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Monasterio G, Morales RA, Bejarano DA, Abalo XM, Fransson J, Larsson L, Schlitzer A, Lundeberg J, Das S, Villablanca EJ. A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract. Nat Protoc 2024:10.1038/s41596-024-01001-2. [PMID: 38906985 DOI: 10.1038/s41596-024-01001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/19/2024] [Indexed: 06/23/2024]
Abstract
Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for proper biological function. To comprehensively characterize and understand the cell circuitry underlying biological processes within tissues, it is crucial to preserve their spatial information. Here we report a simple mounting technique to maximize the area of the tissue to be analyzed, encompassing the whole length of the murine gastrointestinal (GI) tract, from mouth to rectum. Using this method, analysis of the whole murine GI tract can be performed in a single slide not only by means of histological staining, immunohistochemistry and in situ hybridization but also by multiplexed antibody staining and spatial transcriptomic approaches. We demonstrate the utility of our method in generating a comprehensive gene and protein expression profile of the whole GI tract by combining the versatile tissue-rolling technique with a cutting-edge transcriptomics method (Visium) and two cutting-edge proteomics methods (ChipCytometry and CODEX-PhenoCycler) in a systematic and easy-to-follow step-by-step procedure. The entire process, including tissue rolling, processing and sectioning, can be achieved within 2-3 d for all three methods. For Visium spatial transcriptomics, an additional 2 d are needed, whereas for spatial proteomics assays (ChipCytometry and CODEX-PhenoCycler), another 3-4 d might be considered. The whole process can be accomplished by researchers with skills in performing murine surgery, and standard histological and molecular biology methods.
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Affiliation(s)
- Gustavo Monasterio
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - David A Bejarano
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Xesús M Abalo
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer Fransson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
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Liu CY, Polk DB. Cellular maps of gastrointestinal organs: getting the most from tissue clearing. Am J Physiol Gastrointest Liver Physiol 2020; 319:G1-G10. [PMID: 32421359 PMCID: PMC7468759 DOI: 10.1152/ajpgi.00075.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of modern methods to induce optical transparency ("clearing") in biological tissues has enabled the three-dimensional (3D) reconstruction of intact organs at cellular resolution. New capabilities in visualization of rare cellular events, long-range interactions, and irregular structures will facilitate novel studies in the alimentary tract and gastrointestinal systems. The tubular geometry of the alimentary tract facilitates large-scale cellular reconstruction of cleared tissue without specialized microscopy setups. However, with the rapid pace of development of clearing agents and current relative paucity of research groups in the gastrointestinal field using these techniques, it can be daunting to incorporate tissue clearing into experimental workflows. Here, we give some advice and describe our own experience bringing tissue clearing and whole mount reconstruction into our laboratory's investigations. We present a brief overview of the chemical concepts that underpin tissue clearing, what sorts of questions whole mount imaging can answer, how to choose a clearing agent, an example of how to clear and image alimentary tissue, and what to do after obtaining the image. This short review will encourage other gastrointestinal researchers to consider how utilizing tissue clearing and creating 3D "maps" of tissue might deepen the impact of their studies.
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Affiliation(s)
- Cambrian Y. Liu
- 1Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Saban Research Institute Children’s Hospital Los Angeles, Los Angeles, California
| | - D. Brent Polk
- 1Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Saban Research Institute Children’s Hospital Los Angeles, Los Angeles, California,2Department of Pediatrics, Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California Los Angeles, California
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Mortazavi F, Stankiewicz AJ, Zhdanova IV. Looking through Brains with Fast Passive CLARITY: Zebrafish, Rodents, Non-human Primates and Humans. Bio Protoc 2019; 9:e3321. [PMID: 33654828 DOI: 10.21769/bioprotoc.3321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/24/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
Recently developed CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ-hybridization-compatible Tis-sue-hYdrogel) technique renders the tissue transparent by removing lipids in the tissue, while preserving and stabilizing the cellular and subcellular structures. This provides effective penetration of diverse labeling probes, from primary and secondary antibodies to complementary DNA and RNA strands. Followed by high-resolution 3D imaging of neuronal cells and their projections in thick sections, tissue blocks, whole brains, or whole animals, CLARITY allows for superior quantitative analysis of neuronal tissue. Here, we provide our detailed protocol for PACT (Passive Clarity Technique) in brain tissue of diverse species, including human, non-human primate, rodents, and zebrafish. We describe the six principal steps: (1) Tissue fixation and preparation, (2) Passive lipid removal, (3) Immuno-labeling, (4) Optical clearing, (5) Imaging, (6) 3D visualization and quantification.
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Affiliation(s)
- Farzad Mortazavi
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alexander J Stankiewicz
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA.,Department of Preclinical Research, BioChron LLC, Worcester, Massachusetts 01605, USA
| | - Irina V Zhdanova
- Department of Preclinical Research, BioChron LLC, Worcester, Massachusetts 01605, USA
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Bossolani GDP, Pintelon I, Detrez JD, Buckinx R, Thys S, Zanoni JN, De Vos WH, Timmermans JP. Comparative analysis reveals Ce3D as optimal clearing method for in toto imaging of the mouse intestine. Neurogastroenterol Motil 2019; 31:e13560. [PMID: 30761698 DOI: 10.1111/nmo.13560] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/26/2018] [Accepted: 01/03/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND The intestinal wall has a complex topographical architecture. The multi-layered network of the enteric nervous system and its intercellular interactions are difficult to map using traditional section-based or whole-mount histology. With the advent of optical clearing techniques, it has become feasible to visualize intact tissue and organs in 3D. However, as yet, a gap still needs to be filled in that no in-depth analysis has been performed yet on the potential of different clearing techniques for the small intestine. AIM The goal of this study was to identify an optimal clearing protocol for in toto imaging of mouse intestinal tissue. METHODS Five aqueous-based clearing protocols (SeeDB2, CUBIC, ScaleS, Ce3D, and UbasM) and four organic reagent-based clearing protocols (3DISCO, iDISCO+, uDISCO, and Visikol® ) were assessed in segments of small intestine from CX3CR1GFP/GFP and wild-type mice. Following clearing, optical transparency, tissue morphology, green fluorescent protein (GFP) fluorescence retention, and compatibility with (immuno-)labeling were analyzed. KEY RESULTS All organic reagent-based clearing protocols-except for Visikol-rendered tissue highly transparent but led to substantial tissue shrinkage and deformation. Of the aqueous-based protocols, only Ce3D yielded full-thickness tissue transparency. In addition, Ce3D displayed excellent GFP retention and preservation of tissue morphology. CONCLUSIONS Ce3D emerged as a most efficient protocol for enabling rapid full-thickness 3D mapping of the mouse intestinal wall.
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Affiliation(s)
- Gleison D P Bossolani
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium.,Department of Morphological Sciences, State University of Maringá, Maringá, Brasil
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Jan D Detrez
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Roeland Buckinx
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
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Sandoval-Skeet N, Kaufman JA, Castro MJ, Al-Nakkash L. Genistein diet does not modify crypt morphology in the ob/ob mouse jejunum: a comparison of cryostat and clearing techniques. Diabetes Metab Syndr Obes 2018; 11:863-873. [PMID: 30568474 PMCID: PMC6276911 DOI: 10.2147/dmso.s182501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Diabetes is commonly associated with gastrointestinal dysfunction. We have previously shown that transepithelial short circuit current, Isc (chloride secretion), is significantly reduced in the jejunum from ob/ob mice vs lean controls, and consumption of 600 mg genistein/kg of diet (600 G) for 4 weeks significantly rescues Isc. We aimed to evaluate whether morphological changes in the jejunal crypts contribute to the rescue of Isc. METHODS Male mice (ob/ob and lean controls) were fed either a genistein-free diet or genistein-containing diet (600 G). Comparisons of crypt morphology were made for crypt depth, length, and numbers of proliferative cells. Assessments of crypt measures using DAPI and 5-ethynyl-2'-deoxyuridine (EdU) were performed using traditional cryostat sectioning and an innovative 3D optical clearing method. RESULTS We found that crypt length in the ob/ob genistein-fed group was significantly greater when measured with cleared tissue (85.19±4.73 µm, P<0.05, n=8) compared to lengths measured with cryostat (65.42±3.48 µm, n=8). In addition, proliferative EdU+ counts were approximately fivefold greater with clearing, compared to counts obtained via single plane images from cryostat sections for all groups measured. The average length to EdU+ ratio was unchanged between groups. CONCLUSION Thus, we conclude that genistein diet does not affect overall cellular proliferation or crypt morphology, other than for the modest increased crypt length measured via clearing in the ob/ob genistein group. The increase in crypt length is likely indicative of the greater accuracy of the 3D measures compared to single plane. Genistein diet-induced increases in the intestinal Isc are therefore likely not attributed to changes in intestinal crypt morphology.
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Affiliation(s)
| | | | | | - Layla Al-Nakkash
- Department of Physiology, Midwestern University, Glendale, AZ 85308, USA,
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