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Ji B, Chen J, Gong H, Li X. Streamlined Full-Length Total RNA Sequencing of Paraformaldehyde-Fixed Brain Tissues. Int J Mol Sci 2024; 25:6504. [PMID: 38928210 PMCID: PMC11204141 DOI: 10.3390/ijms25126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Paraformaldehyde (PFA) fixation is the preferred method for preserving tissue architecture for anatomical and pathological observations. Meanwhile, PFA reacts with the amine groups of biomolecules to form chemical cross-linking, which preserves RNA within the tissue. This has great prospects for RNA sequencing to characterize the molecular underpinnings after anatomical and pathological observations. However, RNA is inaccessible due to cross-linked adducts forming between RNA and other biomolecules in prolonged PFA-fixed tissue. It is also difficult to perform reverse transcription and PCR, resulting in low sequencing sensitivity and reduced reproducibility. Here, we developed a method to perform RNA sequencing in PFA-fixed tissue, which is easy to use, cost-effective, and allows efficient sample multiplexing. We employ cross-link reversal to recover RNA and library construction using random primers without artificial fragmentation. The yield and quality of recovered RNA significantly increased through our method, and sequencing quality metrics and detected genes did not show any major differences compared with matched fresh samples. Moreover, we applied our method for gene expression analysis in different regions of the mouse brain and identified unique gene expression profiles with varied functional implications. We also find significant dysregulation of genes involved in Alzheimer's disease (AD) pathogenesis within the medial septum (MS)/vertical diagonal band of Broca (VDB) of the 5×FAD mouse brain. Our method can thus increase the performance of high-throughput RNA sequencing with PFA-fixed samples and allows longitudinal studies of small tissue regions isolated by their in situ context.
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Affiliation(s)
- Bingqing Ji
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jiale Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215125, China
| | - Xiangning Li
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215125, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
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Tian J, Chen Y, Jiang T, Jia X, Gong H, Li X. Low-temperature resin embedding of the whole brain for various precise structures dissection. iScience 2023; 26:106705. [PMID: 37216109 PMCID: PMC10192521 DOI: 10.1016/j.isci.2023.106705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/03/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Resin embedding combined with ultra-thin sectioning has been widely used in microscopic and electron imaging to acquire precise structural information of biological tissues. However, the existing embedding method was detrimental to quenchable fluorescent signals of precise structures and pH-insensitive fluorescent dyes. Here, we developed a low-temperature chemical polymerization method named HM20-T to maintain weak signals of various precise structures and to decrease background fluorescence. The fluorescence preservation ratio of green fluorescent protein (GFP) tagged presynaptic elements and tdTomato labeled axons doubled. The HM20-T method was suitable for a variety of fluorescent dyes, such as DyLight 488 conjugated Lycopersicon esculentum lectin. Moreover, the brains also retained immunoreactivity after embedding. In summary, the HM20-T method was suitable for the characterization of multi-color labeled precise structures, which would contribute to the acquisition of complete morphology of various biological tissues and to the investigation of composition and circuit connection in the whole brain.
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Affiliation(s)
- Jiaojiao Tian
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yingying Chen
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Tao Jiang
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainmatics, JITRI, Suzhou 215125, China
| | - Xueyan Jia
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainmatics, JITRI, Suzhou 215125, China
| | - Hui Gong
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainmatics, JITRI, Suzhou 215125, China
| | - Xiangning Li
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainmatics, JITRI, Suzhou 215125, China
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Tao W, Rubart M, Ryan J, Xiao X, Qiao C, Hato T, Davidson MW, Dunn KW, Day RN. A practical method for monitoring FRET-based biosensors in living animals using two-photon microscopy. Am J Physiol Cell Physiol 2015; 309:C724-35. [PMID: 26333599 DOI: 10.1152/ajpcell.00182.2015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/25/2015] [Indexed: 01/07/2023]
Abstract
The commercial availability of multiphoton microscope systems has nurtured the growth of intravital microscopy as a powerful technique for evaluating cell biology in the relevant context of living animals. In parallel, new fluorescent protein (FP) biosensors have become available that enable studies of the function of a wide range of proteins in living cells. Biosensor probes that exploit Förster resonance energy transfer (FRET) are among the most sensitive indicators of an array of cellular processes. However, differences between one-photon and two-photon excitation (2PE) microscopy are such that measuring FRET by 2PE in the intravital setting remains challenging. Here, we describe an approach that simplifies the use of FRET-based biosensors in intravital 2PE microscopy. Based on a systematic comparison of many different FPs, we identified the monomeric (m) FPs mTurquoise and mVenus as particularly well suited for intravital 2PE FRET studies, enabling the ratiometric measurements from linked FRET probes using a pair of experimental images collected simultaneously. The behavior of the FPs is validated by fluorescence lifetime and sensitized emission measurements of a set of FRET standards. The approach is demonstrated using a modified version of the AKAR protein kinase A biosensor, first in cells in culture, and then in hepatocytes in the liver of living mice. The approach is compatible with the most common 2PE microscope configurations and should be applicable to a variety of different FRET probes.
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Affiliation(s)
- Wen Tao
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Michael Rubart
- Riley Heart Research Center, Wells Center for Pediatric Research, and Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jennifer Ryan
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Xiao Xiao
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Chunping Qiao
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Takashi Hato
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Michael W Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, Florida
| | - Kenneth W Dunn
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Richard N Day
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana
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Torlakovic EE, Brynes RK, Hyjek E, Lee SH, Kreipe H, Kremer M, McKenna R, Sadahira Y, Tzankov A, Reis M, Porwit A. ICSH guidelines for the standardization of bone marrow immunohistochemistry. Int J Lab Hematol 2015; 37:431-49. [DOI: 10.1111/ijlh.12365] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/02/2015] [Indexed: 12/25/2022]
Affiliation(s)
- E. E. Torlakovic
- Department of Laboratory Hematology; University Health Network; University of Toronto; Toronto ON Canada
| | - R. K. Brynes
- Department of Pathology; Keck School of Medicine; University of Southern California; Los Angeles CA USA
| | - E. Hyjek
- Department of Pathology; University of Chicago; Chicago IL USA
| | - S.-H. Lee
- Department of Haematology; St George Hospital; SEALS Central; Sydney NSW Australia
| | - H. Kreipe
- Department of Pathology; Hannover Medical School; Hannover Germany
| | - M. Kremer
- Munich Municipal Hospital; Institute of Pathology; Munich Germany
| | - R. McKenna
- Special Hematology; Department of Laboratory Medicine and Pathology; University of Minnesota; Minneapolis MN USA
| | - Y. Sadahira
- Department of Pathology; Kawasaki Medical School; Kurashiki Japan
| | - A. Tzankov
- Institute of Pathology; University Hospital Basel; Basel Switzerland
| | - M. Reis
- Department of Clinical Pathology; Sunnybrook Health Sciences Centre; Toronto ON Canada
| | - A. Porwit
- Department of Laboratory Hematology; University Health Network; University of Toronto; Toronto ON Canada
- Department of Pathology; Karolinska Institute; Stockholm Sweden
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Lemarié F, Chang CW, Blatchford DR, Amor R, Norris G, Tetley L, McConnell G, Dufès C. Antitumor activity of the tea polyphenol epigallocatechin-3-gallate encapsulated in targeted vesicles after intravenous administration. Nanomedicine (Lond) 2012; 8:181-92. [PMID: 22891867 DOI: 10.2217/nnm.12.83] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM The therapeutic potential of epigallocatechin-3-gallate (EGCG), a green tea polyphenol with anticancer properties, is limited by its inability to specifically reach tumors following intravenous administration. The purpose of this study was to determine whether a tumor-targeted vesicular formulation of EGCG would suppress the growth of A431 epidermoid carcinoma and B16-F10 melanoma in vitro and in vivo. MATERIALS & METHODS Transferrin-bearing vesicles encapsulating EGCG were administered intravenously to mice bearing subcutaneous A431 and B16-F10 tumors. RESULTS The intravenous administration of EGCG encapsulated in transferrin-bearing vesicles resulted in tumor suppression in 40% of A431 and B16-F10 tumors. Animal survival was improved by more than 20 days compared with controls. CONCLUSION Encapsulation of EGCG in transferrin-bearing vesicles is a promising therapeutic strategy.
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Affiliation(s)
- Fanny Lemarié
- Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
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Amor R, Norris G, Dempster J, Amos WB, McConnell G. A compact instrument for adjusting laser beams to be accurately coincident and coaxial and its use in biomedical imaging using wave-mixed laser sources. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:083705. [PMID: 22938301 DOI: 10.1063/1.4745373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biomedical imaging applications that involve nonlinear optical processes such as sum-frequency generation (SFG) and four-wave mixing require that the pulses are synchronized in time and the beams are coaxial to better than 400 μrad. For this reason, folding mirrors are normally used to extend the beam path over a few meters so that detectors can be put into the beams to check their overlap at the start of a long path and also at the end of it. We have made a portable instrument with a footprint of only 22 cm × 11 cm × 16 cm that uses a short focal length lens and a telephoto combination for viewing the near-field and far-field simultaneously. Our instrument is simple to build and use, and we show its application in coherent anti-Stokes Raman scattering microscopy and SFG-based two-photon fluorescence microscopy.
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Affiliation(s)
- R Amor
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom.
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