Chinese Journal of Tissue Engineering Research ›› 2024, Vol. 28 ›› Issue (16): 2561-2567.doi: 10.12307/2024.321
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Xia Tian1, Li Binglin1, Xiao Fayuan1, Zheng Enze1, Chen Yueping2
Received:
2023-03-15
Accepted:
2023-05-10
Online:
2024-06-08
Published:
2023-07-31
Contact:
Chen Yueping, MD, Chief physician, Doctoral supervisor, Department of Orthopedic Trauma and Hand Surgery, Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning 530000, Guangxi Zhuang Autonomous Region, China
About author:
Xia Tian, MD candidate, Associate professor, Guangxi University of Chinese Medicine, Nanning 530000, Guangxi Zhuang Autonomous Region, China
Supported by:
CLC Number:
Xia Tian, Li Binglin, Xiao Fayuan, Zheng Enze, Chen Yueping. CeRNA interaction network and immune manifestation of ferroptosis-related signature genes in rheumatoid arthritis[J]. Chinese Journal of Tissue Engineering Research, 2024, 28(16): 2561-2567.
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.3 机器学习方法筛选铁死亡疾病特征基因 运用LASSO回归方法,通过R软件中的“glmnet”对差异基因的表达量进行过滤,取误差最小值的前16 个基因为疾病特征基因,并绘制相关可视化图形,见图5A,基因误差按高到低排名依次获得SLC1A5、GABARAPL1、SAT1、PEBP1、MAPK8、MTCH1、SLC39A7、TRIM21、CIRBP、ADAM23、MEG3、RRM2、GDF15、AHCY、AR、BEX1;然后运用SVM-RFE方法筛选疾病特征基因,通过R软件中的“e1071、kernlab、caret”包对差异基因的表达量进行过滤,通过交叉验证寻找误差最小的疾病特征基因并做可视化分析,见图5B,发现误差表达最小的点共有3 个基因。接着将两者各自获得的疾病特征基因相交,并绘制VENN图,见图6,获得GABARAPL1、SAT1共2 个疾病特征基因。然后对获得的2 个疾病特征基因进行ROC曲线绘制,发现10 个疾病特征基因的AUC值都在80%以上,最后并对检测模型进行检测发现AUC值在0.95以上,说明GABARAPL1、SAT1为疾病的特征基因,具有一定的准确性,见图7。"
2.5 RA铁死亡疾病特征基因的免疫浸润分析 将矫正后的2 个芯片的基因表达量通过使用 CIBERSORT 算法进行分析,其中RA有22 个滑膜组织样本,正常组有19 个滑膜组织样本,同时筛选得到符合条件的有RA 22 个与正常组19 个之间的22 个免疫细胞的免疫浸润差异,通过与正常滑膜相比,RA滑膜中的浆细胞、T 细胞CD8、记忆静息T细胞CD4、记忆激活T细胞CD4、T细胞滤泡辅助器、激活的NK细胞、单核细胞、巨噬细胞M1、活化的肥大细胞等9种免疫细胞与正常组织存在明显差异,见图9,其中浆细胞、T细胞CD8、T细胞滤泡辅助器在疾病组中为高表达状态,其余为低表达。通过比较单个疾病特征基因与免疫细胞的相关性,发现GABARAPL1在树突状静息细胞、激活的NK细胞、巨噬细胞M1等为正相关,其中与树突状静息细胞的相关性最为显著,SAT1与T细胞CD4与γδT细胞为正相关,与NK静息细胞为负相关,见图10。通过GSVA分析发现SAT1在抗坏血酸和醛酸代谢上是上调的,而SAT1在B细胞受体信号通路、自身免疫性甲状腺疾病、TOLL样受体信号通路、T细胞受体信号通路、1型糖尿病、胞浆dna传感通路、自然杀伤细胞介导的细胞毒性、烟酸盐和烟酰胺的代谢是下调的;GABARAPL1在PPAR信号通路、泛酸与coa生物合成、药物代谢细胞色素P450、烟酸盐和烟酰胺的代谢、苯丙氨酸代谢、色氨酸代谢、脂肪酸代谢、类固醇生物合成等是下调的,见图11。通过将疾病特征基因对验证发现,疾病组的GABARAPL1与SAT1与正常组存在显著差异,且疾病组处于低表达的状态,这与以上的研究结果内容符合,见图12。"
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