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免疫相关基因signature 用于肺腺癌预后的开发和验证。

Development and validation of an immune-related gene signature for prognosis in Lung adenocarcinoma.

机构信息

The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.

The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.

出版信息

IET Syst Biol. 2023 Feb;17(1):27-38. doi: 10.1049/syb2.12057. Epub 2023 Feb 2.

Abstract

The most common type of lung cancer tissue is lung adenocarcinoma. The TCGA-LUAD cohort retrieved from the TCGA dataset was considered the internal training cohort, while GSE68465 and GSE13213 datasets from the GEO database were used as the external test cohort. The TCGA-LUAD cohort was classified into two immune subtypes using single-sample gene set enrichment analysis of the immune gene set and unsupervised clustering analysis. The ESTIMATE algorithm, the CIBERSORT algorithm, and HLA family expression levels again validated the reliability of this typing. We performed Venn analysis using immune-related genes from the immport dataset and differentially expressed genes from the subtypes to retrieve differentially expressed immune genes (DEIGs). In addition, DEIGs were used to construct a prognostic model with the least absolute shrinkage and selection operator regression analysis. A reliable risk model consisting of 11 DEIGs, including S100P, INHA, SEMA7A, INSL4, CD40LG, AGER, SERPIND1, CD1D, CX3CR1, SFTPD, and CD79A, was then built, and its reliability was further confirmed by ROC curve and calibration plot analysis. The high-risk score subgroup had a poor prognosis and a lower tumour immune dysfunction and exclusion score, indicating a greater likelihood of anti-PD-1/cytotoxic T lymphocyte antigen 4 benefit.

摘要

最常见的肺癌组织类型是肺腺癌。从 TCGA 数据库中检索到的 TCGA-LUAD 队列被视为内部训练队列,而 GEO 数据库中的 GSE68465 和 GSE13213 数据集则被用作外部测试队列。使用免疫基因集的单样本基因集富集分析和无监督聚类分析对 TCGA-LUAD 队列进行了两种免疫亚型分类。ESTIMATE 算法、CIBERSORT 算法和 HLA 家族表达水平再次验证了这种分型的可靠性。我们使用 immport 数据集中的免疫相关基因和亚型中差异表达的基因进行 Venn 分析,以检索差异表达的免疫基因(DEIGs)。此外,使用 DEIGs 构建了一个预后模型,使用最小绝对收缩和选择算子回归分析。然后构建了一个由 11 个 DEIGs 组成的可靠风险模型,包括 S100P、INHA、SEMA7A、INSL4、CD40LG、AGER、SERPIND1、CD1D、CX3CR1、SFTPD 和 CD79A,并通过 ROC 曲线和校准图分析进一步验证了其可靠性。高风险评分亚组预后不良,肿瘤免疫功能障碍和排除评分较低,提示更有可能从抗 PD-1/细胞毒性 T 淋巴细胞抗原 4 获益。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c9/9931057/d5c1c547890f/SYB2-17-27-g009.jpg

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