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.