Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection to Infer Contact-dependent Immune Cell Transcription.
Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection to Infer Contact-dependent Immune Cell Transcription.
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DOI：
10.1097/tp.0000000000004762
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发表时间：
2024-02-01
期刊：
影响因子：
6.2
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中科院分区：
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排斥反应需要涉及免疫细胞的细胞-细胞接触。从单细胞RNA测序（scRNA-seq）数据推断细胞-细胞相互作用的转录程序是具有挑战性的，因为空间信息丢失。我们将CD 45 pos富集策略与通过基于测序的白细胞表面蛋白定量的转录组和表位的细胞索引相结合，以分析11例人肾移植活检中的细胞-细胞相互作用，包括一系列排斥诊断。使用10 X Genomics平台进行scRNA-seq。我们应用测序物理相互作用细胞计算方法去卷积异型物理相互作用细胞的转录谱。11例同种异体移植物活检产生了31203个高质量的单细胞文库。通过结合转录组和表位的细胞索引，通过来自6种不同白细胞特异性表面蛋白的测序数据进一步细化聚类。6个双联体簇中的3个被鉴定为物理相互作用的细胞复合物;巨噬细胞或树突细胞与B细胞或浆细胞结合;自然杀伤（NK）或T细胞与巨噬细胞或树突细胞结合，以及NK或T细胞与内皮细胞结合。骨髓淋巴细胞物理相互作用细胞复合物表达激活和促炎基因。与内皮细胞物理相互作用的淋巴细胞富集NK和CD 4 T细胞。NK细胞-内皮细胞接触导致内皮促炎基因CXCL 9和CXCL 10以及NK细胞促炎基因CCL 3、CCL 4和GNLY的表达增加。来自人肾移植活检的物理相互作用细胞的转录谱可以使用测序物理相互作用细胞方法从scRNA-seq数据推断。这种方法补充了先前从scRNA-seq数据估计细胞-细胞物理接触的方法。
Rejection requires cell–cell contact involving immune cells. Inferring the transcriptional programs of cell–cell interactions from single-cell RNA-sequencing (scRNA-seq) data is challenging as spatial information is lost. We combined a CD45pos enrichment strategy with Cellular Indexing of Transcriptomes and Epitopes by sequencing based quantification of leukocyte surface proteins to analyze cell–cell interactions in 11 human kidney transplant biopsies encompassing a spectrum of rejection diagnoses. scRNA-seq was performed using the 10X Genomics platform. We applied the sequencing physically interacting cells computational method to deconvolute the transcriptional profiles of heterotypic physically interacting cells. The 11 human allograft biopsies generated 31 203 high-quality single-cell libraries. Clustering was further refined by combining Cellular Indexing of Transcriptomes and Epitopes by sequencing data from 6 different leukocyte-specific surface proteins. Three of 6 doublet clusters were identified as physically interacting cell complexes; macrophages or dendritic cells bound to B cells or plasma cells; natural killer (NK) or T cells bound to macrophages or dendritic cells and NK or T cells bound to endothelial cells. Myeloid-lymphocyte physically interacting cell complexes expressed activated and proinflammatory genes. Lymphocytes physically interacting with endothelial cells were enriched for NK and CD4 T cells. NK cell–endothelial cell contact caused increased expression of endothelial proinflammatory genes CXCL9 and CXCL10 and NK cell proinflammatory genes CCL3, CCL4, and GNLY. The transcriptional profiles of physically interacting cells from human kidney transplant biopsies can be inferred from scRNA-seq data using the sequencing physically interacting cells method. This approach complements previous methods that estimate cell–cell physical contact from scRNA-seq data.