POL Scientific / JBM / Volume 0 / Issue 0 / DOI: 10.14440/jbm.2025.0101
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RESEARCH ARTICLE

3D visualization of human colon tissue using a modified CUBIC-based tissue-clearing technique

Pavel Pavlov1† Andreas Kontny1† Neele Wagner1 Nikola Kolev2 Alexander Zlatarov2 Turgay Kalinov2 Anton B. Tonchev1*
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1 Department of Anatomy and Cell Biology, Faculty of Medicine, Medical University Varna, Varna 9002, Bulgaria
2 Department of General and Operative Surgery, Faculty of Medicine, Medical University Varna, Varna 9002, Bulgaria
JBM null , 0(0), e99010052; https://doi.org/10.14440/jbm.2025.0101
Submitted: 15 October 2024 | Revised: 19 December 2024 | Accepted: 7 January 2025 | Published: 4 February 2025
© by the Journal of Biological Methods published by POL Scientific. Licensee POL Scientific, USA. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

Background: Colorectal cancer represents one of the most common neoplastic diseases worldwide, making it a frequent focus in routine pathological analyses. Visualizing complex three-dimensional (3D) structures, such as nerves within tumors, requires thick tissue sections, which necessitates the use of optical tissue-clearing methods to achieve transparency. However, following tissue clearing, samples typically require advanced imaging techniques such as light-sheet and two-photon confocal microscopy, which are usually unavailable in standard histological laboratories. Objective: We aimed to demonstrate how a well-established tissue-clearing approach can be adapted for use in a routine histological laboratory, enabling a robust 3D visualization of nerve fibers in samples of both normal human colon and colon cancer tissues. Methods: We modified the “clear unobstructed brain/body imaging cocktails” method, originally developed for whole-brain imaging in mice, and applied it to human colon tissue samples measuring approximately 10 mm3, a standard size typically processed in pathological laboratories. Results: Our protocol, which integrates a tissue-clearing technique, enabled reliable immunofluorescent visualization of colonic nerve fibers labeled with anti-β3-tubulin antibodies. The labeled nerve fibers could be observed using a standard epifluorescence microscope, and high-quality 3D reconstructions were generated through a simple image analysis approach using the open-source software ilastik, which eliminates the need for confocal microscopy. Conclusion: The proposed steps provide a valuable method for researchers to visualize complex 3D structures, such as neural cells and processes, in both normal and tumor-transformed tissue settings.

Keywords
Clear unobstructed brain/body imaging cocktails
CUBIC
Tissue clearing
3D-imaging
Colon
Colorectal cancer
Funding
This work was supported by the European Regional Development Fund through the Operational Program “Science and Education for Smart Growth” (contract #BG05M2OP001- 1.002-0010-C01), the European Commission Horizon 2020 Framework Program (Project 856871–TRANSTEM), and the MU-Varna intramural research grants (16007/2016 and 19012/2019).
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Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be perceived as a potential conflict of interest.
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Journal of Biological Methods, Electronic ISSN: 2326-9901 Print ISSN: TBA, Published by POL Scientific