A novel protein-preserving passive tissue clearing approach using sodium cholate and urea for whole-organ imaging

The recent advancements in tissue-clearing techniques have opened new possibilities for non-invasive three-dimensional (3D) volumetric imaging of a wide range of biological specimens. Passive tissue-clearing methods use diffusion-based processes to infiltrate clearing reagents into samples without mechanical forces or energy input, aiming to minimize the sample disruption while preserving the tissue architecture and molecular information. Nevertheless, these methods often rely on sodium dodecyl sulfate (SDS) as a delipidating detergent, which has a risk of causing tissue damage and protein disruptions, thus necessitating the development of a reliable yet accessible approach for passive tissue clearing. Here we replaced SDS with sodium cholate (SC), combined it with urea and developed OptiMuS-prime as a novel passive tissue clearing technique to achieve a better passive infiltration of clearing reagents while retaining structural integrity. SC, a non-denaturing detergent with small micelles, enhances tissue transparency while preserving proteins in their native state, whereas urea disrupts hydrogen bonds and induces hyperhydration to enhance probe penetration. Through the optimization of composition and protocols, we found that OptiMuS-prime enables the 3D imaging of immunolabeled neural structures and vasculature networks across multiple rodent organs, including the brain, intestine and lung. The method demonstrated robust clearing and immunostaining capabilities, particularly for detecting subcellular structures in densely packed organs such as the kidney, spleen and heart, as well as in post-mortem human tissues and human induced pluripotent stem cell-derived brain organoids. Together, OptiMuS-prime offers a fully accessible and customizable solution for passive clearing and immunostaining, enabling 3D cellular connectivity analysis across whole organisms without the need for extensive tissue-clearing expertise.