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基于机器学习的脑胶质瘤免疫浸润新分类。

Machine learning-based new classification for immune infiltration of gliomas.

机构信息

Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.

Department of Internal Medicine III, University Hospital Munich, Ludwig-Maximilians- University Munich, Munich, Germany.

出版信息

PLoS One. 2024 Oct 25;19(10):e0312071. doi: 10.1371/journal.pone.0312071. eCollection 2024.


DOI:10.1371/journal.pone.0312071
PMID:39453922
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11508054/
Abstract

BACKGROUND: Glioma is a highly heterogeneous and poorly immunogenic malignant tumor, with limited efficacy of immunotherapy. The characteristics of the immunosuppressive tumor microenvironment (TME) are one of the important factors hindering the effectiveness of immunotherapy. Therefore, this study aims to reveal the immune microenvironment (IME) characteristics of glioma and predict different immune subtypes using machine learning methods, providing guidance for immune therapy in glioma. METHODS: We first performed unsupervised cluster analysis on the genes and arrays of 693 gliomas in CGGA database and 702 gliomas in TCGA database. Then establish and verify the classification model through Machine Learning (ML). Then, use DAVID to perform functional enrichment analysis for different immune subtypes. Next step, analyze the immune cell distribution, stemness maintenance, mesenchymal phenotype, neuronal phenotype, tumorigenic cytokines, molecular and clinical characteristics of different immune subtypes of gliomas. RESULTS: Firstly, we divide the IME of gliomas in the CGGA database into four different subtypes, namely IM1, IM2, IM3, and IM4; similarly, the IME of gliomas in the TCGA database can also be divided into four different subtypes (IMA, IMB, IMC, and IMD). Next, based on ML, we developed a highly reliable model for predicting different immune subtypes of glioma. Then, we found that Monocytic lineage, Myeloid dendritic cells, NK cells and CD8 T cells had the highest enrichment in the IM1/IMD subtypes. Cytotoxic lymphocytes were highest expressed in the IM4/IMA subtypes. Next step, Enrichment analysis revealed that the IM1-IMD subtypes were mainly closely related to the production and secretion of IL-8 and TNF signaling pathway. The IM2-IMB subtypes were strongly associated with leukocyte activation and NK cell mediated cytotoxicity. The IM3-IMC subtypes were closely related to mitotic nuclear division and mitotic cell cycle process. The IM4-IMA subtypes were strongly associated with Central Nervous System (CNS) development and striated muscle tissue development. Afterwards, Single sample gene set enrichment analysis (ssGSEA) showed that stemness maintenance phenotypes were mainly enriched in the IM4/IMA subtypes; Neuronal phenotypes were closely associated with the IM2/IMB subtypes; and mesenchymal phenotypes and tumorigenic cytokines were highly correlated with the IM2 /IMB subtypes. Finally, we found that compared with patients in the IM2/IMB and IM4/IMA subtypes, the IM1/IMD and IM3/IMC subtypes have the highest proportion of GBM patients, the shortest average overall survival of patients and the lowest proportion of patients with IDH mutation and 1p36/19q13 co-deletion. CONCLUSIONS: We developed a highly reliable model for predicting different immune subtypes of glioma by ML. Then, we comprehensively analyzed the immune infiltration, molecular and clinical features of different immune subtypes of gliomas and defined gliomas into four subtypes: immunogenic subtype, adaptive immune resistance subtype, mesenchymal subtype, and immune tolerance subtype, which represent different TMEs and different stages of tumor development.

摘要

背景:胶质瘤是一种高度异质性和免疫原性差的恶性肿瘤,免疫治疗效果有限。肿瘤免疫抑制微环境(TME)的特征之一是阻碍免疫治疗效果的重要因素之一。因此,本研究旨在通过机器学习方法揭示胶质瘤的免疫微环境(IME)特征,并预测不同的免疫亚型,为胶质瘤的免疫治疗提供指导。

方法:我们首先对 CGGA 数据库中的 693 例胶质瘤和 TCGA 数据库中的 702 例胶质瘤的基因和数组进行无监督聚类分析。然后通过机器学习(ML)建立和验证分类模型。接下来,使用 DAVID 对不同免疫亚型进行功能富集分析。下一步,分析不同免疫亚型胶质瘤的免疫细胞分布、干性维持、间充质表型、神经元表型、致瘤细胞因子、分子和临床特征。

结果:首先,我们将 CGGA 数据库中胶质瘤的 IME 分为四个不同的亚型,即 IM1、IM2、IM3 和 IM4;同样,TCGA 数据库中胶质瘤的 IME 也可以分为四个不同的亚型(IMA、IMB、IMC 和 IMD)。接下来,基于 ML,我们开发了一种高度可靠的预测胶质瘤不同免疫亚型的模型。然后,我们发现单核细胞谱系、髓样树突状细胞、NK 细胞和 CD8 T 细胞在 IM1/IMD 亚型中表达最高。细胞毒性淋巴细胞在 IM4/IMA 亚型中表达最高。下一步,富集分析表明,IM1-IMD 亚型主要与 IL-8 的产生和分泌以及 TNF 信号通路密切相关。IM2-IMB 亚型与白细胞激活和 NK 细胞介导的细胞毒性密切相关。IM3-IMC 亚型与有丝分裂核分裂和有丝分裂细胞周期过程密切相关。IM4-IMA 亚型与中枢神经系统(CNS)发育和横纹肌组织发育密切相关。随后,单细胞基因集富集分析(ssGSEA)表明,干性维持表型主要在 IM4/IMA 亚型中富集;神经元表型与 IM2/IMB 亚型密切相关;间充质表型和致瘤细胞因子与 IM2/IMB 亚型高度相关。最后,我们发现与 IM2/IMB 和 IM4/IMA 亚型的患者相比,IM1/IMD 和 IM3/IMC 亚型的 GBM 患者比例最高,患者的平均总生存期最短,IDH 突变和 1p36/19q13 共缺失的患者比例最低。

结论:我们通过 ML 开发了一种高度可靠的预测胶质瘤不同免疫亚型的模型。然后,我们全面分析了不同免疫亚型胶质瘤的免疫浸润、分子和临床特征,并将胶质瘤定义为四个亚型:免疫原性亚型、适应性免疫抵抗亚型、间充质亚型和免疫耐受亚型,它们代表不同的 TME 和不同的肿瘤发展阶段。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/874e48f71e00/pone.0312071.g007.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/01e504c31a8d/pone.0312071.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/874e48f71e00/pone.0312071.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/7d3ed9912dd1/pone.0312071.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/7ca3084b6443/pone.0312071.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/0a8b098db2b6/pone.0312071.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/8ec3a55263f4/pone.0312071.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/d54819a3896f/pone.0312071.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/01e504c31a8d/pone.0312071.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95f9/11508054/874e48f71e00/pone.0312071.g007.jpg

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