Analysis of specificity of expressed transcripts according to clinical results after kidney transplantation

Abstract

Background: After kidney transplantation, approximately 30% of patients develop BK viremia and 7% develop BK nephropathy. We performed transcriptome-based clustering at the single-cell level to identify these patients to be effective in monitoring and treating allograft dysfunction after transplantation. Methods: Single-cell libraries were generated using the 10× Genomics Chromium Platform from peripheral blood mononuclear cells from each of one posttransplant stable patient, two patients with BK viremia, and three patients with BK virus-associated nephropathy (BKVAN). We analyzed multiplexing data in Cell-Ranger pipeline and used R and "Seurat" packages for downstream analysis. Results: A total of 5,811 differentially expressed genes (DEGs) in 17 cell clusters were identified using 5,473 stable cells, 9,068 BK viremia cells, and 17,238 BKVAN cells for analysis. In the BK virus infection group, CENPF, MKI67, TOP2A, UBE2C, and HIST1H1B were overexpressed in gamma-delta T cells (logarithm two of fold change [log 2 FC] difference, 8.2-63.8), and TSC22D1, C2orf88, RGS18, and ACRBP in platelets than in the stable group (log 2 FC difference, 3.5-153). Among them, CENPF, MKI67, and TOP2A were more expressed in gamma-delta T cells of BKVAN group than in BK viremia group (log 2 FC difference, 53.5-56.5), whereas PF4, PPBP, and GNG11 in platelets were more overexpressed in BK viremia group than in the BKVAN group (log 2 FC difference, 27.6-70.9). In the stable group, LGALS3, CTSD, CD68, CST3, and GRN were overexpressed in FCGR3A monocytes (log 2 FC difference, 12.0-244.7) and TVP23A in CD16 monocytes (log 2 FC difference, 14.1 or more) than in the BK infection group. Conclusions: In patients with reactivated BK virus, the relationship to specific genomes can determine progression to nephropathy. In the case of gamma-delta T cells, the expression level was very low, so the difference in expression of each sample could be confirmed through single-cell RNA analysis. The developed marker is expected to enable more careful management of patients after kidney transplantation.