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* These authors contributed equally
The present protocol provides a step-by-step procedure for rapid and simultaneous optical clearing, muti-round labeling, and 3D volumetric reconstruction of tens of postmortem human brain sections by combining the (SWITCH - H2O2 - Antigen Retrieval - 2,2'-thiodiethanol [TDE]) SHORT tissue transformation technique with light-sheet fluorescence microscopy imaging in a routinely high-throughput protocol.
Despite the numerous clearing techniques that emerged in the last decade, processing postmortem human brains remains a challenging task due to its dimensions and complexity, which make imaging with micrometer resolution particularly difficult. This paper presents a protocol to perform the reconstruction of volumetric portions of the human brain by simultaneously processing tens of sections with the SHORT (SWITCH - H2O2 - Antigen Retrieval - 2,2'-thiodiethanol [TDE]) tissue transformation protocol, which enables clearing, labeling, and sequential imaging of the samples with light-sheet fluorescence microscopy (LSFM). SHORT provides rapid tissue clearing and homogeneous multi-labeling of thick slices with several neuronal markers, enabling the identification of different neuronal subpopulations in both white and grey matter. After clearing, the slices are imaged via LSFM with micrometer resolution and in multiple channels simultaneously for a rapid 3D reconstruction. By combining SHORT with LSFM analysis within a routinely high-throughput protocol, it is possible to obtain the 3D cytoarchitecture reconstruction of large volumetric areas at high resolution in a short time, thus enabling comprehensive structural characterization of the human brain.
Analyzing the 3D molecular organization and cytoarchitecture of large volumes of the human brain requires optical transparency of specimens, achieved through protocols with extensive processing time. Optical clearing techniques were developed to minimize heterogeneity in refractive index (RI) within the tissues, thereby reducing light scattering and increasing the light penetration depth for high-resolution imaging1,2,3,4,5. Current advances in clearing and deep tissue-labeling methods allow volumetric imaging of intact rodent organs and embryos by exploiting cutting-edge microscopy techniques6,7,8,9,10,11,12.
However, volumetric 3D reconstruction of large areas of the postmortem human brain still represents a challenging task compared with model organisms. The complex biological composition and the variable postmortem fixation and storage conditions can compromise the tissue clearing efficiency, the antibody penetration depth, and the epitope recognition13,14,15,16,17,18,19. Moreover, mechanical tissue sectioning and subsequent clearing and labeling of each slice is still required to achieve an efficient clearing and uniform labeling of large human brain areas, resulting in long processing times and the need for sophisticated custom equipment, compared with model organisms15,20,21,22.
The SWITCH - H2O2 - antigen Retrieval -TDE (SHORT) tissue transformation technique has been developed specifically to analyze large volumes of the human brain18,23. This method employs the tissue structural preservation of the SWITCH protocol11 and high concentrations of peroxide hydrogen to decrease tissue autofluorescence, in combination with epitope restoration. SHORT allows uniform staining of human brain slices with markers for different neuronal subtypes, glial cells, vasculature, and myelinated fibers18,24. Its results are compatible with the analysis of both low- and high-density proteins. The resulting high transparency levels and uniform labeling enable volumetric reconstruction of thick slices with fluorescence microscopy, in particular, for fast acquisition light-sheet apparatus can be used18,24,25,26,27.
In this work, we describe how the SHORT tissue transformation technique can be used for simultaneous clearing and multi-round labeling of tens of formalin-fixed human brain sections. Four different fluorescent markers can be used together, leading to the identification of different cellular sub-populations. After clearing, high-resolution volumetric imaging can be performed with fluorescence microscopy. Here, we used a custom-made inverted LSFM18,24,25,26,27, which enables fast optical sectioning of the sample and rapid acquisition of multiple channels in parallel. With this routinely high-throughput protocol, it is possible to obtain a comprehensive cellular and structural characterization with a sub-cellular resolution of large areas of the human brain as already demonstrated in the mapping of an entire Broca's area23.
Formalin-fixed human tissue samples were provided by the Department of Neuropathology at the Massachusetts General Hospital (MGH) Autopsy Service (Boston, USA). Written consent was obtained from healthy participants prior to death, following IRB-approved tissue collection protocols from the Partners Institutional Biosafety Committee (PIBC, protocol 2003P001937). The authorization documents are kept with the MGH Autopsy Services in Boston, MA, United States, and are available upon request.
1. Agarose embedding and sample cutting
2. Tissue fixation
NOTE: All the solutions used in the following protocol are prepared in large volumes, sufficient to process all the slices of the same tissue block and minimize the technical variability and reduce the time for individual steps.
3. Inactivation and clearing
NOTE: Reactive glutaraldehyde in the samples must be inactivated by incubation with an inactivation solution consisting of 1x PBS pH 7.4, 4% w/v acetamide, 4% w/v glycine, pH 9.0. The solution can be stored at 4 °C for up to 3 months. To remove lipids and make the tissue transparent, we use the clearing solution consisting of 200 mM sodium dodecyl sulfate (SDS), 20 mM sodium sulfite (Na2SO3), and 20 mM boric acid (H3BO3), pH 9.0. The solution must be stored at RT as SDS precipitates at 4 °C. All the following steps will be done in tubes filled with the solution.
4. Immunolabeling
NOTE: Before the labeling step, it is necessary to remove the residual SDS, reduce the autofluorescence, and unmask the epitopes with an antigen retrieval solution consisting of 10 mM Tris base, 1 mM EDTA, and 0.05% v/v Tween 20, pH 9. The solution's pH of 9 is optimized for an efficient retrieval process; Tris base acts as a buffering agent to maintain a stable pH environment; EDTA, which is a chelating agent, enhances the antigen's accessibility. The nonionic detergent Tween 20 aids in improving the permeability of the tissue. This solution can be stored at 4 °C. It is important to note that hydrogen peroxide combined with the antigen retrieval step have a synergistic effect in reducing the autofluorescence signal, by breaking down and/or modifying the endogenous fluorophores responsible for non-specific background signal (such as lipofuscin).
5. Refractive index matching
NOTE: To achieve a high level of transparency, it is necessary to homogenize the tissue refractive index. Here we use 2,2'-thiodiethanol (TDE) diluted in 1x PBS. TDE solutions must be stored at RT.
6. Sample mounting
NOTE: To facilitate sample mounting and LSFM image acquisition, we use a custom-made, sealed sample holder (termed "sandwich"), which consists of three parts: a microscope slide, a spacer, and a coverslip.
7. Stripping
NOTE: The structural preservation and the enhanced epitope accessibility of SHORT allow multi-round labeling of slices by removing the antibodies and restaining the samples with other markers.
The protocol described here enables the simultaneous treatment of multiple slices, ranging in thickness from 100 µm to 500 µm, using the SHORT method. This approach significantly reduces the overall processing time for the entire procedure. In this work, we provide a comprehensive description of the entire pipeline (Figure 1) for processing multiple postmortem human brain thick sections simultaneously and we demonstrate the protocol on 24 slices at once (Figure...
High-resolution imaging and 3D reconstruction of large human brain areas require mechanical tissue sectioning followed by optical clearing and immunolabeling of single slices. The protocol presented here describes how the SHORT tissue transformation method can be used for rapid and simultaneous processing of multiple human brain thick sections for 3D brain reconstruction with a subcellular resolution with LSFM.
Unlike other approaches, with the SHORT method the clearing and multi-labeling step...
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
We thank Bruce Fischl, Massachusetts General Hospital, A.A. Martinos Center for Biomedical Imaging, Department of Radiology, for providing the human brain specimens analyzed in this study. This project received funding from the European Union's Horizon 2020 Research and Innovation Framework Programme under grant agreement No. 654148 (Laserlab-Europe), from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3), from the General Hospital Corporation Center of the National Institutes of Health under award number U01 MH117023, and from the Italian Ministry for Education in the framework of Euro-Bioimaging Italian Node (ESFRI research infrastructure). Finally, this research was carried out with the contribution of "Fondazione CR Firenze." The content of this work is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Figure 1 was created with BioRender.com.
Name | Company | Catalog Number | Comments |
2,2'-thiodiethanol | Merck Life Science S.R.L. | 166782 | |
Acetamide >= 99.0% (GC) | Merck Life Science S.R.L. | 160 | |
Agarose High EEO | Merck Life Science S.R.L. | A9793 | |
Boric Acid | Merck Life Science S.R.L. | B7901 | |
Compressome VF-900-0Z Microtome | Precisionary | / | |
Coverslips | LaserOptex | / | customized |
Ethylenediaminetetraacetic acid disodium salt dihydrate | Merck Life Science S.R.L. | E5134 | |
Glutaraldehyde | Merck Life Science S.R.L. | G7651 | |
Glycine | Santa Cruz Biotechnology | SC_29096 | |
Hydrogen Peroxide 30% | Merck Life Science S.R.L. | ||
Incubator ISS-4075 | Lab companion | / | |
Light-sheet fluorescence microscopy (LSFM) | / | / | custom-made |
Loctite Attak | Henkel Italia srl | / | |
Microscope slides | Laborchimica | / | customized |
Phospate buffer saline tablet | Merck Life Science S.R.L. | P4417 | |
Picodent Twinsil | Picodent | 13005002 | out of production |
Potassium Hydrogen Phtalate | Merck Life Science S.R.L. | P1088 | |
Sodium Azide | Merck Life Science S.R.L. | S2002 | |
Sodium Dodecyl Sulfate | Merck Life Science S.R.L. | L3771 | |
Sodium Sulfite | Merck Life Science S.R.L. | S0505 | |
Spacers | Microlaser srl | customized | |
Sputum Containers (dishes with screw lids) | Paul Boettger GmbH & Co. KG | 07.061.2000 | |
Tris Base | PanReac AppliChem (ITW reagents) | A4577,0500 | |
Triton X-100 | Merck Life Science S.R.L. | T8787 | |
Tubes | Sarstedt | 62 547254 | |
Tween 20 | Merck Life Science S.R.L. | P9416 | |
Vibratome VT1000S | Leica Biosystem | / | |
Water bath | Memmert | WNB 7-45 | |
Antibodies and Dyes | |||
Alexa Fluor 488 AffiniPure Alpaca Anti-Rabbit IgG (H+L) | Jackson Immuno Reasearch | 611-545-215 | Dilution used, 1:200 |
Alexa Fluor 488 AffiniPure Bovine Anti-Goat IgG (H+L) | Jackson Immuno Reasearch | 805-545-180 | Dilution used, 1:200 |
Alexa Fluor 647 AffiniPure Alpaca Anti-Rabbit IgG (H+L) | Jackson Immuno Reasearch | 611-605-215 | Dilution used, 1:200 |
Anti-NeuN Antibody | Merck Life Science S.R.L. | ABN91 | Dilution used, 1:100 |
Anti-Parvalbumin antibody (PV) | Abcam | ab32895 | Dilution used, 1:200 |
Anti-Vimentin antibody [V9] - Cytoskeleton Marker (VIM) | Abcam | ab8069 | Dilution used, 1:200 |
Calretinin Polyclonal antibody | ProteinTech | 12278_1_AP | Dilution used, 1:200 |
DAPI | ThermoFisher | D3571 | Dilution used, 1:100 |
Donkey Anti-Mouse IgG H&L (Alexa Fluor 568) | Abcam | ab175700 | Dilution used, 1:200 |
Donkey Anti-Mouse IgG H&L (Alexa Fluor 647) | Abcam | ab150107 | Dilution used, 1:200 |
Donkey Anti-Rabbit IgG H&L (Alexa Fluor 568) | Abcam | ab175470 | Dilution used, 1:200 |
Donkey Anti-Rat IgG H&L (Alexa Fluor 568) preadsorbed | Abcam | ab175475 | Dilution used, 1:200 |
Goat Anti-Chicken IgY H&L (Alexa Fluor 488) | Abcam | ab150169 | Dilution used, 1:500 |
Goat Anti-Chicken IgY H&L (Alexa Fluor 568) | Abcam | ab175711 | Dilution used, 1:500 |
Goat Anti-Chicken IgY H&L (Alexa Fluor 647) | Abcam | ab150171 | Dilution used, 1:500 |
Goat Anti-Rabbit IgG H&L (Alexa Fluor 488) | Abcam | ab150077 | Dilution used, 1:200 |
Recombinant Alexa Fluor 488 Anti-GFAP antibody | Abcam | ab194324 | Dilution used, 1:200 |
Somatostatin Antibody YC7 | Santa Cruz Biotechnology | sc-47706 | Dilution used, 1:200 |
Vasoactive intestinal peptide (VIP) | ProteinTech | 16233-1-AP | Dilution used, 1:200 |
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