Liu Zhenjie, Liu Fengxun, Xie Junwei, Zhao Zihao, Pan Shaokang, Liu Dongwei, Xia Zongping, Liu Zhangsuo
Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China.
Research Institute of Nephrology, Zhengzhou University, Zhengzhou 450052, Henan Province, China.
J Transl Int Med. 2024 Oct 1;12(4):367-383. doi: 10.2478/jtim-2024-0013. eCollection 2024 Sep.
Systemic lupus erythematosus (SLE) is distinguished by dysregulated immune system activity, resulting in a spectrum of clinical manifestations, with lupus nephritis being particularly prominent. This study endeavors to discern novel targets as potential therapeutic markers for this condition.
Weighted correlation network analysis (WGCNA) was used to construct the network and select the key hub genes in the co-expression module based on the gene expression dataset GSE81622. Subsequently, functional enrichment and pathway analysis were performed for SLE and lupus nephritis. In addition, also identify genes and differences in SLE with lupus nephritis and methylation site. Finally, qRT-PCR and western blot were used to verify the up-regulated expression levels of the selected key genes.
Within the co-expression modules constructed by WGCNA, the MElightcyan module exhibited the strongest positive correlation with lupus nephritis (0.4, = 0.003), while showing a weaker correlation with the control group SLE (0.058) and a negative correlation with the control group (-0.41, = 0.002). Additionally, the MEgreenyellow module displayed the highest positive correlation with SLE (0.25), but its P value was 0.06, which did not reach statistical significance(P > 0.05). Furthermore, it had a negative correlation with the control group was (-0.38, = 0.004). The module associated with lupus nephritis was characterized by processes such as neutrophil activation (neutrophil_activation), neutrophil degranulation (neutrophil_degranulation), neutrophil activation involved in immune response (neutrophil_activation_involved_in_immune_response), neutrophils mediated immune (neutrophil_mediated_immunity) and white blood cells degranulation (leukocyte_degranulation) and so on the adjustment of the process. Secondly, in the analysis of SLE samples, the identification of differentially expressed genes revealed 125 genes, with 49 being up-regulated and 76 down-regulated. In the case of lupus nephritis samples, 156 differentially expressed genes were discerned, include in 70 up-regulated and 86 down-regulated genes. When examining differential methylation sites, we observed 12432 such sites in the SLE sample analysis, encompassing 2260 hypermethylation sites and 10172 hypomethylation sites. In the lupus nephritis samples analysis, 9613 differential methylation sites were identified, comprising 4542 hypermethylation sites and 5071 hypomethylation sites. Substantiating our findings, experimental validation of the up-regulated genes in lupus nephritis confirmed increased levels of gene expression and protein expression for CEACAM1 and SLC2A5.
We have identified several genes, notably CEACAM1 and SLC2A5, as potential markers for lupus nephritis. Their elevated expression levels and reduced DNA methylation in lupus nephritis contribute to a more comprehensive understanding of the aberrant epigenetic regulation of expression in this condition. These findings hold significant implications for the diagnosis and therapeutic strategies of lupus nephritis.
系统性红斑狼疮（SLE）的特征是免疫系统活动失调，导致一系列临床表现，其中狼疮性肾炎尤为突出。本研究旨在识别新的靶点，作为该疾病潜在的治疗标志物。
基于基因表达数据集GSE81622，采用加权基因共表达网络分析（WGCNA）构建网络并选择共表达模块中的关键枢纽基因。随后，对SLE和狼疮性肾炎进行功能富集和通路分析。此外，还鉴定了SLE伴狼疮性肾炎的基因及差异，并分析了甲基化位点。最后，采用qRT-PCR和蛋白质免疫印迹法验证所选关键基因的上调表达水平。
在WGCNA构建的共表达模块中，MElightcyan模块与狼疮性肾炎呈最强正相关（0.4，P = 0.003），而与SLE对照组相关性较弱（0.058），与正常对照组呈负相关（-0.41，P = 0.002）。此外，MEgreenyellow模块与SLE呈最高正相关（0.25），但其P值为0.06，未达到统计学意义（P>0.05）。此外，它与正常对照组呈负相关（-0.38，P = 0.004）。与狼疮性肾炎相关的模块的特征是中性粒细胞活化（neutrophil_activation）、中性粒细胞脱颗粒（neutrophil_degranulation）、参与免疫反应的中性粒细胞活化（neutrophil_activation_involved_in_immune_response）、中性粒细胞介导的免疫（neutrophil_mediated_immunity）和白细胞脱颗粒（leukocyte_degranulation）等过程的调节。其次，在SLE样本分析中，差异表达基因鉴定出125个基因，其中49个上调，76个下调。在狼疮性肾炎样本中，识别出156个差异表达基因，包括70个上调和86个下调基因。在检测差异甲基化位点时，我们在SLE样本分析中观察到12432个此类位点，包括2260个高甲基化位点和10172个低甲基化位点。在狼疮性肾炎样本分析中，鉴定出9613个差异甲基化位点，包括4542个高甲基化位点和5071个低甲基化位点。为证实我们的发现，对狼疮性肾炎中上调基因的实验验证证实了癌胚抗原相关细胞黏附分子1（CEACAM1）和溶质载体家族2成员5（SLC2A5）的基因表达水平和蛋白表达水平均升高。
我们已确定几个基因，特别是CEACAM1和SLC2A5，作为狼疮性肾炎的潜在标志物。它们在狼疮性肾炎中的表达水平升高和DNA甲基化降低有助于更全面地了解该疾病中异常的表观遗传调控表达。这些发现对狼疮性肾炎的诊断和治疗策略具有重要意义。
