A set of three new advancements allows for clear and efficient imaging of human brain tissue at various scales and mapping the connections between neurons at the individual cell level. In order to showcase this progress, scientists compared a brain region in both an Alzheimer’s patient and a control sample. This achievement has been a long-standing goal in neuroscience, and now, a team based at MIT has described a technology pipeline in a new study in Science that made it possible to carefully process, label, and share detailed observations of anything within the human brain, no matter how large or small, while keeping it fully intact.Displaying complete hemispheric images of the brains of two individuals, one with Alzheimer’s and one without, at a high resolution and speed. “We performed comprehensive imaging of human brain tissues at various resolutions, from individual synapses to entire brain hemispheres, and have made that data accessible,” stated Kwanghun Chung, 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. “This technology pipeline truly allows us to study the human brain.”The new study is not yet a complete map of the entire brain, but it demonstrates a set of three technologies that could potentially be used to map the human brain at multiple scales. The study provides examples of what the pipeline makes possible, including imaging of thousands of neurons within whole brain regions and individual cells within diverse forests. This could enable long-sought neuroscience investigations, such as fully mapping human brains.The article displays detailed images of subcellular structures within the extracellular molecules. The researchers compare quantitative analytical data from a specific area in both Alzheimer’s and non-Alzheimer’s hemispheres. Being able to image entire human brain hemispheres intact and at the level of individual synapses is crucial for understanding the brain in both health and disease, according to Chung. This capability allows scientists to explore questions using the same brain, rather than different brains.The new technology pipeline allows scientists to study various phenomena in the same brain without causing any damage to the tissue. This makes it possible to create a comprehensive picture of the entire system. This technology makes the tissues highly resistant and allows them to be re-labeled multiple times in order to study different cells or molecules for years. Chung’s team has already used 20 different antibody labels to highlight different cells and proteins, and they plan to expand that to a hundred or more in the future.”We are able to observe various functional components such as cells, their shape, connectivity, subcellular structures, and synaptic connections within the same brain. This is particularly important due to the significant individual differences in the human brain and the value of human brain samples,” Chung explained. “With this technology pipeline, we can effectively extract all these crucial features from the same brain in a fully integrated way.”
Additionally, the pipeline has a relatively high scalability and throughput, allowing us to image an entire brain hemisphere in just 100 hours once it is prepared, as opposed to many
Having a large number of brain images from different sources and modalities allows for a diverse representation of demographics, disease states, and other factors, which can lead to more reliable comparisons and stronger statistical power. Chung envisions the creation of a brain bank with fully imaged brains that can be analyzed and re-labeled for new studies, similar to the comparisons made in the new paper between Alzheimer’s and non-Alzheimer’s hemispheres.
Three key innovations
Chung faced significant challenges in achieving the advancements described in the paper.
background in optics and imaging, developed a system for rapidly imaging the entire brain slice at high resolution, which they called “tomo-seq.”
MIT has assembled a team of three highly skilled and accomplished scientists to work on a groundbreaking project. These individuals, Ji Wang, Juhyuk Park, and Webster Guan, have played pivotal roles in developing three major innovations. Ji Wang created the “Megatome,” a device capable of slicing intact human brain hemispheres without causing any damage. Juhyuk Park developed a special chemistry that allows the brain slices to be clear, flexible, durable, expandable, and easily labeled repeatedly, known as “mELAST.” Webster Guan, with a background in optics and imaging, contributed by creating a system called “tomo-seq” that rapidly images the entire brain slice at a high resolution.Wang, a software developer, has a talent for creating computational systems. One of his creations, “UNSLICE,” is able to reconstruct each hemisphere of the brain in full 3D, including the precise alignment of blood vessels and neural axons. This technology allows for imaging the entire human brain at subcellular resolution without the need to slice it first, which is a challenge due to its thickness and opacity. This innovation has been developed at LifeCanvas Technologies, a company founded by Chung.The vibratome slicer has been improved to vibrate faster from side to side and create wider slices than previous models. This new design also ensures that the instrument stays perfectly aligned, resulting in slices that retain all anatomical information without any loss during separation. Additionally, the vibratome can cut thicker slabs of tissue at a faster rate, allowing for an entire hemisphere to be sliced in a day rather than over the course of months.
One of the key factors enabling thicker slabs in the pipeline is the mELAST hydrogel, engineered by Park. This hydrogel infuses the brain sample, making it optically clear and virtually indestructible.The samples in Chung’s lab are both compressible and expandable, making them adaptable to other chemical engineering technologies developed recently. They can be quickly infused with antibody labels that highlight cells and proteins of interest. The lab has also customized a light sheet microscope, which can image a whole hemisphere down to individual synapses in about 100 hours, according to the authors of the study. Park, who is now an assistant professor at Seoul National University in South Korea, collaborated on this technology. The advanced polymeric network fine-tunes the physicochemical properties of tissues, enabling multiplexed multiscale imaging of the intact human body.During the rainy season, it is important to take precautions,” Park explained. Once each slab is completely imaged, the goal is to then use computational methods to reconstruct a complete image of the entire hemisphere. Guan’s UNSLICE accomplishes this at various scales. For example, at the intermediate, or “meso” scale, it algorithmically follows the blood vessels entering one layer from neighboring layers and connects them. However, it also takes a more detailed approach. In order to further align the slabs, the team intentionally marked adjacent neural axons with different colors (similar to the wires in an electrical fixture). This allowed UNSLICE to match layers based on the tracing of the axons, Chung explained. Guan is currently working at LifeCanvas.The researchers in the study provide numerous examples of the capabilities of the pipeline. The first figure illustrates how the imaging allows for comprehensive labeling of an entire hemisphere and then the ability to zoom in from brainwide structures to circuits, individual cells, and even subcellular components like synapses. Other visual aids show the variety of labeling, revealing long axonal connections and the abundance and shape of different cell types, including neurons, astrocytes, and microglia.
Investigating Alzheimer’s
For years, the study has been exploring, Aris Chung and co-author Matthew Frosch, who is an Alzheimer’s researcher and the director of the brain bank at Massachusetts General Hospital, have worked together to study and analyze Alzheimer’s disease brains. Using a new pipeline, they began exploring without a specific plan, starting by identifying where they observed the most significant loss of neurons in the disease sample compared to the control within a slab of tissue. They then followed their curiosity, taking advantage of the technology to conduct a series of detailed investigations, which are discussed in the paper.
Chung explained, “We didn’t plan out all of these experiments in advance. We just let our curiosity guide us as the technology allowed us to do.”It began with the statement, “Alright, let’s visualize this section and observe what we find.” We pinpointed areas of the brain with significant loss of neurons, so let’s examine what’s happening there. “Let’s delve deeper.” We then utilized a variety of markers to identify and understand the connections between disease-causing factors and various cell types.
“This method allows us to have nearly unlimited access to the tissue,” Chung explained. “We can always revisit and explore something new.”
They concentrated most of their analysis on the orbitofrontal cortex in each hemisphere. One of the numerous findings they made was that the loss of synapses was focused in areas where the
There was a direct overlap with amyloid plaques. In areas without plaques, the brain with Alzheimer’s had the same high synapse density as the one without the disease.
Chung said that with just two samples, the team is not drawing any conclusions about the nature of Alzheimer’s disease. The study’s purpose is to show that there is now the capability to fully image and deeply analyze whole human brain hemispheres for research.
It’s important to note that the technology can be applied to many other tissues in the body, not just brains.
“We believe that this scalable technology platform will advance our research”
The authors concluded that understanding human organ functions and disease mechanisms is crucial for the development of new therapies. In addition to Park, Wang, Guan, Chung and Frosch, other authors of the paper include Lars A. Gjesteby, Dylan Pollack, Lee Kamentsky, Nicholas B. Evans, Jeff Stirman, Xinyi Gu, Chuanxi Zhao, Slayton Marx, Minyoung E. Kim, Seo Woo Choi, Michael Snyder, David Chavez, Clover Su-Arcaro, Yuxuan Tian, Chang Sin Park, Qiangge Zhang, Dae Hee Yun, Mira Moukheiber, Guoping Feng, X. William Yang, C. Dirk Keene, Patrick R. Hof, Satrajit S. Ghosh, and Laura J. Brattain. The National Institute of Health provided the primary funding for the work.The organizations involved in this project include the Institutes of Health, The Picower Institute for Learning and Memory, The JPB Foundation, and the NCSOFT Cultural Foundation.