Quantitative validation of immunofluorescence and lectin staining using reduced CLARITY acrylamide formulations
- 364 Downloads
The CLARITY technique enables three-dimensional visualization of fluorescent-labeled biomolecules in clarified intact brain samples, affording a unique view of molecular neuroanatomy and neurocircuitry. It is therefore, essential to find the ideal combination for clearing tissue and detecting the fluorescent-labeled signal. This method requires the formation of a formaldehyde–acrylamide fixative-generated hydrogel mesh through which cellular lipid is removed with sodium dodecyl sulfate. Several laboratories have used differential acrylamide and detergent concentrations to achieve better tissue clearing and antibody penetration, but the potential effects upon fluorescent signal retention is largely unknown. In an effort to optimize CLARITY processing procedures we performed quantitative parvalbumin immunofluorescence and lectin-based vasculature staining using either 4 or 8% sodium dodecyl sulfate detergent in combination with different acrylamide formulas in mouse brain slices. Using both confocal and CLARITY-optimized lightsheet microscope-acquired images, we demonstrate that 2% acrylamide monomer combined with 0.0125% bis-acrylamide and cleared with 4% sodium dodecyl sulfate generally provides the most optimal signal visualization amongst various hydrogel monomer concentrations, lipid removal times, and detergent concentrations.
KeywordsCLARITY Immunofluorescence Imaging Cortex Vasculature
We would like to thank Drs. Maria Waselus and Aram Parsegian in reviewing the present manuscript. We also greatly appreciate the efforts of Mr. James Stewart and Drs. Qiang Wei and Elaine Hebda-Bauer for assistance with animal care and obtaining animals for preliminary experiments. For technical advice regarding CLARITY procedures we wish to thank Drs. Robert Thompson and Hui Li as well as Mr. Tom Dixon. This work was supported by NIH: R01MH104261, ONR N00014-12-1-0366, Hope for Depression Research Foundation, and Pritzker Neuropsychiatric Research Consortium.
Compliance with ethical standards
Conflict of interest
For the current study, we report no financial or non-financial conflict of interest.
Human rights and animal participants statements
All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.
This work was supported by NIH: R01MH104261, ONR N00014-12-1-0366, Hope for Depression Research Foundation, and Pritzker Neuropsychiatric Research Consortium.
ESM_4: 3D visualization of PV+ interneurons after surface rendering using Amira. Color coding represents segmented individual neurons immunostained for PV (white) with signal above threshold and assigned automatically in Amira software during quantitation. Video can be viewed using QuickTime or VLC media player. (MPG 409690 KB)
ESM_5: 3D visualization of cortical PV+ interneurons and lectin-stained vasculature. Mouse brains were perfused with 2% acrylamide and cleared with 4% SDS. This movie first shows a series of xy-plane images acquired on a confocal microscope followed by a maximum intensity projection 3D volume rendering of PV cells (red) and vasculature (green) in Imaris software. Video can be viewed using QuickTime or VLC media player. (MP4 170795 KB)
ESM_6: Maximum intensity projected 3D visualization of coronal slice images acquired with a COLM system. Imaris rendering shows neurons immunostained for PV (red) and tyrosine hydroxylase (white) with lectin-stained vasculature (green) in brain perfused with 2% acrylamide and cleared with 4% SDS. Fly through cortical area represents the region of interest considered for quantitation which was kept consistent across samples and groups. TH+ fibers represent nigrostriatal efferents. Video can be viewed using QuickTime or VLC media player. (MP4 166521 KB)
ESM_7: Magnified right hemisphere view of raw images acquired using a COLM system. Dorsal half of the right hemisphere from a coronal brain slice is visualized in a series of xy-plane images recorded in Amira. PV+ neurons and vasculature are in red and green, respectively. Video can be viewed using QuickTime or VLC media player. (MPG 170208 KB)
ESM_8: Surface-rendered post-quantification animation in Amira. Color coded individual PV+ neurons and lectin-stained vasculature (blue) within the quantified region of interest captured with a COLM system. Video can be viewed using QuickTime or VLC media player. (MPG 287748 KB)
ESM_9: Tyrosine hydroxylase (TH) expressing neuronal cell bodies and fibers. A series of xy-plane images show TH positive cell bodies in substantia nigra pars compacta (SNc) and ventral tegmental area (VTA). Projections from SNc can be seen innervating striatum via nigrostriatal pathway whereas projections from VTA are directed towards cortex. TH positive cell bodies can also be seen around paraventricular nucleus and zona incerta regions in hypothalamus. Movie derived from brain perfused with 2% acrylamide monomer, cleared with 4% SDS and imaged using a COLM with 10x objective. (MPG 65662 KB)
- Ando K, Laborde Q, Lazar A, Godefroy D, Youssef I, Amar M, Pooler A, Potier MC, Delatour B, Duyckaerts C (2014) Inside Alzheimer brain with CLARITY: senile plaques, neurofibrillary tangles and axons in 3-D. Acta Neuropathol 128(3):457–459. https://doi.org/10.1007/s00401-014-1322-y CrossRefPubMedPubMedCentralGoogle Scholar
- Chang EH, Argyelan M, Aggarwal M, Chandon TS, Karlsgodt KH, Mori S, Malhotra AK (2017) The role of myelination in measures of white matter integrity: Combination of diffusion tensor imaging and two-photon microscopy of CLARITY intact brains. Neuroimage 147:253–261. https://doi.org/10.1016/j.neuroimage.2016.11.068 CrossRefPubMedGoogle Scholar
- Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K (2013) Structural and molecular interrogation of intact biological systems. Nature 497(7449):332–337. https://doi.org/10.1038/nature12107 CrossRefPubMedPubMedCentralGoogle Scholar
- Costantini I, Ghobril JP, Di Giovanna AP, Allegra Mascaro AL, Silvestri L, Mullenbroich MC, Onofri L, Conti V, Vanzi F, Sacconi L, Guerrini R, Markram H, Iannello G, Pavone FS (2015) A versatile clearing agent for multi-modal brain imaging. Sci Rep 5:9808. https://doi.org/10.1038/srep09808 CrossRefPubMedPubMedCentralGoogle Scholar
- Kim SY, Cho JH, Murray E, Bakh N, Choi H, Ohn K, Ruelas L, Hubbert A, McCue M, Vassallo SL, Keller PJ, Chung K (2015) Stochastic electrotransport selectively enhances the transport of highly electromobile molecules. Proc Natl Acad Sci USA 112(46):E6274–E6283. https://doi.org/10.1073/pnas.1510133112 CrossRefPubMedPubMedCentralGoogle Scholar
- Lee H, Park JH, Seo I, Park SH, Kim S (2014) Improved application of the electrophoretic tissue clearing technology, CLARITY, to intact solid organs including brain, pancreas, liver, kidney, lung, and intestine. BMC Dev Biol 14:48. https://doi.org/10.1186/s12861-014-0048-3 CrossRefPubMedPubMedCentralGoogle Scholar
- Lerner TN, Shilyansky C, Davidson TJ, Evans KE, Beier KT, Zalocusky KA, Crow AK, Malenka RC, Luo L, Tomer R, Deisseroth K (2015) Intact-brain analyses reveal distinct information carried by SNc dopamine subcircuits. Cell 162(3):635–647. https://doi.org/10.1016/j.cell.2015.07.014 CrossRefPubMedPubMedCentralGoogle Scholar
- Magliaro C, Callara AL, Mattei G, Morcinelli M, Viaggi C, Vaglini F, Ahluwalia A (2016) clarifying CLARITY: quantitative optimization of the diffusion based delipidation protocol for genetically labeled tissue. Front Neurosci 10:179. https://doi.org/10.3389/fnins.2016.00179 CrossRefPubMedPubMedCentralGoogle Scholar
- Paxinos G, Franklin KBJ (2001) The mouse brain in stereotaxic coordinates. 2nd edn, Academic Press, San DiegoGoogle Scholar
- Phillips J, Laude A, Lightowlers R, Morris CM, Turnbull DM, Lax NZ (2016) Development of passive CLARITY and immunofluorescent labelling of multiple proteins in human cerebellum: understanding mechanisms of neurodegeneration in mitochondrial disease. Sci Rep 6:26013. https://doi.org/10.1038/srep26013 CrossRefPubMedPubMedCentralGoogle Scholar
- Stefaniuk M, Gualda EJ, Pawlowska M, Legutko D, Matryba P, Koza P, Konopka W, Owczarek D, Wawrzyniak M, Loza-Alvarez P, Kaczmarek L (2016) Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene. Sci Rep 6:28209. https://doi.org/10.1038/srep28209 CrossRefPubMedPubMedCentralGoogle Scholar
- Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V (2015) Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Protoc 10(11):1860–1896. https://doi.org/10.1038/nprot.2015.122 CrossRefPubMedPubMedCentralGoogle Scholar
- Ye L, Allen WE, Thompson KR, Tian Q, Hsueh B, Ramakrishnan C, Wang AC, Jennings JH, Adhikari A, Halpern CH, Witten IB, Barth AL, Luo L, McNab JA, Deisseroth K (2016) Wiring and molecular features of prefrontal ensembles representing distinct experiences. Cell 165(7):1776–1788. https://doi.org/10.1016/j.cell.2016.05.010 CrossRefPubMedPubMedCentralGoogle Scholar
- Zhang MD, Tortoriello G, Hsueh B, Tomer R, Ye L, Mitsios N, Borgius L, Grant G, Kiehn O, Watanabe M, Uhlen M, Mulder J, Deisseroth K, Harkany T, Hokfelt TG (2014) Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury. Proc Natl Acad Sci USA 111(12):E1149–E1158. https://doi.org/10.1073/pnas.1402318111 CrossRefPubMedPubMedCentralGoogle Scholar