Transcriptome and proteome profiling reveals TREM2-dependent and -independent glial response and metabolic perturbation in an Alzheimers mouse model

Elucidating the intricate molecular mechanisms of Alzheimer's disease (AD) requires a multidimensional analysis incorporating various omics data. In this study, we employed transcriptome and proteome profiling of AppNL-G-F, a human APP knock-in model of amyloidosis, at the early and mid-stages of amyloid-beta (A) pathology, to delineate the impacts of A deposition on brain cells. By contrasting AppNL-G-F mice with TREM2 (Triggering receptor expressed on myeloid cells 2) knockout models, our study further investigates the role of TREM2, a well-known AD risk gene, in influencing microglial responses to A pathology. Our results highlight microglial activation as a central feature of A pathology, characterized by the significant upregulation of microglia-specific genes related to immune responses such as complement system and antigen presentation, and catabolic pathways such as phagosome formation and lysosome biogenesis. The absence of TREM2 markedly diminishes the induction of these genes, impairs A clearance, and exacerbates dystrophic neurite formation. Importantly, TREM2 is required for the microglial engagement with A plaques and the formation of compact A plaque cores. Furthermore, this study reveals substantial disruptions in energy metabolism and protein synthesis, signaling a shift from anabolism to catabolism in response to A deposition. This metabolic alteration, coupled with a decrease in synaptic protein abundance, occurs independently of TREM2, suggesting the direct effects of A deposition on synaptic integrity and plasticity. In summary, our findings demonstrate significant microglial activation and metabolic disruption following A deposition, offering mechanistic insights into A pathology and highlighting the potential of targeting these pathways in AD therapy. We performed transcriptome and proteome profiling of single human APP knock-in AppNL-G-F mice at the onset and middle stages of A pathology to comprehensively investigate the pathway alterations and molecular mechanisms associated with A deposition. AppNL-G-F knock-in mice were selected as they eliminate artifacts related to APP overexpression, such as the mis-localization of APP and the accumulation of APP fragments including CTF- (C-terminal fragment of APP) and AICD (APP intracellular domain). Furthermore, we also profiled AppNL-G-F, TREM2 knockout mice to examine how the absence of TREM2 affects the responses of microglia and other glial cells to A deposition.阐明阿尔茨海默病（Alzheimer's Disease, AD）复杂的分子机制，需要整合多组学数据开展多维分析。本研究针对淀粉样变性的人源APP敲入模型AppNL-G-F，在β淀粉样蛋白（A）病理的早期和中期阶段开展转录组与蛋白质组谱分析，以厘清A沉积对脑细胞的影响。通过对比AppNL-G-F小鼠与髓系细胞触发受体2（Triggering receptor expressed on myeloid cells 2, TREM2）敲除模型，本研究进一步探究了这一已知AD风险基因TREM2在小胶质细胞应对A病理过程中的作用。本研究结果显示，小胶质细胞激活是A病理的核心特征，具体表现为与免疫应答相关的小胶质细胞特异性基因（如补体系统、抗原呈递相关基因）以及吞噬体形成、溶酶体生物发生等分解代谢通路的显著上调。TREM2缺失会显著削弱这些基因的诱导表达，损害A清除能力，并加重营养不良性神经突的形成。尤为重要的是，TREM2是小胶质细胞与A斑块结合以及形成致密A斑块核心所必需的。此外，本研究还揭示了能量代谢与蛋白质合成的显著紊乱，表明机体在应对A沉积时出现了从合成代谢到分解代谢的转变。这一代谢改变伴随突触蛋白丰度的降低，且该过程不依赖于TREM2，提示A沉积可直接影响突触完整性与突触可塑性。综上，本研究发现A沉积后会出现显著的小胶质细胞激活与代谢紊乱，为A病理提供了机制层面的见解，并凸显了靶向这些通路用于AD治疗的潜力。为全面探究A沉积相关的通路改变与分子机制，我们对处于A病理起始与中期阶段的单只人源APP敲入AppNL-G-F小鼠开展了转录组与蛋白质组谱分析。选择AppNL-G-F敲入小鼠的原因在于，其可消除APP过表达相关的实验伪影，如APP的错误定位以及包括APP羧基末端片段（C-terminal fragment of APP, CTF-）和APP细胞内结构域（APP intracellular domain, AICD）在内的APP片段积累。此外，我们还对AppNL-G-F、TREM2敲除小鼠进行了谱分析，以探究TREM2缺失如何影响小胶质细胞及其他胶质细胞对A沉积的应答。