title: Structural and molecular interrogation of intact biological systems.
abstract: Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
authors.forename: Kwanghun
authors.initials: K
authors.lastname: Chung
authors.forename: Jenelle
authors.initials: J
authors.lastname: Wallace
authors.forename: Sung-Yon
authors.initials: SY
authors.lastname: Kim
authors.forename: Sandhiya
authors.initials: S
authors.lastname: Kalyanasundaram
authors.forename: Aaron S
authors.initials: AS
authors.lastname: Andalman
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Davidson
authors.forename: Julie J
authors.initials: JJ
authors.lastname: Mirzabekov
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Zalocusky
authors.forename: Joanna
authors.initials: J
authors.lastname: Mattis
authors.forename: Aleksandra K
authors.initials: AK
authors.lastname: Denisin
authors.forename: Sally
authors.initials: S
authors.lastname: Pak
authors.forename: Hannah
authors.initials: H
authors.lastname: Bernstein
authors.forename: Charu
authors.initials: C
authors.lastname: Ramakrishnan
authors.forename: Logan
authors.initials: L
authors.lastname: Grosenick
authors.forename: Viviana
authors.initials: V
authors.lastname: Gradinaru
authors.forename: Karl
authors.initials: K
authors.lastname: Deisseroth
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D003432:Cross-Linking Reagents / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate / Q000737:chemistry; D021621:Imaging, Three-Dimensional / Q000379:methods*; D017403:In Situ Hybridization / Q000379:methods; D008055:Lipids / Q000302:isolation & purification; D051379:Mice; D057054:Molecular Imaging / Q000379:methods*; D010539:Permeability; D010641:Phenotype; D012542:Scattering, Radiation
chemical_list: D003432:Cross-Linking Reagents; D008055:Lipids; D005557:Formaldehyde; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate