Healthcare (Commonwealth Union) – MIT has developed an innovative technology that allows scientists to label proteins across millions of individual cells within fully intact 3D tissues with unmatched speed, consistency, and flexibility. This breakthrough technology enabled the team to label large tissue samples comprehensively in just one day. In their recent study published in Nature Biotechnology, the researchers demonstrate how labeling proteins with antibodies at the single-cell level in large tissue samples reveals valuable insights that other common labeling techniques miss.
Profiling the proteins produced by cells is essential in fields like biology, neuroscience, and more, as the proteins a cell produces can offer crucial information about its current functions or response to conditions like diseases or treatments. Despite significant advances in microscopy and labeling technologies, scientists have struggled to track protein expression in millions of densely packed cells within whole, 3D tissues. Typically limited to thin slices of tissue on slides, researchers have lacked the tools to fully understand cellular protein expression in the complex, interconnected systems where it naturally occurs.
“Conventionally, investigating the molecules within cells requires dissociating tissue into single cells or slicing it into thin sections, as light and chemicals required for analysis cannot penetrate deep into tissues. Our lab developed technologies such as CLARITY and SHIELD, which enable investigation of whole organs by rendering them transparent, but we now needed a way to chemically label whole organs to gain useful scientific insights,” explained the study senior author Kwanghun Chung, who is an associate professor in The Picower Institute for Learning and Memory, the departments of Chemical Engineering and Brain and Cognitive Sciences, and the Institute for Medical Engineering and Science at MIT. “If cells within a tissue are not uniformly processed, they cannot be quantitatively compared. In conventional protein labeling, it can take weeks for these molecules to diffuse into intact organs, making uniform chemical processing of organ-scale tissues virtually impossible and extremely slow.”
The newly introduced method, known as “CuRVE,” marks a significant breakthrough after years of development, offering a revolutionary approach to uniformly processing large and dense tissues in their entirety. In their study, the researchers explain how they overcame technical challenges by implementing a version of CuRVE named “eFLASH.” They provide detailed demonstrations of this technology, including its role in uncovering new insights in neuroscience.
The lead author Dae Hee Yun, PhD ’24, a recent MIT graduate who now works as a senior application engineer at LifeCanvas Technologies, a startup founded by Kwanghun Chung to commercialize the lab’s innovations. The other lead author is Young-Gyun Park, a former MIT postdoc now serving as an assistant professor at KAIST in South Korea. He indicated that it is a major advancement, particularly in terms of how the technology performs.
The main challenge in labeling large, 3D tissue samples uniformly lies in the slow penetration of antibodies into tissues, contrasted with their rapid binding to target proteins. This mismatch in speed causes proteins at the outer layers of the tissue to be thoroughly labeled, while the antibodies struggle to reach deeper cells and proteins inside, resulting in incomplete labeling.
To enhance the labeling process, the team developed a method central to CuRVE that addresses the speed discrepancy. Their approach involved continuously regulating the rate at which antibodies bind to proteins, while simultaneously accelerating their movement throughout the tissue. To refine this method, they designed and ran an advanced computational simulation that allowed them to test various variables, including binding speeds, tissue density, and composition.
The next step was applying this approach to actual tissues. The team began by building upon a previous technology called “SWITCH,” created by Chung’s lab, which involved temporarily halting antibody binding to allow antibodies to penetrate the tissue before restarting the binding process. While this technique was effective, Yun points out that they identified opportunities for improvement, specifically by controlling antibody binding speed more precisely.
