Table_1_Integrating peripheral blood and brain transcriptomics to identify immunological features associated with Alzheimer’s disease in mild cognitive impairment patients.xlsx

BackgroundImmune system dysfunction has been proven to be an important pathological event in Alzheimer’s disease (AD). Mild cognitive impairment (MCI), as a transitional stage between normal cognitive function and AD, was an important research object for the screening of early diagnostic markers and therapeutic targets for AD. However, systematic assessment of peripheral immune system changes in MCI patients and consistent analysis with that in the CNS were still lacking.
MethodsPeripheral blood transcriptome data from the AddNeuroMed Cohort (n = 711) was used as a training dataset to assess the abundance of 24 immune cells through ImmuCellAI and to identify MCI-related immune signaling pathways and hub genes. The expression level of the immune hub gene was validated in peripheral blood (n = 587) and brain tissue (78 entorhinal cortex, 140 hippocampi, 91 temporal cortex, and 232 frontal cortex) validation datasets. Finally, reliable immune hub genes were applied for Gene Set Enrichment Analysis and correlation analysis of AD pathological characteristics.
ResultsMCI patients have early changes in the abundance of various types of immune cells in peripheral blood, accompanied by significant changes in NF-kB, TNF, JAK-STAT, and MAPK signaling pathways. Five hub immune-related differentially expressed genes (NFKBIA, CD4, RELA, CASP3, and HSP90AA1) were screened by the cytoHubba plugin in Cytoscape and the least absolute shrinkage and selection operator (LASSO) regression. Their expression levels were significantly correlated with infiltration score and the abundance of monocytes, natural killer cells, Th2 T cells, T follicular helper cells, and cytotoxic T cells. After validation with independent datasets derived from peripheral blood and brain, RELA and HSP90AA1 were identified as two reliable immune hub genes in MCI patients and had consistent changes in AD. The Gene Set Enrichment Analysis (GSEA) showed that their expression levels were closely associated with Alzheimer’s disease, JAK-STAT, calcium signaling pathway, etc. In addition, the expression level of RELA was positively correlated with β- and γ-secretase activity and Braak stage. The expression level of HSP90AA1 was negatively correlated with α- and β-secretase activity.
ConclusionImmune system dysfunction was an early event in AD. It provides a new target for the early diagnosis and treatment of AD.

背景
免疫功能异常已被证实为阿尔茨海默病（Alzheimer’s Disease, AD）的重要病理事件。轻度认知障碍（Mild Cognitive Impairment, MCI）作为正常认知功能与阿尔茨海默病之间的过渡阶段，是阿尔茨海默病早期诊断标志物与治疗靶点筛选的重要研究对象。然而，目前尚缺乏对轻度认知障碍患者外周免疫系统变化的系统性评估，以及与中枢神经系统（Central Nervous System, CNS）变化的一致性分析。

方法
本研究以AddNeuroMed队列（n=711）的外周血转录组数据作为训练集，通过ImmuCellAI工具评估24种免疫细胞的浸润丰度，并筛选与轻度认知障碍相关的免疫信号通路及核心基因（hub gene）。随后，在外周血验证集（n=587）及脑组织验证集（78例内嗅皮层样本、140例海马样本、91例颞皮层样本、232例额叶皮层样本）中对该免疫核心基因的表达水平进行验证。最终，选取可靠的免疫核心基因开展基因集富集分析（Gene Set Enrichment Analysis, GSEA）及阿尔茨海默病病理特征相关性分析。

结果
轻度认知障碍患者外周血中多种免疫细胞的丰度已出现早期改变，同时伴随NF-κB、TNF、JAK-STAT及MAPK等信号通路的显著异常。本研究通过Cytoscape的cytoHubba插件及最小绝对收缩和选择算子（Least Absolute Shrinkage and Selection Operator, LASSO）回归分析，筛选出5个与免疫相关的差异表达核心基因：NFKBIA、CD4、RELA、CASP3及HSP90AA1。上述基因的表达水平与免疫浸润评分及单核细胞、自然杀伤细胞、Th2型T细胞、滤泡辅助性T细胞、细胞毒性T细胞的丰度均呈显著相关。经外周血及脑组织独立数据集验证后，RELA与HSP90AA1被确定为轻度认知障碍患者中两个可靠的免疫核心基因，且在阿尔茨海默病中呈现一致的表达变化。基因集富集分析（GSEA）结果显示，二者的表达水平与阿尔茨海默病、JAK-STAT信号通路、钙信号通路等密切相关。此外，RELA的表达水平与β、γ分泌酶活性及Braak分期呈正相关；HSP90AA1的表达水平则与α、β分泌酶活性呈负相关。

结论
免疫功能异常是阿尔茨海默病的早期事件，可为阿尔茨海默病的早期诊断与治疗提供全新靶点。