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Kaufman JA, Castro MJ, Sandoval-Skeet N, Al-Nakkash L. Optical clearing of small intestine for three-dimensional visualization of cellular proliferation within crypts. J Anat 2017; 232:152-157. [PMID: 28967147 DOI: 10.1111/joa.12711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 12/31/2022] Open
Abstract
New methods on optical clearing provide a valuable alternative to traditional physical section histology. Optical clearing allows investigation of relatively large tissue samples at histological resolution while maintaining the three-dimensional architecture of the intact system. There is significant potential for applying optical clearing to gastrointestinal tissues. In particular, intestinal crypts contain high concentrations of stem cells, making these structures especially important for research on cellular proliferation in the intestinal epithelium. The objective of our study is to demonstrate an optical clearing method that is easy to implement and is compatible with mitotic fluorescent labeling. The optical clearing method we present utilizes a Triton/DMSO delipidization step followed by refractive index matching, rendering the tissue nearly transparent. We use EdU click chemistry to fluorescently label mitotic cell nuclei. Our results demonstrate successful clearing of jejunal samples with readily visible EdU staining by means of confocal microscopy. Three-dimensional reconstruction of labeled samples reveals preservation of intestinal cytoarchitecture including muscular, submucosal, and mucosal layers. Additionally, the morphology of intestinal crypts and individual EdU-positive mitotic nuclei are visible in sharp detail within their intact three-dimensional organization. In summary, we present an optical clearing method that is easy to implement and has the potential to provide more accurate assessment of cellular proliferation within the gastrointestinal tract in both healthy and disease states.
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Affiliation(s)
- Jason A Kaufman
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Monica J Castro
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Noemy Sandoval-Skeet
- Masters of Biomedical Science Program, College of Health Sciences, Midwestern University, Glendale, AZ, USA
| | - Layla Al-Nakkash
- Department of Physiology, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
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53
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Nojima S, Susaki EA, Yoshida K, Takemoto H, Tsujimura N, Iijima S, Takachi K, Nakahara Y, Tahara S, Ohshima K, Kurashige M, Hori Y, Wada N, Ikeda JI, Kumanogoh A, Morii E, Ueda HR. CUBIC pathology: three-dimensional imaging for pathological diagnosis. Sci Rep 2017; 7:9269. [PMID: 28839164 PMCID: PMC5571108 DOI: 10.1038/s41598-017-09117-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.
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Affiliation(s)
- Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kyotaro Yoshida
- Department of Pathology, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Hiroyoshi Takemoto
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Naoto Tsujimura
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Shohei Iijima
- Department of Nutrition Oncology, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka-shi, Osaka, 541-8567, Japan
| | - Ko Takachi
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Yujiro Nakahara
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenji Ohshima
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masako Kurashige
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yumiko Hori
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naoki Wada
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun-Ichiro Ikeda
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kumanogoh
- Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Respiratory Medicine, Allergy and Rheumatic Disease, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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54
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Zhang Y, Shin Y, Sung K, Yang S, Chen H, Wang H, Teng D, Rivenson Y, Kulkarni RP, Ozcan A. 3D imaging of optically cleared tissue using a simplified CLARITY method and on-chip microscopy. SCIENCE ADVANCES 2017; 3:e1700553. [PMID: 28819645 PMCID: PMC5553818 DOI: 10.1126/sciadv.1700553] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 07/12/2017] [Indexed: 05/07/2023]
Abstract
High-throughput sectioning and optical imaging of tissue samples using traditional immunohistochemical techniques can be costly and inaccessible in resource-limited areas. We demonstrate three-dimensional (3D) imaging and phenotyping in optically transparent tissue using lens-free holographic on-chip microscopy as a low-cost, simple, and high-throughput alternative to conventional approaches. The tissue sample is passively cleared using a simplified CLARITY method and stained using 3,3'-diaminobenzidine to target cells of interest, enabling bright-field optical imaging and 3D sectioning of thick samples. The lens-free computational microscope uses pixel super-resolution and multi-height phase recovery algorithms to digitally refocus throughout the cleared tissue and obtain a 3D stack of complex-valued images of the sample, containing both phase and amplitude information. We optimized the tissue-clearing and imaging system by finding the optimal illumination wavelength, tissue thickness, sample preparation parameters, and the number of heights of the lens-free image acquisition and implemented a sparsity-based denoising algorithm to maximize the imaging volume and minimize the amount of the acquired data while also preserving the contrast-to-noise ratio of the reconstructed images. As a proof of concept, we achieved 3D imaging of neurons in a 200-μm-thick cleared mouse brain tissue over a wide field of view of 20.5 mm2. The lens-free microscope also achieved more than an order-of-magnitude reduction in raw data compared to a conventional scanning optical microscope imaging the same sample volume. Being low cost, simple, high-throughput, and data-efficient, we believe that this CLARITY-enabled computational tissue imaging technique could find numerous applications in biomedical diagnosis and research in low-resource settings.
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Affiliation(s)
- Yibo Zhang
- Electrical Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yoonjung Shin
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Kevin Sung
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Sam Yang
- Electrical Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Harrison Chen
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hongda Wang
- Electrical Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Da Teng
- Computer Science Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yair Rivenson
- Electrical Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rajan P. Kulkarni
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aydogan Ozcan
- Electrical Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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