头颈鳞状细胞癌（HNSCC）占头颈肿瘤的超过一半，大约90%。本研究重点是利用单细胞和批量转录组数据构建异质性景观，以识别原发性和淋巴转移性头颈鳞状细胞癌微环境的分子特征。本研究纳入了23例具有scRNA-seq数据的HNSCC样本和546例TCGA的HNSCC样本。我们使用了Monocle对细胞进行排序，并使用CellPhoneDB来探索细胞间的相互作用。Infercnv是用来根据单细胞测序转录组数据推断出具有明显拷贝数变异的细胞的工具。我们重新评估了HNSCC批量RNA转录组数据，以表征不同细胞类型在塑造HNSCC的免疫微环境中的功能。我们结合了谱系重构、CNV推断和细胞相互作用来揭示不同疾病状态下不同细胞群体的特征，癌细胞和免疫细胞系谱的分化轨迹以及非免疫和免疫细胞之间的相互作用。PD-1和PD-L1/PD-L2在T细胞中表达非常罕见，免疫检查点分子KLRB1-CLEC2D达到高水平表达。我们鉴定了与HNSCC患者预后相关的基于微环境的三种HNSCC亚型。总之，本研究对原发性和转移性HNSCC的肿瘤内异质性和免疫微环境进行了解剖，对揭示不同疾病状态下HNSCC对免疫疗法抵抗机制的重要性至关重要，并有望有助于进一步研究HNSCC细胞转移机制和指导临床患者的治疗。版权所有©2023 Elsevier Ltd.

Head and neck squamous cell carcinoma (HNSCC) accounts for more than half of head and neck tumors, roughly 90%. This study focused on constructing the heterogeneous landscape using single-cell and bulk transcriptomic data to identify molecular characteristics of the microenvironment in primary and lymphatic metastatic head and neck squamous carcinomas.The study enrolled 23 HNSCC samples with scRNA-seq data and 546 HNSCC samples from TCGA. We used Monocle to sort the cells and used CellPhoneDB to explore the cell-cell interactions. Infercnv, which was used to infer cells with apparent copy number variation based on single-cell sequencing transcriptome data. We re-evaluated HNSCC bulk RNA transcriptome data to characterize the functions of different cell types in shaping the immune microenvironment of HNSCC.We combined genealogical reconstruction, CNV inference, and cellular interactions to uncover the characteristics of distinct cell populations in different disease states, differences in cancer and immune cell lineages of differentiation trajectories, and interactions between non-immune and immune cell. PD-1 and PD-L1/PD-L2 expressed extremely rare in T cells, the immune checkpoint molecule KLRB1-CLEC2D achieved a high-level expression. We identified three microenvironment-based HNSCC subtypes associated with the prognosis of HNSCC patients.In summary, the present study dissected the intratumoral heterogeneity and immune microenvironment of primary and metastatic HNSCC, which is crucial to reveal the mechanisms of resistance to immunotherapy in HNSCC in different disease states and is expected to assist in the further investigation of the mechanism of HNSCC cell metastasis and guide the treatment of clinical patients.Copyright © 2023. Published by Elsevier Ltd.