Circadian Control of Heparan Sulfate Levels Times Phagocytosis of Amyloid Beta Aggregates

The following datasets are from the manuscript entitled “Circadian Control of Heparan Sulfate Levels Times Phagocytosis of Amyloid Beta Aggregates” published in PLOS Genetics. This paper investigates the link between Alzheimer’s disease and circadian disruption by looking at naïve macrophages and the phagocytosis of a neurotoxic protein involved in Alzheimer’s Disease, amyloid-beta (1-42). We found that there is a circadian oscillation in the phagocytosis of amyloid-beta (1-42) with the peak of phagocytosis at Post Shock time (PS) 32 and the trough at PS 16. To confirm the observed rhythm, we repeated our phagocytosis experiment in PER1-/-/PER2-/- knockout cells, which lack a circadian rhythm, and observed a change in the rhythm, confirming circadian influence. We then probed a previously published macrophage proteomic dataset (Collins et al., Genome Research, 2021) and found genes involved in the heparan sulfate and chondroitin sulfate biosynthesis pathways to be circadianly controlled. To demonstrate the circadian control of cells surface heparan sulfate and chondroitin sulfate proteoglycans, we performed liquid chromatography tandem mass spectrometry on our macrophages and found that there is a circadian rhythm to both heparan sulfate and chondroitin sulfate proteoglycan expression. We found that the rhythm of heparan sulfate expression was anti-phase to the oscillation of amyloid-beta phagocytosis, indicating an inhibitory relationship. Therefore, we performed phagocytosis experiments in the presence of heparan sulfate cleaving enzymes (heparinases I, II, and III) and found an ablation of the previously observed rhythm of amyloid-beta phagocytosis. Furthermore, we investigated if this oscillation was unique to amyloid-beta (1-42) by repeating our phagocytosis experiments with other homologs of amyloid-beta, amyloid-beta (1-40) and mouse amyloid-beta (1-42). These homologs were of interest as they do not rapidly aggregate like amyloid-beta (1-42) and mouse amyloid-beta contains mutations in the known heparan sulfate proteoglycan binding region. We found that the amyloid-beta homologs did not have an oscillation in phagocytosis, demonstrating that aggregation and heparan sulfate proteoglycan binding are essential to the observed rhythm. The attached datasets are from all the above-mentioned experiments. For the phagocytosis experiments, the fluorescent microscopy images as well as the determined pixel intensity data are included. For the liquid chromatography tandem mass spectrometry data, the normalization method as well as the raw and normalized data are available.

本数据集源自于发表于《PLOS Genetics》杂志上的手稿《昼夜节律对肝素硫酸酯水平调控与淀粉样蛋白β聚集吞噬作用的关系》。该研究探讨了阿尔茨海默病与昼夜节律紊乱之间的联系，通过研究原始巨噬细胞对参与阿尔茨海默病的神经毒性蛋白——淀粉样蛋白β（1-42）的吞噬作用。研究发现，淀粉样蛋白β（1-42）的吞噬作用存在昼夜节律性波动，吞噬作用峰值出现在冲击后时间（PS）32，谷值出现在PS 16。为证实观察到的节律，研究者在缺乏昼夜节律的PER1-/-/PER2-/-敲除细胞中重复了吞噬实验，并观察到节律变化，从而证实了昼夜节律的影响。随后，研究者对先前发表的巨噬细胞蛋白质组学数据集（Collins等，《基因组研究》，2021年）进行了探究，发现参与肝素硫酸酯和透明质酸硫酸酯生物合成途径的基因受到昼夜节律调控。为了展示细胞表面肝素硫酸酯和透明质酸硫酸酯蛋白聚糖的昼夜节律调控，研究者对巨噬细胞进行了液相色谱串联质谱分析，发现肝素硫酸酯和透明质酸硫酸酯蛋白聚糖的表达均存在昼夜节律。研究发现，肝素硫酸酯的表达节律与淀粉样蛋白β吞噬作用的振荡呈反相，表明存在抑制作用。因此，研究者在存在肝素硫酸酯裂解酶（肝素酶I、II和III）的情况下进行了吞噬实验，发现之前观察到的淀粉样蛋白β吞噬作用节律消失。此外，研究者还探讨了这种振荡是否仅限于淀粉样蛋白β（1-42），通过重复使用其他淀粉样蛋白同源物——淀粉样蛋白β（1-40）和鼠淀粉样蛋白β（1-42）进行吞噬实验。这些同源物因其不像淀粉样蛋白β（1-42）那样迅速聚集，且鼠淀粉样蛋白β在其已知的肝素硫酸酯蛋白聚糖结合区域存在突变，因此备受关注。研究发现，淀粉样蛋白β同源物在吞噬作用中不存在振荡，证明了聚集和肝素硫酸酯蛋白聚糖结合对于观察到的节律是必要的。所附数据集涵盖了上述所有实验。对于吞噬实验，包括荧光显微镜图像以及确定的像素强度数据。对于液相色谱串联质谱数据，提供了标准化方法以及原始和标准化数据。