Mining GEO and TCGA Database for Immune Microenvironment of Lung Squamous Cell Carcinoma Patients With or Without Chemotherapy.

Huiping Qiang,Tianqing Chu,Qing Chang,Yinchen Shen,Jiaqi Li,Jialin Qian

doi:10.3389/fonc.2022.835225

Huiping Qiang, Tianqing Chu + Show 4 more

Open Access

https://doi.org/10.3389/fonc.2022.835225

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Abstract

BackgroundChemotherapy is the main treatment for patients with lung squamous cell carcinoma (LUSC). However, how chemotherapy affects their immune system is rarely reported. This study was aimed to compare the differences in the immune microenvironment of LUSC patients with or without chemotherapy.MethodsA total of 494 LUSC samples were obtained from The Cancer Genome Atlas (TCGA) database. The immune cell infiltration was evaluated by the ssGSEA algorithm, and the tumor subtype was assayed by ConsensusClusterPlus. The differences in tumor mutation burden (TMB) and clinical information between the two types were then compared. Additionally, the differentially expressed genes (DEGs) between two types were analyzed and hub genes were validated in the GEO database.ResultsLSCC samples in TCGA were divided into three subtypes. Then, combining the tumor subtype and immune scores, the samples were divided into hot and cold tumors. Regardless of whether LUSC patients received chemotherapy, the survival of the hot tumor group was not significantly prolonged compared with that of the cold tumor group. For LUSC patients who received chemotherapy, the TMB value in hot tumor group was significantly higher. Total 501 DEGs were identified between two groups. The high expressions of hub genes CD19, CTLA4, FCGR3B, CD80, IL-10, etc. were also validated in the GSE37745 dataset.ConclusionChemotherapy does not affect the survival and prognosis of LUSC patients, but it significantly increases the TMB value of patients with hot tumor. The DEGs, especially hub genes, such as CD19, CTLA4, and FCGR3B, may serve as biomarkers to distinguish cold and hot tumors in LUSC.

Highlights

Lung cancer is one of the most common malignant tumors with a 5-year overall survival rate of 16%–20% [1, 2]
Non-small cell lung cancer (NSCLC) accounts for about 80% of all lung cancer types [3], which consist of two main histologic subtypes: lung squamous cell carcinoma (LUSC; accounting for 55% of all NSCLCs) and lung adenocarcinoma (LUAD; accounting for 30%) [4]
LUSC is often diagnosed at the advanced stage with poor prognosis and lacks targeted therapies available compared to LUAD

Summary

Introduction

Lung cancer is one of the most common malignant tumors with a 5-year overall survival rate of 16%–20% [1, 2]. Non-small cell lung cancer (NSCLC) accounts for about 80% of all lung cancer types [3], which consist of two main histologic subtypes: lung squamous cell carcinoma (LUSC; accounting for 55% of all NSCLCs) and lung adenocarcinoma (LUAD; accounting for 30%) [4]. Immune cells are normal cell types that are commonly symbiotic with cancer cells [6]. In recent years, accumulating evidence has illustrated the correlation between immunotherapy and immune microenvironment [7]. Chemotherapy is the main treatment for patients with lung squamous cell carcinoma (LUSC). This study was aimed to compare the differences in the immune microenvironment of LUSC patients with or without chemotherapy

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