The separate effects of lipids and proteins on brain MRI contrast revealed through tissue clearing

Despite the widespread use of magnetic resonance imaging (MRI) of the brain, the relative contribution of different biological components (e.g. lipids and proteins) to structural MRI contrasts (e.g., T1, T2, T2*, proton density, diffusion) remains incompletely understood. This limitation can undermine the interpretation of clinical MRI and hinder the development of new contrast mechanisms. Here, we determine the respective contribution of lipids and proteins to MRI contrast by removing lipids and preserving proteins in mouse brains using the tissue clearing method CLARITY. Our results show that although lipids and proteins account for approximately the same percentage of brain matter by weight, the lipids are by far the dominant source of tissue contrast. While proteins may influence relaxivity, we observed minimal T2 contrast and no contrast at all for all the other MRI sequences when the lipids are removed by clearing (Fig.1). Our data also provides evidence that hindered water diffusion in brain tissue is mainly caused by lipids and bi-lipid cell membranes, while the preserved cytoskeleton has no observable effect on water diffusion rates or anisotropy (Fig.2).

Leuze C., Aswendt M., Ferenczi E., Liu C., Hsueh B., Goubran M., Tian Q., Steinberg G., Zeineh M., Deisseroth K., McNab J. The separate effects of lipids and proteins on brain MRI contrast revealed through tissue clearing. NeuroImage, 2017;

Figure 1: Mouse brain during the different stages of tissue clearing. MRI contrast decreases with increasing transparency of the brain (top to bottom).

Figure 2: (A) While the protein content is mainly preserved in the cleared tissue, most other components such as phosphorus present in the phospholipids are washed out. (B) Staining the cleared tissue with propidium iodide for cells (red) and neurofilaments (green) shows that the nucleic acids and proteins are preserved at their original locations in the tissue.