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Expediting 3D Analysis of Normal and Diseased Tissues

CLARITY enables the formation of a hydrogel matrix by crosslinking biological molecules to a 3D network of hydrophilic polymers followed by lipid removal to generate a transparent, structurally intact tissue. The tissue retains its original structural features, can be labeled with macromolecules, and subsequently imaged without destruction of tissue morphology.

Human lung cancer images courtesy of ClearLight Biotechnologies

The current gold standard for tissue analysis, formalin fixation paraffin embedding (FFPE) followed by 2D thin sectioning, has been around for more than a century. And like any 100-year-old technology, it has key limitations.. So, ClearLight Biotechnologies is on a mission to significantly improve the field by automating nondestructive processing of tissue in 3D as a means to initially facilitate preclinical and clinical research applications. Laurie Goodman, PhD, CEO and board manager of ClearLight Biotechnologies, explained the process in an interview with MD+DI.

ClearLight’s founder, Karl Deisseroth, MD, PhD, invented CLARITY at Stanford University, as he was trying to discover a way to understand neuronal pathways in the intact mouse brain, Goodman explained. “They needed a way to keep the brain intact and be able to study long-range neuronal projections and understand the differences between normal and diseased tissue," she said. “Prior to the invention of these 3D technologies, the researchers had to rely on trying to recapitulate a 3D structure by piecing together information from thinly sectioned brain slices.”

The essential question that Deisseroth posed, Goodman said: “How do I lock in the biology of a tissue in 3D, yet remove what impedes the ability to image deeply into the brain? In the case of the brain, it’s very lipid rich, and lipids are inherently light scattering.”

“Dr. Deisseroth created the method called CLARITY, which is pretty simple, yet quite elegant in its form and function.” Goodman said.

The process uses hydrogel monomers to create a covalent intact tissue scaffold and then employs a very simple detergent to extract the light scattering lipids, Goodman explained. “The next step is interrogating with various fluorescently labeled macromolecules that can be used to identify key analytes that can be imaged in 3D (proteins or nucleic acids).

“It allows a way to spatially observe how a variety of different biological molecules interact with each other in a 3D space,” she continued. “Additionally, it allows you to make more measurements of a particular molecule of interest over a thick volume of tissue, and chances are that your statistics are going to be a lot more accurate than if you’re just looking at a small fraction of that volume.”

CLARITY can be applied to any biological area that relies on 2D thin section analysis of tissue. A current focus of the company is oncology prognostic and predictive applications with an emphasis on predictive biomarker applications for immune-oncology T-cell-based drugs. “Common sense would say if you’re trying to predict drug response and outcome in the oncology field, if you’re only analyzing a 5-micron slice of a tumor, then you’re likely not getting the full picture of the biology of that patient’s tumor," said Goodman.

ClearLight Biotechnologies was recently nominated by StartupCity magazine as one of the 15 Most Promising BioTech Startups for 2018. In terms of future applications for the technology, Goodman said the company’s timeline includes building a beta platform, for limited use externally as well as internally to build a robust service model.

The company has key researchers who will be testing the technologies to see what improvements can be made within a three- to five-year strategy, and this will aid to inform the market and future commercialization strategy for introducing the platform into the research market.

“I am confident that next-generation tissue analysis in 3D will be the standard in the future. However, as any revolutionary technology, it will take time to get there, just as it did with next-generation sequencing. It will not be an overnight process, but the rewards will be great for patients,” said Goodman.

Susan Shepard

Susan Shepard

Susan Shepard is a freelance contributor to MD + DI.

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