PPP1R14A基因与头颈鳞状细胞癌免疫治疗耐药相关：综合分析单细胞和批量测序结果

doi:10.24920/004354

摘要/Abstract

摘要： 目的分析接受纳武利尤单抗治疗的头颈鳞状细胞癌（head and neck squamous cell carcinoma,HNSCC）患者的单细胞和批量RNA测序数据,发现与耐药相关的基因。
方法下载基因表达总库（the Gene Expression Omnibus database,GEO）数据库中接受纳武利尤单抗治疗HNSCC患者的单细胞和批量RNA测序数据,采用R软件筛选在耐药患者和药物敏感患者之间的差异表达基因（differentially expressed genes,DEGs）。采用最小绝对收缩和选择算法（The Least Absolute Shrinkage Selection Operator,LASSO）和递归特征消除（Recursive Feature Elimination,RFE）算法,鉴别与耐药相关的关键基因。利用基因本体和京都基因组百科全书分析DEGs的功能富集。之后,研究关键基因表达与免疫细胞浸润、细胞分化轨迹、动态基因表达谱以及配体-受体相互作用的关系。
结果我们共发现83个DEGs。它们主要富集在T细胞分化、PD-1和PD-L1检查点通路以及T细胞受体等通路中。在机器学习方法筛选出的6个关键基因中,仅PPP1R14A基因表达在耐药组与药物敏感组的差异有统计学意义,这种现象既存在于治疗前,也存在于治疗后（P < 0.05）。PPP1R14A基因高表达组的免疫得分较低（P < 0.01）、高免疫抑制因子表达较高（如PDCD1、CTLA4和PDCD1LG2等）（R > 0, P < 0.05）、免疫细胞浸润水平较低,HLA与CD4的相互作用程度较高（P < 0.05）。
结论 PPP1R14A基因与HNSCC患者对纳武利尤单抗耐药性相关。因此,PPP1R14A基因可能是改善HNSCC患者纳武利尤单抗耐药性的靶点。

关键词: PPP1R14A, 头颈鳞状细胞癌, 免疫治疗, 耐药

Abstract: Objective To identify nivolumab resistance-related genes in patients with head and neck squamous cell carcinoma (HNSCC) using single-cell and bulk RNA-sequencing data.
Methods The single-cell and bulk RNA-sequencing data downloaded from the Gene Expression Omnibus database were analyzed to screen out differentially expressed genes (DEGs) between the nivolumab resistant and nivolumab sensitive patients using R software. The Least Absolute Shrinkage Selection Operator (LASSO) regression and Recursive Feature Elimination (RFE) algorithm were performed to identify key genes associated with nivolumab resistance. Functional enrichment of DEGs was analyzed with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The relationships of key genes with immune cell infiltration, differentation trajectory, dynamic gene expression profiles, and ligand-receptor interaction were explored.
Results We found 83 DEGs. They were mainly enriched in T-cell differentiation, PD-1 and PD-L1 checkpoint pathways, and T-cell receptor pathways. In six key genes identified using machine learning algorithms, only PPP1R14A gene was differentially expressed between the nivolumab resistant and nivolumab sensitive groups both before and after immunotherapy (P < 0.05). The high PPP1R14A gene expression group had lower immune score (P < 0.01), higher expression of immunosuppressive factors (such as PDCD1, CTLA4, and PDCD1LG2) (r > 0, P < 0.05), lower differentiation of infiltrated immune cells (P < 0.05), and a higher degree of interaction between HLA and CD4 (P < 0.05).
Conclusions PPP1R14A gene is closely associated with resistance to nivolumab in HNSCC patients. Therefore, PPP1R14A may be a target to ameliorate nivolumab resistance of HNSCC patients.

Key words: PPP1R14A, head and neck squamous cell carcinoma, immunotherapy, drug resistance

基金资助: 国家级大学生创新创业训练项目（202210367002）; 安徽省重点实验室开放项目（AHCM2022Z004）

Jun-Jie Ma, Lei Zhang, Jin Lu, Hao-Xuan Zhang. PPP1R14A is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing[J/OL].Chinese Medical Sciences Journal, .DOI:10.24920/004354.[Epub ahead of print].

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