Kidney transplantation is an ideal treatment modality for patients with ESKD [1], and patients who undergo kidney transplantation have a better quality of life and significant survival advantages [3]. However, the occurrence of allograft rejection after kidney transplantation significantly reduces the success rate of kidney transplantation [6]. Antibody- or cell-mediated immune rejection leading to allograft loss is one of the main reasons for the low success rate of kidney transplantation [13, 14]. Accurate detection of rejection and nonrejection in the immune infiltrate landscape becomes extremely important for the treatment of rejection after kidney transplantation.
The CIBERSORT algorithm was used to calculate the infiltration of 22 known immune cell subtypes in the GSE21374 sample. After removing samples with CIBERSORT P < 0.05, a total of 218 samples, including 73 rejection and 145 nonrejection samples in the GSE21374 dataset, were reserved for CIBERSORT analysis. The proportions of most immune cells were shown to correlate with other immune cells by correlation analysis. CIBERSORT analysis revealed that the proportions and numbers of memory B cells, plasma cells, and resting mast cells were downregulated, but the proportions and numbers of follicular helper T cells, CD8 T cells, M1 macrophages, memory CD4 T cells, and gamma delta T cells were upregulated in the rejection samples compared to the nonrejection samples. Previous studies have shown that resting mast cells are increased in nonrejected kidneys compared to rejected kidneys [28] and that under "resting" conditions, mast cells can maintain tissue homeostasis [29]. Mast cells can produce large amounts of cytokines that can affect the activation and development of T and B cells [30, 31]. It was shown that the levels of M1 macrophages, T cells, CD8 T cells and gamma delta T cells were significantly increased in rejected kidneys compared to nonrejected kidneys [28]. Consistent with our findings, it has been shown that an increase in M1-type macrophages predominates in the rejection of transplanted kidneys [32]. After kidney transplantation, CD8 T cells play an important role in the process of allograft rejection by invading allograft tissues and activating other types of immune cells, and the phenotypic and molecular characteristics of CD8 T cells correlate significantly with the development of the T-cell-mediated immune rejection response (TCMR) [33]. gamma delta T cells are a subset of T cells; although the role of gamma delta T cells in transplanted kidneys remains controversial [34], gamma delta T cells have also been reported to perform multiple effector functions [35].
This study is based on WGCNA. A total of 270 genes were identified as infiltrating immune cell-related genes, and these genes were mainly involved in immune-related functions. They were analyzed by GO annotation and KEGG pathway enrichment. Notably, these 270 infiltrating immune cell-related genes were mainly involved in immune-related BPs, CCs, MFs, and KEGG pathways. GO enrichment results showed that for BP, rejection-associated genes were mainly associated with T-cell activation, adaptive immune response, and leukocyte proliferation. For CC, rejection-associated genes were mainly associated with the outer side of the plasma membrane, mast cell granule, and T-cell receptor complex. For MF, rejection-associated genes were mainly associated with interleukin-15 receptor activity, MHC protein complex binding, and T-cell receptor binding. KEGG pathway enrichment analysis also showed that rejection-associated genes were mainly associated with natural killer cell-mediated cytotoxicity, chemokine signaling pathways, Th1 and Th2 cell differentiation, and B-cell receptor signaling pathways. Thus, these results suggested that these 270 infiltrating immune cell-related genes might play key roles in kidney transplant rejection by regulating the immune response.
Based on K‒M survival analysis, we found that 212 genes among 270 infiltrating immune cell-related genes were associated with the prognosis of patients. Thus, 270 immune cell-related genes were retained for further analysis. Finally, overlapping genes obtained by the XGBoost and LASSO algorithms identified a total of 5 hub genes, including WARS, CD8A, CRTAM, GBP2, and VAMP5. Studies have shown that allograft rejection is associated with molecular alterations [36, 37]. Our study found that WARS, CD8A, CRTAM, GBP2 and VAMP5 play key roles in the rejection of kidney allografts. Tryptophan-tRNA synthetase (WARS) is a very important housekeeping enzyme [38] that plays a unique role in immune control and immunomodulation, where WARS binds to WHEP (helix-turn-helix motif) upon infection, leading to the initiation of an inflammatory response and elimination of invading pathogens [39, 40]. Studies suggest that WARS levels and activity may play a key role in the immunopathogenesis of CKD [41]. Indeed, tryptophan-tRNA synthetase is overexpressed at the protein level in several cell types during antibody-mediated rejection and shows a distinct microcirculatory pattern by immunohistochemistry in antibody-mediated rejection in kidney transplantation [42]. Studies have shown that CD8A encodes the CD8 antigen, so CD8A expression may be associated with immune cell infiltration and immunotherapy response, and CD8A may serve as a useful biomarker for immunotherapy [43]. Studies have shown that CRTAM, a transmembrane protein of the immunoglobulin superfamily, can dynamically influence adaptive immune responses [44]. The expression of GBP2 was shown to correlate significantly with the level of immune infiltration and immune regulation [45]. GBP2 is a novel prognostic biomarker and potential indicator of the immune microenvironment in renal cell carcinoma [46]. A study showed that VAMP5 is an important immune-related gene [47].