*Purpose: Our study was to investigate the potential associations between the single nucleotide polymorphisms (SNPs) in NFATC1 and the risk of T cell-mediated rejection (TCMR) in kidney transplanted recipients.

*Methods: A total of 200 patients were enrolled in our cohort and blood samples were collected. Total DNA was extracted and examined by target sequencing (TS) based on next-generation sequencing technology. Then, SNPs were genotyped and analyzed. Multivariable analysis was performed to identify the potential confounding factors of the results. Logistic regression analysis adjusted by confounding factors was carried out to evaluate the association of SNPs in NFATC1 and risk of TCMR in our cohort. Haplotype analysis was also used. Significant SNPs with TCMR were further investigated with the Banff score and rejection degree based on the pathological examination. Furthermore, to confirm the biological function of significant SNPs, we conducted the wild-type and mutation plasmids, which was co-cultured with T cells in vitro, respectively. T cell proliferation and inflammation cytokines were tested. Flow cytometry (FCM) assay was carried to explore the effects of mutations on SNPs on the T cell sub-populations. NFATC1 mRNA and proteins were also examined by PCR and western blotting.

*Results: As a result, 55 SNPs on NFATC1 were detected by primary sequencing. After minor allele frequency and Hardy-Weinberg equilibrium (HWE) tests followed by linkage disequilibrium analysis, a total of 14 tagger SNPs with 4 haplotypes were considered for further analysis. Then, 4 significant SNPs were identified with the risk of TCMR following renal transplant. No significance was observed in 4 haplotypes. The mutations of rs2290154 were found to be significant correlated with the Banff scores of TCMR cohort. In vitro, we found the mutation plasmids of rs2290154 could increase the expression of NFATC1 mRNA and proteins in CD3+ T lymphocytes, as well as promote the proliferation of T cells. Moreover, we found the accelerated secretion of IL-2 cytokines in supernatant of cell culture. FCM assay suggested the cell numbers of CD3+CD4+ and CD3+CD8+ T lymphocytes were both significant increased treated by mutation plasmids, as well as the proportion of CD4+/CD8+ ratio.

*Conclusions: In conclusion, our in vivo and vitro study suggested that SNPs of NFATC1 rs2290154 could significantly increase the risk of TCMR of recipients following kidney transplantation by promoting the activation and proliferation of T lymphocytes, and accelerating the polarization of CD3+ T lymphocytes.

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