RF1 - Chung 1RF1MH121270-01

Highly specific, renewable, and cost-effective antibody toolbox for 3D proteomic phenotyping of the brain

Overlay of multi-round immunostained images registered based on preserved YFP signals. YFP: green, NeuN: red; Neurofilament-H: rhite; Calretinin: dark blue; Calbindin: light blue; GFAP: dark purple; Parvalbumin: light blue; SMI-32: yellow.


System-wide analysis of cell types in the brain is essential for understanding how complex cellular interactions give rise to various brain functions. Rapidly evolving tissue transformation and clearing technologies have enabled three-dimensional (3D) imaging and phenotyping of intact brains at unprecedented resolution. In particular, proteomic imaging techniques can provide multiscale anatomical, morphological, molecular, and functional information in both non-human and human brains. Highly specific antibodies, once rigorously validated, should enable spatial mapping of the brain proteome and corresponding cellular architectures; however, the unique potential of the 3D proteomic imaging is fundamentally limited by (1) incompatibility of existing antibodies with the emerging tissue transformation approaches, (2) poor specificity of commercially available antibodies, (3) lack of antibodies for newly identified targets, and (4) prohibitively high antibody cost for brain-wide labeling applications. The goal of this project is to democratize the 3D proteomic imaging approaches by creating a comprehensive open-source library of high-quality monoclonal antibodies (mAbs) that are truly renewable, scalable, and compatible with a wide range of conventional and emerging tissue processing technologies. In addition, we will develop robust and scalable protocols for uniform staining of intact brain tissues with new mAb tools. We envision that this antibody library and protocols will allow the research community to interrogate brain structure and function, including complex intercellular relationships at multiple scales.

Project Leadership

Kwanghun Chung, Ph.D. (Multiple Principal Investigator)
Associate Professor, Department of Chemical Engineering
Institute for Medical Engineering and Science (IMES)
Picower Institute for Learning and Memory
Massachusetts Institute of Technology


Heng Zhu, Ph.D. (Multiple Principal Investigator)
Professor, Dept. of Pharmacology & Mol Sciences
Johns Hopkins School of Medicine


Daniel Eichinger, Ph.D. (Multiple Principal Investigator)
Chief Scientific Officer
CDI Laboratories


Ignacio Pino, D.V.M. (Multiple Principal Investigator)
Chief Executive Officer
CDI Laboratories

Project Data Types

  • 3000 mouse monoclonal antibodies to 300 targets
  • An openly available database of staining information and fluorescent microscopy images for each antibody
  • Recombinant antibody library consisting of cloned sequences of specific antibodies
  • Staining protocols for optimal, cost effective use of created antibodies

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