Del Barrio Calvo Carla, Bindila Laura
Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center, Mainz, Germany.
Front Cell Dev Biol. 2024 Aug 23;12:1450971. doi: 10.3389/fcell.2024.1450971. eCollection 2024.
Recent progress in cell isolation technologies and high-end omic technologies has allowed investigation of single cell sets across multiple omic domains and a thorough exploration of cellular function and various functional stages. While most multi-omic studies focused on dual RNA and protein analysis of single cell population, it is crucial to include lipid and metabolite profiling to comprehensively elucidate molecular mechanisms and pathways governing cell function, as well as phenotype at different functional stages. To address this gap, a cellular lipidomics and transcriptomics phenotyping approach employing simultaneous extraction of lipids, metabolites, and RNA from single cell populations combined with untargeted cellular 4 dimensional (4D)-lipidomics profiling along with RNA sequencing was developed to enable comprehensive multi-omic molecular profiling from the lowest possible number of cells. Reference cell models were utilized to determine the minimum number of cells required for this multi-omics analysis. To demonstrate the feasibility of higher resolution cellular multi-omics in early-stage identification of cellular phenotype changes in pathological and physiological conditions we implemented this approach for phenotyping of macrophages in two different activation stages: MyD88-knockout macrophages as a cellular model for atherosclerosis protection, and wild type macrophages. This multi-omic study enabled the determination of the lipid content remodeling in macrophages with anti-inflammatory and atherosclerotic protective function acquired by MyD88-KO, hence expedites the understanding of the molecular mechanisms behind immune cells effector functionality and of possible molecular targets for therapeutic intervention. An enriched functional role of phosphatidylcholine and plasmenyl/plasmalogens was shown here to accompany genetic changes underlying macrophages acquisition of anti-inflammatory function, finding that can serve as reference for macrophages reprogramming studies and for general immune and inflammation response to diseases.
细胞分离技术和高端组学技术的最新进展使得能够跨多个组学领域研究单细胞集，并深入探索细胞功能和各种功能阶段。虽然大多数多组学研究集中于单细胞群体的RNA和蛋白质双重分析，但纳入脂质和代谢物分析对于全面阐明调控细胞功能的分子机制和途径以及不同功能阶段的表型至关重要。为了填补这一空白，开发了一种细胞脂质组学和转录组学表型分析方法，该方法从单细胞群体中同时提取脂质、代谢物和RNA，并结合非靶向细胞四维（4D）脂质组学分析以及RNA测序，以实现从尽可能少的细胞中进行全面的多组学分子分析。利用参考细胞模型来确定这种多组学分析所需的最少细胞数量。为了证明高分辨率细胞多组学在病理和生理条件下细胞表型变化早期识别中的可行性，我们将这种方法应用于两种不同激活阶段巨噬细胞的表型分析：MyD88基因敲除巨噬细胞作为动脉粥样硬化保护的细胞模型，以及野生型巨噬细胞。这项多组学研究能够确定MyD88基因敲除巨噬细胞获得的具有抗炎和动脉粥样硬化保护功能的巨噬细胞中的脂质含量重塑，从而加快了对免疫细胞效应功能背后分子机制以及治疗干预可能的分子靶点的理解。本文显示了磷脂酰胆碱和缩醛磷脂/缩醛磷脂原的丰富功能作用伴随着巨噬细胞获得抗炎功能的潜在基因变化，这一发现可为巨噬细胞重编程研究以及对疾病的一般免疫和炎症反应提供参考。
