Evan Murray,1,2,10 Jae Hun Cho,3,10 Daniel Goodwin,5,10 Taeyun Ku,2,4,10 Justin Swaney,3,10 Sung-Yon Kim,2 Heejin Choi,2,4 Young-Gyun Park,2,4 Jeong-Yoon Park,2,4 Austin Hubbert,3 Margaret McCue,1,4 Sara Vassallo,2,4 Naveed Bakh,3 Matthew P. Frosch,6 Van J. Wedeen,7 H. Sebastian Seung,5,8 and Kwanghun Chung1,2,3,4,9,*
1Department of Brain and Cognitive Sciences
2Institute for Medical Engineering and Science
3Department of Chemical Engineering
4Picower Institute for Learning and Memory Massachusetts Institute of Technology, Cambridge, MA 02139, USA
5Simons Center for Data Analysis, 160 Fifth Avenue, 8th Floor, New York, NY 10010, USA
6C.S. Kubik Laboratory of Neuropathology, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
7Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
8Princeton Neuroscience Institute and Computer Science Department, Princeton University, Princeton, NJ 08544, USA
9Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
10Co-first author
*Correspondence: Kwanghun Chung
Summary
Combined measurement of diverse molecular and anatomical traits that span multiple levels remains a major challenge in biology. Here, we introduce a simple method that enables proteomic imaging for scalable, integrated, high-dimensional phenotyping of both animal tissues and human clinical samples. This method, termed SWITCH, uniformly secures tissue architecture, native biomolecules, and antigenicity across an entire system by synchronizing the tissue preservation reaction. The heat- and chemical-resistant nature of the resulting framework permits multiple rounds (>20) of relabeling. We have performed 22 rounds of labeling of a single tissue with precise co-registration of multiple datasets. Furthermore, SWITCH synchronizes labeling reactions to improve probe penetration depth and uniformity of staining. With SWITCH, we performed combinatorial protein expression profiling of the human cortex and also interrogated the geometric structure of the fiber pathways in mouse brains. Such integrated high-dimensional information may accelerate our understanding of biological systems at multiple levels.