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

Cell Research
Yu-Pei ChenJun Ma

Abstract

Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumor 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 7581 malignant cells and 40,285 immune cells from fifteen primary NPC tumors and one normal sample. We revealed malignant signatures capturing intratumoral 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 prov...Continue Reading

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Citations

Jan 5, 2021·Journal of Cancer Research and Clinical Oncology·Nguyen Hoang VietJ Luis Espinoza
Jan 23, 2021·Oncogene·Nicholas J CampionGhassan Alusi
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Methods Mentioned

BETA
scRNA-seq
RNA-seq
biopsy
FACS
flow cytometry
transfection
biopsies
Chip
PCR
density gradient centrifugation

Software Mentioned

R Base package
Seurat R package
inferCNV
GenePattern
RcisTarget
ssGSEA
BWA
pySCENIC
CellRanger
Gene set variation analysis ( GSVA )

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