Integrated analysis of cell-specific gene expression in peripheral blood using ISG15 as a marker of rejection in kidney transplantation.
Integrated analysis of cell-specific gene expression in peripheral blood using ISG15 as a marker of rejection in kidney transplantation.
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DOI：
10.3389/fimmu.2023.1153940
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发表时间：
2023
影响因子：
7.3
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中科院分区：
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移植肾排斥反应可导致移植物功能障碍和移植物丢失。常规活检给肾功能正常的受者带来了额外的风险。外周血单个核细胞(PBMCs)转录组蕴含着丰富的信息，在非侵入性诊断中具有潜在的应用价值。从基因表达总览数据库中，我们收集了三个数据集，包含109个拒绝样本和215个正常对照。经过数据过滤和归一化后，我们对大量的RNA测序数据进行去卷积，以预测细胞类型和细胞类型特异性基因的表达。随后，我们用张量-细胞2cell计算细胞通讯分析，并进行最小绝对收缩和选择算子(LASSO)Logistic回归，筛选出稳健的差异表达基因(Deg)。这些基因的表达水平在小鼠肾移植急性排斥模型中得到了验证。通过基因敲除和淋巴细胞刺激实验进一步证实了新基因ISG15在单核细胞中的功能。大量的RNA-seq很难准确预测肾移植排斥反应。从基因表达数据中预测了七种免疫细胞和转录特征。单核细胞在排斥反应的数量和基因表达上存在显著差异。细胞间通讯显示抗原提呈和T细胞激活配体-受体对的丰富。通过Lasso回归分析发现了10个新基因，其中一个新基因ISG15在公共数据和动物模型中均在排斥样本和正常对照的单核细胞中保持差异表达。此外，ISG15还显示出促进T细胞增殖的关键作用。本研究发现并验证了一个与肾移植后外周血排斥反应相关的新基因ISG15，这是一个重要的非侵入性诊断和潜在的治疗靶点。
Allograft kidney rejection can lead to graft dysfunction and graft loss. Protocol biopsy poses additional risk for recipients with normal renal function. The transcriptome of peripheral blood mononuclear cells (PBMCs) contains tremendous information and has potential application value for non-invasive diagnosis. From the Gene Expression Omnibus database, we collected three datasets containing 109 rejected samples and 215 normal controls. After data filter and normalization, we performed deconvolution of bulk RNA sequencing data to predict cell type and cell-type specific gene expression. Subsequently, we calculated cell communication analysis by Tensor-cell2cell and conducted the least absolute shrinkage and selection operator (LASSO) logistic regression to screen the robust differentially expressed genes (DEGs). These gene expression levels were validated in mice kidney transplantation acute rejection model. The function of the novel gene ISG15 in monocytes was further confirmed by gene knockdown and lymphocyte-stimulated assay. The bulk RNA-seq hardly predicted kidney transplant rejection accurately. Seven types of immune cells and transcriptomic characteristics were predicted from the gene expression data. The monocytes showed significant differences in amount and gene expression of rejection. The cell-to-cell communication indicated the enrichment of antigen presentation and T cell activation ligand-receptor pairs. Then 10 robust genes were found by Lasso regression and a novel gene ISG15 remained differential expression in monocytes between rejection samples and normal control both in public data and animal model. Furthermore, ISG15 also showed a critical role in promoting the proliferation of T cells. This study identified and validated a novel gene ISG15 associated with rejection in peripheral blood after kidney transplantation, which is a significant non-invasive diagnosis and a potential therapeutic target.