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整合多组学分析和机器学习识别出用于软组织肉瘤诊断及临床获益的G蛋白偶联受体相关特征。

Integrated multi-omics analysis and machine learning identify G protein-coupled receptor-related signatures for diagnosis and clinical benefits in soft tissue sarcoma.

作者信息

Wang Duo, Tu Jihao, Liu Jianfeng, Piao Yuting, Zhao Yiming, Xiong Ying, Wang Jianing, Zheng Xiaotian, Liu Bin

机构信息

Department of Hand and Foot Surgery, Orthopedics Center, The First Hospital of Jilin University, Jilin University, Changchun, China.

Engineering Laboratory of Tissue Engineering Biomaterials of Jilin Province, Jilin University, Changchun, China.

出版信息

Front Immunol. 2025 Jul 21;16:1561227. doi: 10.3389/fimmu.2025.1561227. eCollection 2025.


DOI:10.3389/fimmu.2025.1561227
PMID:40761790
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12318986/
Abstract

BACKGROUND: G protein-coupled receptors (GPRs) are associated with tumor development and prognosis. However, there were fewer reports of GPR-related signatures (GPRSs) in soft tissue sarcomas (STSs), and we aim to combine GPR-related genes with cellular landscape to construct diagnostic and prognostic models in STSs. METHODS: Based on AddModuleScore, single-sample gene set enrichment analysis (ssGSEA), differentially expressed genes (DEGs), and weighted gene co-expression network analysis (WGCNA), GPR-related genes (GPRs) were screened at both the single-cell and bulk RNA-seq levels based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We developed a novel machine learning framework that incorporated 12 machine learning algorithms and their 127 combinations to construct a consensus GPRS to screen biomarkers with diagnostic significance and clinical translation, which was assessed by the internal and external validation datasets. Moreover, the GPR-TME classifier as the prognosis model was constructed and further performed for immune infiltration, functional enrichment, somatic mutation, immunotherapy response prediction, and scRNA-seq analyses. RESULTS: We identified 151 GPR-related genes at both the single-cell and bulk transcriptome levels, and identified a Stepglm[both]+Enet[alpha=0.6] model with seven GPR-related genes as the final diagnostic predictive model with high accuracy and translational relevance using a 127-combination machine learning computational framework, and the GPR-integrated diagnosis nomogram provided a quantitative tool in clinical practice. Moreover, we identified seven prognosis GPRs and five prognosis-good immune cells constructing the GPR score and TME score, respectively. The findings indicate that high expression of GPRs is associated with a poor prognosis in patients with STS, highlighting the significant role of GPRs and the tumor microenvironment (TME) in STS development. Building up a GPR-TME classifier, low GPR combined with high TME exhibited the most favorable prognosis and immunotherapeutic efficacy, which was further performed for immune infiltration, functional enrichment, somatic mutation, immunotherapy response prediction, and scRNA-seq analyses. CONCLUSIONS: Our study constructed a GPRS that can serve as a promising tool for diagnosis and prognosis prediction, targeted prevention, and personalized medicine in STS.

摘要

背景:G蛋白偶联受体(GPRs)与肿瘤的发生发展及预后相关。然而,关于软组织肉瘤(STSs)中GPR相关特征(GPRSs)的报道较少,我们旨在将GPR相关基因与细胞图谱相结合,构建STSs的诊断和预后模型。 方法:基于AddModuleScore、单样本基因集富集分析(ssGSEA)、差异表达基因(DEGs)和加权基因共表达网络分析(WGCNA),在单细胞和批量RNA测序水平上,基于癌症基因组图谱(TCGA)和基因表达综合数据库(GEO)筛选GPR相关基因(GPRs)。我们开发了一种新颖的机器学习框架,该框架整合了12种机器学习算法及其127种组合,以构建一个共识GPRS,用于筛选具有诊断意义和临床转化价值的生物标志物,并通过内部和外部验证数据集进行评估。此外,构建了GPR-TME分类器作为预后模型,并进一步进行免疫浸润、功能富集、体细胞突变、免疫治疗反应预测和单细胞RNA测序分析。 结果:我们在单细胞和批量转录组水平上鉴定了151个GPR相关基因,并使用127种组合的机器学习计算框架,确定了一个包含7个GPR相关基因的Stepglm[both]+Enet[alpha=0.6]模型作为最终诊断预测模型,该模型具有较高的准确性和转化相关性,并且GPR综合诊断列线图为临床实践提供了一种定量工具。此外,我们鉴定了7个预后GPR和5个预后良好的免疫细胞,分别构建了GPR评分和TME评分。研究结果表明,GPRs的高表达与STSs患者的不良预后相关,突出了GPRs和肿瘤微环境(TME)在STSs发生发展中的重要作用。构建GPR-TME分类器,低GPR与高TME结合显示出最有利的预后和免疫治疗效果,并进一步进行免疫浸润、功能富集、体细胞突变、免疫治疗反应预测和单细胞RNA测序分析。 结论:我们的研究构建了一种GPRS,可作为STSs诊断、预后预测、靶向预防和个性化医疗的有前景的工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/33d453327599/fimmu-16-1561227-g012.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/e14ab858de18/fimmu-16-1561227-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/95818249ca04/fimmu-16-1561227-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/914bd20e10ce/fimmu-16-1561227-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/5ad88cc91dfe/fimmu-16-1561227-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/22f1c73ad462/fimmu-16-1561227-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/fc8a2b5ba70f/fimmu-16-1561227-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/16bd8e847cae/fimmu-16-1561227-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/33d453327599/fimmu-16-1561227-g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/1da636b6221f/fimmu-16-1561227-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/bdb278b1aa4d/fimmu-16-1561227-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/55b9f3dce9ce/fimmu-16-1561227-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/e3041ddb7601/fimmu-16-1561227-g004.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/95818249ca04/fimmu-16-1561227-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/914bd20e10ce/fimmu-16-1561227-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/5ad88cc91dfe/fimmu-16-1561227-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/22f1c73ad462/fimmu-16-1561227-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/fc8a2b5ba70f/fimmu-16-1561227-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/16bd8e847cae/fimmu-16-1561227-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3209/12318986/33d453327599/fimmu-16-1561227-g012.jpg

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Combined signature of G protein-coupled receptors and tumor microenvironment provides a prognostic and therapeutic biomarker for skin cutaneous melanoma.

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