ClearLight Biotechnologies
CLARITY Tissue Clearing Beyond the Brain

Researchers and scientists studying the tissues inside the brain have faced two challenges. First, the brain is rich in lipids that cloud any attempts at light microscopy. And secondly, slicing biological tissues into thin sections, as has been the convention with Formalin-Fixed Paraffin-Embedded (FFPE) 2D thin sections, disrupts the spatial and morphological analysis of the tissue microenvironment. Researchers need a competent way to see beyond the tissue surface to study structures in soft tissue—especially very small, delicate structures, like neurons in a brain or cancerous lesions in breast tissue. With the advantages of working with larger tissue samples and being able to see more biology within them, scientists are better equipped to create the cures of tomorrow.

Enter ClearLight Biotechnologies, a California-based company that empowers researchers to See More Biology™within the tissue microenvironment. The company provides CLARITY Tissue Clearing, 3D Immunohistochemistry (IHC), and Tru3D® Image Analysis services to pharmaceutical, biotechnology, and academic researchers. The company works with larger undisturbed tissue volumes as compared to 2D thin section tissue slices. Tissues are cleared of light scattering lipids and then immunostained and imaged in 3D. Researchers gain greater insights into the tissue’s subcellular structure when the third dimension is added. This technology has the potential to reduce the cost and failure rates of potential drug candidates during the costly drug development process. “Our goal is to make sure that we can reduce risk and provide better insights so clients don’t invest as much time in a product that by the time it gets to clinical, is going to fail, “ offered Sharla White, PhD, Vice President - Research and Development at ClearLight Biotechnologies.

It all started in a laboratory at Stanford University where Karl Deisseroth MD, PhD, the founder of ClearLight Biotechnologies, developed CLARITY to overcome the opacity of lipids in brain tissue that caused light to scatter during microscopic visualization of neurons, thereby obscuring image quality. Since then, the company broadened the applicability of the CLARITY method to other tissues—from the brain to bone. “We started developing CLARITY for immuno-oncology to look at breast cancer and other cancers, and elevated CLARITY to the next level by applying it to other tissues as well,” shared Dr. White.

The company’s CLARITY Tissue Clearing method allows a tissue sample to be rendered optically clear, retain its three-dimensional integrity, and enables tissue staining and re-interrogation multiple times.

In this method, a tissue sample is first embedded in a hydrogel. The hydrogel provides a three-dimensional matrix that supports the tissue sample and retains the structural integrity and spatial orientation of the critical tissue components. Subsequently, lipids are removed using detergent solutions, making the tissues transparent. This enables researchers to immunostain and image the tissues using fluorescent microscopy for closer examination and to garner greater insights into their subcellular structure. “We create a hybrid tissue scaffold using CLARITY that allows us to see beyond the surface of the tissues and see deeper for spatial analysis,” states Dr. White. While other techniques immunostain the tissue before applying the clearing reagent, CLARITY is the only technique to employ tissue lipid-clearing before immunostaining, followed by refractive index (RI) matching.

ClearLight has built upon the original CLARITY protocol, optimizing the reagents, developing expertise in thick tissue immunostaining penetration, and expanding beyond the brain to include organoids, eye, lymph nodes, skin, bone, kidney, liver, tonsil, and other human and animal tissues. The company’s CLARITY expertise beyond the brain has paid off.

One story Dr. White shared is about a biomedical startup that was working on an implantable device. Rather than taking a one-size-fits-all approach, ClearLight Biotechnologies first understands the researchers’ requirements before designing a custom solution for them.

The biomedical company wanted to design the device in such a way that it was completely removable after use, a requirement needed to gain FDA approval and widespread acceptance in the market. After initially getting unsatisfactory answers to questions about the effect of the drug outside the device, cell growth, among others, the company abandoned competing technologies and instead collaborated with ClearLight Biotechnologies. ClearLight not only provided this biomedical startup with images to answer their initial queries but also gave them the certainty whether their device was working according to their initial goals. It wasn’t. That prompted a return to the drawing board, saving them years of costly development down a faulty path.

Where ClearLight is Taking CLARITY

ClearLight Biotechnologies pushes the envelope of tissue clearing with continued innovation of its products and services. Currently, tissue clearing and staining is a weeks-long process that delays the analysis of tissues. The ClearLight team envisions an automated clearing and staining platform to complete the entire process in less than a week. The platform will allow the company to streamline the complete CLARITY workflow—clearing, staining, imaging, and quantitative analysis. “We keep listening to preclinical researchers and are always expanding our antibody library, tissue library, and technology stack to help them at each step of the way. All of this contributes toward a future with more non-destructive tissue processing and digital tissue image analysis in 3D. This platform has the potential for scientists and researchers to develop next-generation cures,” concludes Dr. White.