Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection

Abstract

Myeloid cells are increasingly recognized as major players in transplant rejection. Here, we used a murine kidney transplantation model and single cell transcriptomics to dissect the contribution of myeloid cell subsets and their potential signaling pathways to kidney transplant rejection. Using a variety of bioinformatic techniques, including machine learning, we demonstrate that kidney allograft–infiltrating myeloid cells followed a trajectory of differentiation from monocytes to proinflammatory macrophages, and they exhibited distinct interactions with kidney allograft parenchymal cells. While this process correlated with a unique pattern of myeloid cell transcripts, a top gene identified was Axl , a member of the receptor tyrosine kinase family Tyro3/Axl/Mertk (TAM). Using kidney transplant recipients with Axl gene deficiency, we further demonstrate that Axl augmented intragraft differentiation of proinflammatory macrophages, likely via its effect on the transcription factor Cebpb. This, in turn, promoted intragraft recruitment, differentiation, and proliferation of donor-specific T cells, and it enhanced early allograft inflammation evidenced by histology. We conclude that myeloid cell Axl expression identified by single cell transcriptomics of kidney allografts in our study plays a major role in promoting intragraft myeloid cell and T cell differentiation, and it presents a potentially novel therapeutic target for controlling kidney allograft rejection and improving kidney allograft survival.

Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice

“…So far, only limited information on the use of scRNA-seq in murine kidney transplantation has been published. Anil Dangi et al reported whole transcriptomics of mouse kidney transplants on day 15 in a single cell level and identified 13 immune cell clusters (13). In the present study, we developed further in-depth analysis of these immune cell types with comprehensive classification and description of cell subtypes including their specific marker genes, functional characteristics, transcriptional regulation, and the proportional dynamics from the renal allograft rejection peak on D7 to the regression phase on D15.…”

“…Similarly 452 cells expressing markers of both T cells and macrophages/neutrophils were filtered as doublets. Next, 4,254 and 2,871 CD45 + leukocytes passing criteria of quality control were extracted from GSM4761000 and GSM4761003, respectively (Supplementary Figures 2, 3A-C) (13). Then, Seurat was used for integrating D7 and D15 data, and unsupervised clustering (14).…”

“…Ly6c lo Mrc1 + macrophages (cluster 1, 16) and IFNIC (cluster 2) specifically expressed ligand Axl and interacted with other cells through Axl-Il15ra, Axl-Pros1 pairs (Figures 12A, C, F, Supplementary Figure 11C). It was reported that Axl augmented intragraft differentiation of certain types of proinflammatory macrophages and enhanced early allograft inflammation (13).…”

Detailed Molecular Mechanism and Potential Drugs for COL1A1 in Carboplatin-Resistant Ovarian Cancer

“…We used the R package edgeR ( 12 ) to normalize and analyze significantly differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) between the carboplatin-resistant OV group (n = 14) and the carboplatin-nonresistant OV group (n = 84). According to the previous study ( 13 ), we wanted to obtain more candidates. So, the cutoff values were |log2 fold change| ≥ 0.4 and p < 0.05.…”

Macrophage Heterogeneity in Kidney Injury and Fibrosis

“…By evaluating the typical C1qa , Cd74 , and Adgre1 expression, macrophages are defined as the predominant immune cells in diabetic glomeruli and mainly M1-like macrophages ( 90 ). The scRNA-seq analysis revealed that both extent and levels of Axl expression increased in F4/80 + macrophages from rejecting allografts compared to tolerized kidneys; and Axl promotes the differentiation of intra-graft myeloid cells towards pro-inflammatory phenotypes after transplantation ( 82 ). Moreover, the combination of scRNA-seq and lineage tracing technique attracts particular attention.…”