Single-cell sequencing reveals the underlying mechanism of antibody-mediated rejection in renal transplant recipients

doi:10.12092/j.issn.1009-2501.2026.03.001

Abstract

Abstract:

AIM: Based on single-cell sequencing analysis, the underlying mechanism of antibody-mediated rejection (ABMR) in kidney transplant recipients. METHODS: Recipients with 6 months or more after kidney transplantation were selected as research subjects, and high-resolution scRNA-seq analysis of immune cell subsets in peripheral blood mononuclear cells (PBMC) was performed using single-cell RNA sequencing (scRNA-seq) technology. Flow cytometry was used to examine the effect of differential genes on renal transplant ABMR in different immune cell populations. RESULTS: This study analyzed differential gene expression between ABMR patients and healthy controls using single-cell sequencing technology, identifying CD69, CD83, CD52, CD74, and CX3CR1 as key differentially expressed genes. In classical monocytes, ABMR patients exhibited increased CD83 and CD52 gene expression levels compared to the control group, which showed a downward trend after treatment. Regarding initial CD4⁺T cells, ABMR patients demonstrated significantly reduced CD69 gene expression. In NK cells, ABMR patients displayed decreased CX3CR1 gene expression initially, with further reduction in its geometric mean value post-treatment. Conversely, the geometric mean value of CD74 showed an increasing trend. CONCLUSION: In classical mononuclear cells, upregulated expression of CD83 and CD52 genes correlates with enhanced antigen-presenting cell functionality, thereby promoting the development of antigen-bonded microenvironment remodeling (ABMR). In initial CD4⁺T cells, elevated CD69 gene expression is associated with T cell activation and proliferation, further contributing to ABMR progression. Conversely, downregulated CX3CR1 gene expression in NK cells relates to impaired immune surveillance mechanisms, which partially inhibits ABMR formation.

Key words: tacrolimus, kidney transplantation, rejection, differential gene, PBMC

CLC Number:

Kaile ZHENG, Jiazhao FU, Jia YOU, Dan WU, Xuebin WANG, Zhuo WANG. Single-cell sequencing reveals the underlying mechanism of antibody-mediated rejection in renal transplant recipients[J]. Chinese Journal of Clinical Pharmacology and Therapeutics, 2026, 31(3): 289-299.

Figures/Tables 12

References 30

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Cell type	Marker genes
T cell	CD3E, CD3D, CD3G
B cell	CD79B, CD19, CD79A
Fibroblast	COL1A1, COL1A2, COL3A1, POSTN
Epithelial cell	EPCAM, CDH1, KRT18, KRT8
Neutrophil	Ly6g, Ncf1, Csf3r, Cd177, Sorl1
Macrophage	CD14, CD68, CD163, CD209, AIF1
Dendritic cell	Flt3, CD1C
Natural killer cell	Nkg7, Ifng, Klrd1, Klrc1, CD56
Endothelial cell	VWF, CDH5, Pecam1
Basophil	TPSB2, TPSAB1, TPSAB2, CPA3
Plasma cell	CD27, CD38, XBP1, JCHAIN
Monocyte	CD14, CD300E, CD244
CD8⁺NKT-like cell	CD3E, CD8A, CD161, KLRC1
Classical monocyte	CD14, LYZ
Na?ve B cell	CD19, CD20, CD79A, IGLL1
Na?ve CD4⁺T cell	CD3E, CD4, CD45RA, LEF1
Na?ve CD8⁺T cell	CD3E, CD8A, CD45RA, LEF1
Non-classical monocyte	CD14, CD16, FCGR3A
Plasmacytoid dendritic cell	CD123, CD303, IRF7, LY6E
Platelet	CD41, CD61, PF4, GPIBα
Pro-B cell	CD19, CD34, CD79A, IGLL1, RAG1

Cell type	Marker genes
T cell	CD3E, CD3D, CD3G
B cell	CD79B, CD19, CD79A
Fibroblast	COL1A1, COL1A2, COL3A1, POSTN
Epithelial cell	EPCAM, CDH1, KRT18, KRT8
Neutrophil	Ly6g, Ncf1, Csf3r, Cd177, Sorl1
Macrophage	CD14, CD68, CD163, CD209, AIF1
Dendritic cell	Flt3, CD1C
Natural killer cell	Nkg7, Ifng, Klrd1, Klrc1, CD56
Endothelial cell	VWF, CDH5, Pecam1
Basophil	TPSB2, TPSAB1, TPSAB2, CPA3
Plasma cell	CD27, CD38, XBP1, JCHAIN
Monocyte	CD14, CD300E, CD244
CD8⁺NKT-like cell	CD3E, CD8A, CD161, KLRC1
Classical monocyte	CD14, LYZ
Na?ve B cell	CD19, CD20, CD79A, IGLL1
Na?ve CD4⁺T cell	CD3E, CD4, CD45RA, LEF1
Na?ve CD8⁺T cell	CD3E, CD8A, CD45RA, LEF1
Non-classical monocyte	CD14, CD16, FCGR3A
Plasmacytoid dendritic cell	CD123, CD303, IRF7, LY6E
Platelet	CD41, CD61, PF4, GPIBα
Pro-B cell	CD19, CD34, CD79A, IGLL1, RAG1

Variable	Recipient 1	Recipient 2	Recipient 3	Recipient 4
Gender	Male	Female	Male	Male
Age	15	48	54	51
Weight (kg)	41	58.1	68.5	85
Clinical diagnosis	AR	ABMR	IgAN	Normal
Organ transplantation	DCD	DCD	DCD	DCD
Immune induction	ATG	basiliximab	ATG	ATG
Immunosuppressant	TAC+MPA	TAC+MPA+Pred	TAC+MPA+Pred	TAC+MPA+Pred
Tacrolimus C₀ (ng/mL)	4.5	11.1	2.1	7.9
Treatment adjustment	Rituximab	Bortezomib	No adjustment	No adjustment
Serum creatinine (μmoI/L)	144	172	680	89
Uric acid (μmol/L)	593	345	303	498
Urea (mmol/L)	15.9	16.1	14.7	4.7
Albumin/globulin	139	1.18	1.19	1.54
Clinical manifestation	Normal body temperature, stable blood pressure	Normal body temperature, stable blood pressure	Normal body temperature, stable blood pressure	Normal body temperature, stable blood pressure

Variable	Recipient 1	Recipient 2	Recipient 3	Recipient 4
Gender	Male	Female	Male	Male
Age	15	48	54	51
Weight (kg)	41	58.1	68.5	85
Clinical diagnosis	AR	ABMR	IgAN	Normal
Organ transplantation	DCD	DCD	DCD	DCD
Immune induction	ATG	basiliximab	ATG	ATG
Immunosuppressant	TAC+MPA	TAC+MPA+Pred	TAC+MPA+Pred	TAC+MPA+Pred
Tacrolimus C₀ (ng/mL)	4.5	11.1	2.1	7.9
Treatment adjustment	Rituximab	Bortezomib	No adjustment	No adjustment
Serum creatinine (μmoI/L)	144	172	680	89
Uric acid (μmol/L)	593	345	303	498
Urea (mmol/L)	15.9	16.1	14.7	4.7
Albumin/globulin	139	1.18	1.19	1.54
Clinical manifestation	Normal body temperature, stable blood pressure	Normal body temperature, stable blood pressure	Normal body temperature, stable blood pressure	Normal body temperature, stable blood pressure

Renal transplant recipient samples	CD83 (PC7-A)	CD52 (APC)
ABMR_pre (03-L1-F1-1)	12173.0	5753.7
ABMR_post (06-L H 17-C1)	7377.2	3130.1
Normal (04-W1-F1)	10419.7	6564.7