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肾移植纤维化中不同的程序性细胞死亡模式和免疫特征:基于机器学习、单核RNA测序和分子对接对肾移植失败的预测

Diverse regulated cell death patterns and immune traits in kidney allograft with fibrosis: a prediction of renal allograft failure based on machine learning, single-nucleus RNA sequencing and molecular docking.

作者信息

Li Yuqing, Zhang Jiandong, Qiu Xuemeng, Zhang Yifei, Wu Jiyue, Bi Qing, Sun Zejia, Wang Wei

机构信息

Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.

Institute of Urology, Capital Medical University, Beijing, China.

出版信息

Ren Fail. 2024 Dec;46(2):2435487. doi: 10.1080/0886022X.2024.2435487. Epub 2024 Dec 4.

Abstract

Post-transplant allograft fibrosis remains a challenge in prolonging allograft survival. Regulated cell death has been widely implicated in various kidney diseases, including renal fibrosis. However, the role of different regulated cell death (RCD) pathways in post-transplant allograft fibrosis remains unclear. Microarray transcriptome profiling and single-nuclei sequencing data of post-transplant fibrotic and normal grafts were obtained and used to identify RCD-related differentially expressed genes. The enrichment activity of nine RCD modalities in tissue and cells was examined using single-sample gene set enrichment analysis, and their relations with immune infiltration in renal allograft samples were also assessed. Parenchymal and non-parenchymal cells displayed heterogeneity in RCD activation. Additionally, cell-cell communication analysis was also conducted in fibrotic samples. Subsequently, weighted gene co-expression network analysis and seven machine learning algorithms were employed to identify RCD-related hub genes for renal fibrosis. A 9-gene signature, termed RCD risk score (RCDI), was constructed using the least absolute shrinkage and selection operator and multivariate Cox regression algorithms. This signature showed robust accuracy in predicting 1-, 2-, and 3-year allograft survival status (area under the curve for 1-, 2-, and 3-year were 0.900, 0.877, 0.858, respectively). Immune infiltration analysis showed a strong correlation with RCDI and the nine model genes. Finally, molecular docking simulation suggested rapamycin, tacrolimus and mycophenolate mofetil exhibit strong interactions with core RCD-related receptors. In summary, this study explored the activation of nine RCD pathways and their relationships with immune traits, identified potential RCD-related hub genes associated with renal fibrosis, and highlighted potential therapeutic targets for renal allograft fibrosis.

摘要

移植后同种异体移植物纤维化仍然是延长移植物存活时间的一大挑战。程序性细胞死亡与包括肾纤维化在内的各种肾脏疾病密切相关。然而,不同的程序性细胞死亡(RCD)途径在移植后同种异体移植物纤维化中的作用仍不清楚。获取了移植后纤维化和正常移植物的微阵列转录组分析和单核测序数据,并用于鉴定RCD相关的差异表达基因。使用单样本基因集富集分析检查了9种RCD模式在组织和细胞中的富集活性,并评估了它们与肾移植样本中免疫浸润的关系。实质细胞和非实质细胞在RCD激活方面表现出异质性。此外,还对纤维化样本进行了细胞间通讯分析。随后,采用加权基因共表达网络分析和七种机器学习算法来识别肾纤维化的RCD相关枢纽基因。使用最小绝对收缩和选择算子以及多变量Cox回归算法构建了一个名为RCD风险评分(RCDI)的9基因特征。该特征在预测1年、2年和3年移植物存活状态方面表现出强大的准确性(1年、2年和3年的曲线下面积分别为0.900、0.877、0.858)。免疫浸润分析显示与RCDI和九个模型基因有很强的相关性。最后,分子对接模拟表明雷帕霉素、他克莫司和霉酚酸酯与核心RCD相关受体表现出强烈的相互作用。总之,本研究探讨了9种RCD途径的激活及其与免疫特征的关系,确定了与肾纤维化相关的潜在RCD相关枢纽基因,并突出了肾移植纤维化的潜在治疗靶点。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f777/11619039/d1e04cc24a3b/IRNF_A_2435487_F0001_C.jpg

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