<italic style="font-style: italic">PPP1R14A</italic> is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing

Jun-Jie Ma; Lei Zhang; Jin Lu; Hao-Xuan Zhang

doi:10.24920/004354

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PPP1R14A is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing

Chinese Medical Sciences Journal Vol. 39, Issue 2, Pages: 111-121(2024)

Research Articles | Updated：2025-03-07

- PPP1R14A is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing
- Affiliations：
  
  1.Department of Clinical Medicine, Bengbu Medical University, Bengbu 233030, Anhui, China
  3.Department of Human Anatomy, Bengbu Medical University, Bengbu 233030, Anhui, China
  4.Anhui Key Laboratory of Computational Medicine and Intelligent Health, Bengbu Medical University, Bengbu 233030, Anhui, China
  2.Department of General Surgery, The Second Affiliated Hospital of Bengbu Medical University, Bengbu 233030, Anhui, China
- Author bio：
  
  E-mail: zhxww@foxmail.com
- Funds：
  
  国家级大学生创新创业训练项目(202210367002)
- DOI：10.24920/004354
  CLC：
- Received：04 March 2024，
  
  Accepted：2024-04-18，
  
  Published Online：18 June 2024，
  
  Published：30 June 2024
- Accepted：
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马俊杰,张磊,陆进等.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[J].中国医学科学杂志（英文）,2024,39(02):111-121.

Ma Jun-Jie,Zhang Lei,Lu Jin,et al.PPP1R14A is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing[J].Chinese Medical Sciences Journal,2024,39(02):111-121.
马俊杰,张磊,陆进等.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[J].中国医学科学杂志（英文）,2024,39(02):111-121. DOI： 10.24920/004354.

Ma Jun-Jie,Zhang Lei,Lu Jin,et al.PPP1R14A is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing[J].Chinese Medical Sciences Journal,2024,39(02):111-121. DOI： 10.24920/004354.

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（

0.05）。

PPP1R14A

基因高表达组的免疫得分较低（

0.01）、高免疫抑制因子表达较高（如

PDCD1

、

CTLA4

和

PDCD1LG2

等）（R

0，

0.05）、免疫细胞浸润水平较低，

HLA

与

CD4

的相互作用程度较高（

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。

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 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

and T-cell receptor pathways. Among 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 (

0.05). The high

PPP1R14A

gene expression group had lower immune score (

0.01)

higher expression of immunosuppressive factors (such as

PDCD1

CTLA4

and

PDCD1LG2

) (

0.05)

lower differentiation of infiltrated immune cells (

0.05)

and a higher degree of interaction between HLA and CD4 (

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.

关键词

Keywords

references

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Jun-Jie Ma

Lei Zhang

Jin Lu

Hao-Xuan Zhang

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Department of Clinical Medicine

Department of Human Anatomy

Anhui Key Laboratory of Computational Medicine and Intelligent Health, Bengbu Medical University

⁰

PPP1R14A is Associated with Immunotherapy Resistance in Head and Neck Squamous Cell Carcinoma Identified by Single-Cell and Bulk RNA-Sequencing

DOI：10.24920/004354

摘要

Abstract

关键词

Keywords

references