Identification of M1 macrophage-related genes in rejection after kidney transplantation based on weighted gene co-expression network analysis
10.3969/j.issn.1674-7445.2023.01.011
- VernacularTitle:基于加权基因共表达网络鉴定肾移植术后排斥反应中巨噬细胞M1亚型相关基因
- Author:
Boqing DONG
1
;
Yang LI
;
Yuting SHI
;
Jing ZHANG
;
Xinshun FENG
;
Jin ZHENG
;
Xiao LI
;
Xiaoming DING
;
Wujun XUE
Author Information
1. Department of Kidney Transplantation, the First Affiliated Hospital of Xi'an Jiaotong University, Institute of Organ Transplantation of Xi'an Jiaotong University, Xi'an 710061, China
- Publication Type:Research Article
- Keywords:
Kidney transplantation;
Rejection;
Renal graft loss;
Macrophages;
M1 subtype;
Weighted gene co-expression network analysis;
Differentially expressed gene;
Immunoreaction;
MicroRNA
- From:
Organ Transplantation
2023;14(1):83-
- CountryChina
- Language:Chinese
-
Abstract:
Objective To identify M1 macrophage-related genes in rejection after kidney transplantation and construct a risk prediction model for renal allograft survival. Methods GSE36059 and GSE21374 datasets after kidney transplantation were downloaded from Gene Expression Omnibus (GEO) database. GSE36059 dataset included the samples from the recipients with rejection and stable allografts. Using this dataset, weighted gene co-expression network analysis (WGCNA) and differential analysis were conducted to screen the M1 macrophage-related differentially expressed gene (M1-DEG). Then, GSE21374 dataset (including the follow-up data of graft loss) was divided into the training set and validation set according to a ratio of 7∶3. In the training set, a multivariate Cox's model was constructed using the variables screened by least absolute shrinkage and selection operator (LASSO), and the ability of this model to predict allograft survival was evaluated. CIBERSORT was employed to analyze the differences of infiltrated immune cells between the high-risk group and low-risk group, and the distribution of human leukocyte antigen (HLA)-related genes was analyzed between two groups. Gene set enrichment analysis (GSEA) was used to further clarify the biological process and pathway enrichment in the high-risk group. Finally, the database was employed to predict the microRNA (miRNA) interacting with the prognostic genes. Results In the GSE36059 dataset, 14 M1-DEG were screened. In the GSE21374 dataset, Toll-like receptor 8 (TLR8), Fc gamma receptor 1B (FCGR1B), BCL2 related protein A1 (BCL2A1), cathepsin S (CTSS), guanylate binding protein 2(GBP2) and caspase recruitment domain family member 16 (CARD16) were screened by LASSO-Cox regression analysis, and a multivariate Cox's model was constructed based on these 6 M1-DEG. The area under curve (AUC) of receiver operating characteristic of this model for predicting the 1- and 3-year graft survival was 0.918 and 0.877 in the training set, and 0.765 and 0.736 in the validation set, respectively. Immune cell infiltration analysis showed that the infiltration of rest and activated CD4+ memory T cells, γδT cells and M1 macrophages were increased in the high-risk group (all P < 0.05). The expression level of HLA I gene was up-regulated in the high-risk group. GSEA analysis suggested that immune response and graft rejection were enriched in the high-risk group. CTSS interacted with 8 miRNA, BCL2A1 and GBP2 interacted with 3 miRNA, and FCGR1B interacted with 1 miRNA. Conclusions The prognostic risk model based on 6 M1-DEG has high performance in predicting graft survival, which may provide evidence for early interventions for high-risk recipients.
