomes present in the TME (10,26,27,31,40). EBV-encoded LMP1 functions as a constitutively active TNF receptor.…”

“…The tumor usually contains a heavy infiltrate of EBV-negative non-malignant leukocytes that are primarily composed of CD8+ and CD4+ T cells and subsets of natural killer (NK) cells, B cells, mast cells and various types of myeloid cells including monocytes, macrophages, and neutrophils. Several infiltrating cell types with known immunosuppressive function are present, including CD4+ CD25+Foxp3+T regulatory cells (Tregs), myeloidderived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) (26,27). Although TILs account for a large fraction of stromal cells in the tumor microenvironment (TME), they seem to have no inhibitory effects on NPC tumor cells.…”

“…In a recent study, single-cell transcriptome analysis identified a subpopulation of tumor cells expressing high levels of immunerelated genes (27). Interestingly, the presence of cells with this "epithelial-immune" dual phenotype in NPC tissues were associated with a poorer prognosis.…”

“…Their presence also correlated strongly with expression of co-inhibitory receptors (PD-1, LAG-3, TIM-3, TIM-4 and CD276) on CD8+ TILs, reflecting a more profound dysfunction of TILs in tumors containing this unique subpopulation of cancer cells. Functional studies also showed that the "epithelial-immune" tumor subpopulation displayed a more substantial capacity for tumorigenesis, a greater potential for immune cell recruitment and modulation, and was able to suppress IFN-g production by T cells (27). Given that LMP1 expression in NPC cells upregulates many cytokines and immunomodulatory molecules that facilitate immunosuppression, the possible correlation between LMP1 expression and the presence of these "epithelial-immune" NPC cells is clear an area worthy of further investigation.…”