3D molecular phenotyping of intact brain tissue via high-throughput active immunohistochemistry

Abstract. Molecular phenotyping has led to a growing appreciation of neural cell type diversity and function thereby transforming our understanding of the brain. Beyond first-order classification of cells as glial or neuronal, excitatory or inhibitory, it is now recognized that there are dozens of molecularly-defined cell types that differ in their morphology, connectivity, physiology, and gene and protein expression. Detection of protein in fixed tissues via immunohistochemistry (IHC) has been a major driver of cell type discovery, with a cell’s precise microenvironment within tissue (e.g. proximity to vasculature and extracellular deposits) providing essential physiological context. Such data have yielded a rich picture of how cellular topography varies by brain region and provides a robust backdrop to assess cell type-specific changes that occur in disease states, such as profound neurological disorders like Alzheimer’s and Parkinson’s disease. Despite the prevalence of IHC, its application has remained encumbered by the slow rate at which reagents such as IgG antibodies passively diffuse into tissue. Due to this bottleneck, tissues have traditionally been thinly sliced (≤ 50 µm) to facilitate uniform staining of features and make quantitative analyses reliable. CLARITY, iDISCO, and related techniques that optically-clear intact tissues by removing cell membrane lipids have offered a means to perform whole-brain IHC, as delipidation grants reagents easier access to deep tissue sites. However, labeling time remains a major bottleneck, with intact samples requiring weeks to months of incubation for labeling to reach the center. If whole organs could be labeled more quickly and practically it would provide a powerful tool to perform unbiased molecular phenotyping in mammalian models of development and neurological disorders. To this end LifeCanvas developed SmartLabel (SL), the world’s first whole-organ active immunostaining device that fully labels an entire mouse brain in just 24 hrs using proprietary stochastic electrotransport technology. SL additionally employs an affinity ramp, a method in which antibodies are evenly distributed throughout the tissue before binding to target proteins to produce labeling that is strikingly uniform in intensity from the sample’s surface to its core. During Phase I, we broadened SL’s applications by (1) extending SL’s rapid immunolabeling capability for tissues processed using iDISCO, (2) ensuring compatibility with key morphological, cell type, and neuronal activity markers such as c-Fos, (3) adapting the technology to work with diverse sample types such as human cerebral organoids, and (4) developing a prototype next-generation SL that performed simultaneous and cost-effective cohort-level immunolabeling of multiple organoids or adult mouse brains. Having completed all the Phase I project goals, we are now poised – in Phase II – to complete the development of the next generation SL, a dual function clearing and labeling device capable of rapid immunostaining and turnkey batch-processing of a wide range of neural sample types including tissues of different CNS/PNS origins and of various mammalian species. Additionally, we will continue in-house research to expand the number of validated antibodies against neuroscience-related targets by three-fold, and further enable DISCO users to adopt SL in their pipeline for rapid and uniform immunolabeling. Our Phase II goals are to commercialize the next generation SL, popularize active immunolabeling and thereby facilitate application of quantitative whole-sample molecular phenotyping analyses for a broader neuroscience community.