Single-cell analysis reveals immune landscape in kidneys of patients with chronic transplant rejection
Single-cell analysis reveals immune landscape in kidneys of patients with chronic transplant rejection
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DOI：
10.7150/thno.48201
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发表时间：
2020-01-01
期刊：
影响因子：
12.4
通讯作者：
Zhao, Ming
中科院分区：
文献类型：
--
作者：
Liu, Yongguang;Hu, Jianmin;Zhao, Ming
基本原理：单细胞RNA测序（scRNA-seq）提供了在单细胞水平上对细胞群体的特异性分析的无偏评估。传统的肾活检和批量RNA-seq只能平均出潜在的差异，而慢性肾移植排斥反应（CKTR）的程度以及它如何被肾脏中的细胞和状态塑造仍然很差。在这里，我们分析了细胞从CKTR和匹配的健康成人肾脏在单细胞resolution.Methods：高品质的转录组产生的三个健康人的肾脏和两个CKTR活检。对活检标本进行无监督聚类分析，以鉴定15种不同的细胞类型，包括主要的免疫细胞、肾细胞和少数类型的基质细胞。结果：自然杀伤T（NKT）细胞可分为5个亚类，分别代表CD 4（+）T细胞、CD 8（+）T细胞、细胞毒性T淋巴细胞（CTL）、调节性T细胞（TcR）和自然杀伤细胞（NK）。记忆B细胞分为两个亚型，代表反向免疫激活。单核细胞形成经典的CD 14（+）组和非经典的CD 16（+）组。我们在成纤维细胞中发现了一个新的亚群[肌成纤维细胞（MyoF）]，它表达胶原蛋白和细胞外基质成分。CKTR组的特点是增加数量的免疫细胞和MyoF，导致增加肾排斥反应和fibrosis.Conclusions：通过评估在单细胞分辨率亚型的功能差异，我们发现不同的亚型，与不同的功能在CKTR。该资源提供了对CKTR生物学的更深入了解，这将有助于CKTR的诊断和治疗。
Rationale: Single-cell RNA sequencing (scRNA-seq) has provided an unbiased assessment of specific profiling of cell populations at the single-cell level. Conventional renal biopsy and bulk RNA-seq only average out the underlying differences, while the extent of chronic kidney transplant rejection (CKTR) and how it is shaped by cells and states in the kidney remain poorly characterized. Here, we analyzed cells from CKTR and matched healthy adult kidneys at single-cell resolution.Methods: High-quality transcriptomes were generated from three healthy human kidneys and two CKTR biopsies. Unsupervised clustering analysis of biopsy specimens was performed to identify fifteen distinct cell types, including major immune cells, renal cells and a few types of stromal cells. Single-sample gene set enrichment (ssGSEA) algorithm was utilized to explore functional differences between cell subpopulations and between CKTR and normal cells.Results: Natural killer T (NKT) cells formed five subclasses, representing CD4(+) T cells, CD8(+) T cells, cytotoxic T lymphocytes (CTLs), regulatory T cells (Tregs) and natural killer cells (NKs). Memory B cells were classified into two subtypes, representing reverse immune activation. Monocytes formed a classic CD14(+) group and a nonclassical CD16(+) group. We identified a novel subpopulation [myofibroblasts (MyoF)] in fibroblasts, which express collagen and extracellular matrix components. The CKTR group was characterized by increased numbers of immune cells and MyoF, leading to increased renal rejection and fibrosis.Conclusions: By assessing functional differences of subtype at single-cell resolution, we discovered different subtypes that correlated with distinct functions in CKTR. This resource provides deeper insights into CKTR biology that will be helpful in the diagnosis and treatment of CKTR.