DataSheet_1_Integrated transcriptomic and metabolomic analysis reveals the metabolic programming of GM-CSF- and M-CSF- differentiated mouse macrophages.docx

Macrophages play a critical role in the inflammatory response and tumor development. Macrophages are primarily divided into pro-inflammatory M1-like and anti-inflammatory M2-like macrophages based on their activation status and functions. In vitro macrophage models could be derived from mouse bone marrow cells stimulated with two types of differentiation factors: GM-CSF (GM-BMDMs) and M-CSF (M-BMDMs), to represent M1- and M2-like macrophages, respectively. Since macrophage differentiation requires coordinated metabolic reprogramming and transcriptional rewiring in order to fulfill their distinct roles, we combined both transcriptome and metabolome analysis, coupled with experimental validation, to gain insight into the metabolic status of GM- and M-BMDMs. The data revealed higher levels of the tricarboxylic acid cycle (TCA cycle), oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), and urea and ornithine production from arginine in GM-BMDMs, and a preference for glycolysis, fatty acid storage, bile acid metabolism, and citrulline and nitric oxide (NO) production from arginine in M-BMDMs. Correlation analysis with the proteomic data showed high consistency in the mRNA and protein levels of metabolic genes. Similar results were also obtained when compared to RNA-seq data of human monocyte derived macrophages from the GEO database. Furthermore, canonical macrophage functions such as inflammatory response and phagocytosis were tightly associated with the representative metabolic pathways. In the current study, we identified the core metabolites, metabolic genes, and functional terms of the two distinct mouse macrophage populations. We also distinguished the metabolic influences of the differentiation factors GM-CSF and M-CSF, and wish to provide valuable information for in vitro macrophage studies.巨噬细胞在炎症应答与肿瘤发生发展中发挥关键作用。根据激活状态与功能差异，巨噬细胞主要可分为促炎型M1样巨噬细胞与抗炎型M2样巨噬细胞。体外巨噬细胞模型可通过两种分化因子刺激小鼠骨髓细胞构建：分别为粒细胞-巨噬细胞集落刺激因子（GM-CSF，GM-BMDMs）与巨噬细胞集落刺激因子（M-CSF，M-BMDMs），以分别模拟M1样与M2样巨噬细胞。鉴于巨噬细胞分化需要协同的代谢重编程与转录重编程以实现其独特功能，本研究整合转录组与代谢组分析，并结合实验验证，以解析GM-BMDMs与M-BMDMs的代谢状态。数据显示，GM-BMDMs中三羧酸循环（TCA循环）、氧化磷酸化（OXPHOS）、脂肪酸氧化（FAO）以及精氨酸代谢生成尿素与鸟氨酸的通路活性更高；而M-BMDMs则更倾向于糖酵解、脂肪酸储存、胆汁酸代谢，以及精氨酸代谢生成瓜氨酸与一氧化氮（NO）的通路。与蛋白质组数据的关联分析显示，代谢相关基因的mRNA与蛋白表达水平具有高度一致性。将本研究数据与GEO数据库中人单核细胞来源巨噬细胞的RNA-seq数据进行比对，也得到了相似的结果。此外，经典巨噬细胞功能如炎症应答与吞噬作用，与上述代表性代谢通路紧密相关。本研究明确了两种不同小鼠巨噬细胞群体的核心代谢物、代谢基因及功能条目，同时阐明了分化因子GM-CSF与M-CSF对巨噬细胞代谢的调控差异，以期为体外巨噬细胞相关研究提供有价值的参考信息。