Structural and molecular interrogation of intact biological systems

By Kwanghun Chung, Jenelle L. Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, A. Andalman, T. J. Davidson, J. J. Mirzabekov, K. Zalocusky, J. Mattis, A. Denisin and 6 more. Nature, 2013

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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.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/880d48407b38b354dab63003ef3058da4059b24f

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Citations in the corpus

Closed-loop and activity-guided optogenetic control. (2015, positive): “…Smith, 2007) and wiring information (see circuit-targeting strategies reviewed below and Bock et al., 2011) could be further obtained (for example, leveraging recent advances in multiround molecular and anatomical analysis in large, intact cleared brains; Chung et al., 2013; Tomer et al., 2014).”
Memory engrams: Recalling the past and imagining the future (2020, methodology): “Roy and colleagues tagged cells active at training and those active at recall throughout the brain in the same mouse using a CLARITYlike tissue-clearing technique (101) dubbed SHIELD (stabilization under harsh conditions via intramolecular epoxide linkages to prevent degradation) (102), thereby perm”
Simple, scalable proteomic imaging for high-dimensional profiling of intact systems (2015, neutral): “For instance, the CLARITY technique has demonstrated three rounds of immunostaining of mouse brain tissue (Chung et al., 2013).”
Gamma frequency entrainment attenuates amyloid load and modifies microglia (2016, positive): “CLARITY.”
Clarifying Tissue Clearing (2015, neutral): “This lipid removal process can result in a high degree of protein loss (24%–41%), which lowers epitope concentrations and potentially weakens immunostaining (Chung et al., 2013).”
Three-dimensional intact-tissue sequencing of single-cell transcriptional states (2018, neutral): “S.V. generated the CLARITY data with PV transgenicmice.”