1
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Du J, Kim K, Chen M. Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations. Nat Commun 2024; 15:3620. [PMID: 38684657 PMCID: PMC11058242 DOI: 10.1038/s41467-024-47789-1] [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: 09/21/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Photobodies (PBs) are membraneless subnuclear organelles that self-assemble via concentration-dependent liquid-liquid phase separation (LLPS) of the plant photoreceptor and thermosensor phytochrome B (PHYB). The current PHYB LLPS model posits that PHYB phase separates randomly in the nucleoplasm regardless of the cellular or nuclear context. Here, we established a robust Oligopaints method in Arabidopsis to determine the positioning of individual PBs. We show surprisingly that even in PHYB overexpression lines - where PHYB condensation would be more likely to occur randomly - PBs positioned at twelve distinct subnuclear locations distinguishable by chromocenter and nucleolus landmarks, suggesting that PHYB condensation occurs nonrandomly at preferred seeding sites. Intriguingly, warm temperatures reduce PB number by inducing the disappearance of specific thermo-sensitive PBs, demonstrating that individual PBs possess different thermosensitivities. These results reveal a nonrandom PB nucleation model, which provides the framework for the biogenesis of spatially distinct individual PBs with diverse environmental sensitivities within a single plant nucleus.
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Affiliation(s)
- Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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2
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Berleant JD, Banal JL, Rao DK, Bathe M. Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.12.24305660. [PMID: 38699348 PMCID: PMC11064994 DOI: 10.1101/2024.04.12.24305660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The surge in nucleic acid analytics requires scalable storage and retrieval systems akin to electronic databases used to organize digital data. Such a system could transform disease diagnosis, ecological preservation, and molecular surveillance of biothreats. Current storage systems use individual containers for nucleic acid samples, requiring single-sample retrieval that falls short compared with digital databases that allow complex and combinatorial data retrieval on aggregated data. Here, we leverage protective microcapsules with combinatorial DNA labeling that enables arbitrary retrieval on pooled biosamples analogous to Structured Query Languages. Ninety-six encapsulated pooled mock SARS-CoV-2 genomic samples barcoded with patient metadata are used to demonstrate queries with simultaneous matches to sample collection date ranges, locations, and patient health statuses, illustrating how such flexible queries can be used to yield immunological or epidemiological insights. The approach applies to any biosample database labeled with orthogonal barcodes, enabling complex post-hoc analysis, for example, to study global biothreat epidemiology.
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Affiliation(s)
- Joseph D. Berleant
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James L. Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Present address: Cache DNA, Inc. 733 Industrial Rd., San Carlos, CA 94070 USA
| | | | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139 USA
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3
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Hirabayashi Y, Lewis TL, Du Y, Virga DM, Decker AM, Coceano G, Alvelid J, Paul MA, Hamilton S, Kneis P, Takahashi Y, Gaublomme JT, Testa I, Polleux F. Most axonal mitochondria in cortical pyramidal neurons lack mitochondrial DNA and consume ATP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579972. [PMID: 38405915 PMCID: PMC10888904 DOI: 10.1101/2024.02.12.579972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In neurons of the mammalian central nervous system (CNS), axonal mitochondria are thought to be indispensable for supplying ATP during energy-consuming processes such as neurotransmitter release. Here, we demonstrate using multiple, independent, in vitro and in vivo approaches that the majority (~80-90%) of axonal mitochondria in cortical pyramidal neurons (CPNs), lack mitochondrial DNA (mtDNA). Using dynamic, optical imaging analysis of genetically encoded sensors for mitochondrial matrix ATP and pH, we demonstrate that in axons of CPNs, but not in their dendrites, mitochondrial complex V (ATP synthase) functions in a reverse way, consuming ATP and protruding H+ out of the matrix to maintain mitochondrial membrane potential. Our results demonstrate that in mammalian CPNs, axonal mitochondria do not play a major role in ATP supply, despite playing other functions critical to regulating neurotransmission such as Ca2+ buffering.
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Affiliation(s)
- Yusuke Hirabayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo; Tokyo, 113-8656, Japan
| | - Tommy L. Lewis
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Yudan Du
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo; Tokyo, 113-8656, Japan
| | - Daniel M. Virga
- Department of Biological Sciences, Columbia University; New York, NY, 10027, USA
- Department of Neuroscience, Columbia University; New York, NY, 10027, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
| | - Aubrianna M. Decker
- Department of Biological Sciences, Columbia University; New York, NY, 10027, USA
| | - Giovanna Coceano
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonatan Alvelid
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technology, Jena, Germany
| | - Maëla A. Paul
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL; Paris, France
| | - Stevie Hamilton
- Department of Neuroscience, Columbia University; New York, NY, 10027, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
| | - Parker Kneis
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Yasufumi Takahashi
- Department of Electronics, Graduate School of Engineering, Nagoya University, 464-8603, Nagoya, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920–1192 Japan
| | - Jellert T. Gaublomme
- Department of Biological Sciences, Columbia University; New York, NY, 10027, USA
| | - Ilaria Testa
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Franck Polleux
- Department of Neuroscience, Columbia University; New York, NY, 10027, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
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4
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Zhao F, Guan Y, Su F, Du Z, Wen S, Zhang L, Jin D. Lanthanide-Complex-Enhanced Bioorthogonal Branched DNA Amplification. Anal Chem 2024; 96:1556-1564. [PMID: 38214216 DOI: 10.1021/acs.analchem.3c04274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Fluorescence in situ hybridization (FISH) is a widely used technique for detecting intracellular nucleic acids. However, its effectiveness in detecting low-copy nucleic acids is limited due to its low fluorescence intensity and background autofluorescence. To address these challenges, we present here an approach of lanthanide-complex-enhanced bioorthogonal-branched DNA amplification (LEBODA) with high sensitivity for in situ nuclear acid detection in single cells. The approach capitalizes on two levels of signal amplification. First, it utilizes click chemistry to directly link a substantial number of bridge probes to target-recognizing probes, providing an initial boost in signal intensity. Second, it incorporates high-density lanthanide complexes into each bridge probe, enabling secondary amplifications. Compared to the traditional "double Z" probes used in the RNAscope method, LEBODA exhibits 4 times the single enhancement for RNA detection signal with the click chemistry approach. Using SARS-CoV-2 pseudovirus-infected HeLa cells, we demonstrate the superiority in the detection of viral-infected cells in rare populations as low as 20% infectious rate. More encouragingly, the LEBODA approach can be adapted for DNA-FISH and single-molecule RNA-FISH, as well as other hybridization-based signal amplification methods. This adaptability broadens the potential applications of LEBODA in the sensitive detection of biomolecules, indicating promising prospects for future research and practical use.
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Affiliation(s)
- Fang Zhao
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yunpeng Guan
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Fei Su
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Zhongbo Du
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shihui Wen
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Le Zhang
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Dayong Jin
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
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5
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Zhang X, Lu W, Feng Y, Zhang Z, Yuan Z. A Chromogenic In Situ Hybridization (CISH) Assay for Detection of HBV RNA, DNA, and cccDNA in Liver Tissue. Methods Mol Biol 2024; 2837:137-148. [PMID: 39044081 DOI: 10.1007/978-1-0716-4027-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Hepatitis B virus (HBV) developed highly intricates mechanisms exploiting host resources for its multiplication within a constrained genetic coding capacity. With the aid of a series of classical analytical methods such as ultrafiltration, and Southern and Northern blots, a general framework of HBV life cycle has been established. However, this picture still lacks many key histological contexts which involves pathophysiological changes of hepatocytes, non-parenchymal cells, infiltrated leukocytes, and associated extracellular matrix. Here, we describe a CISH protocol modified from the ViewRNA assay that allows direct visualization of HBV RNA, DNA, and cccDNA in liver tissue of chronic hepatitis B patients. By coupling it with immunohistochemistry and other histological stains, much richer information regarding the HBV-induced pathological changes can be harvested.
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Affiliation(s)
- Xiaonan Zhang
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Wei Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yanling Feng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhanqing Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE & NHC), Research Unit of Cure of Chronic Hepatitis B Virus Infection (CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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6
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Duckworth AD, Slupsky JR, Kalakonda N. Highly Multiplexed and Simultaneous Characterization of Protein and RNA in Single Cells by Flow or Mass Cytometry Platforms Using Proximity Ligation Assay for RNA. Methods Mol Biol 2024; 2752:143-165. [PMID: 38194033 DOI: 10.1007/978-1-0716-3621-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
In situ hybridization of oligonucleotide probes to intracellular RNA allows quantification of predefined gene transcripts within millions of single cells using cytometry platforms. Previous methods have been hindered by the number of RNA that can be analyzed simultaneously. Here we describe a method called proximity ligation assay for RNA (PLAYR) that permits highly multiplexed RNA analysis that can be combined with antibody staining. Potentially any number of RNA combined with antigen can be analyzed together, being limited only by the number of analytes that can be measured simultaneously.
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Affiliation(s)
- Andrew D Duckworth
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nagesh Kalakonda
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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7
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Luo M, Lan F, Li W, Chen S, Zhang L, Situ B, Li B, Liu C, Pan W, Gao Z, Zhang Y, Zheng L. Design strategies and advanced applications of primer exchange reactions in biosensing: A review. Anal Chim Acta 2023; 1283:341824. [PMID: 37977767 DOI: 10.1016/j.aca.2023.341824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/19/2023]
Abstract
Early disease diagnosis relies on the sensitive detection and imaging of biomarkers. Signal amplification is one of the most commonly used methods to improve detection sensitivity. Primer exchange reaction (PER) is a novel signal amplification technique that has garnered attention because of its simple and sensitive features. The classical PER involves a single catalytic hairpin, which enables the attachment of custom sequences to the primer chain, generating a long repeat sequence that can bind numerous signaling molecules and achieve powerful signal amplification. Currently, numerous PER-based signal amplification strategies are available that can improve detection sensitivity and promote the development of the signal amplification field. This review focuses on the mechanism of typical PER, the diversification of PER, and PER-based biosensors for various targets. Finally, the challenges and prospects of PER development are discussed.
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Affiliation(s)
- Min Luo
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Fei Lan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Wenbin Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Siting Chen
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Lifeng Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Bo Situ
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Bo Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Chunchen Liu
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Weilun Pan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Zhuowei Gao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Ye Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Lei Zheng
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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8
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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9
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Bressan D, Battistoni G, Hannon GJ. The dawn of spatial omics. Science 2023; 381:eabq4964. [PMID: 37535749 PMCID: PMC7614974 DOI: 10.1126/science.abq4964] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
Spatial omics has been widely heralded as the new frontier in life sciences. This term encompasses a wide range of techniques that promise to transform many areas of biology and eventually revolutionize pathology by measuring physical tissue structure and molecular characteristics at the same time. Although the field came of age in the past 5 years, it still suffers from some growing pains: barriers to entry, robustness, unclear best practices for experimental design and analysis, and lack of standardization. In this Review, we present a systematic catalog of the different families of spatial omics technologies; highlight their principles, power, and limitations; and give some perspective and suggestions on the biggest challenges that lay ahead in this incredibly powerful-but still hard to navigate-landscape.
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Affiliation(s)
- Dario Bressan
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
| | - Gregory J. Hannon
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
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10
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Jiang M, Wei K, Li M, Lin C, Ke R. Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH. RNA (NEW YORK, N.Y.) 2023; 29:836-846. [PMID: 36813533 PMCID: PMC10187679 DOI: 10.1261/rna.079482.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/05/2023] [Indexed: 05/18/2023]
Abstract
Although RNA plays a vital role in gene expression, it is less used as an in situ biomarker for clinical diagnostics than DNA and protein. This is mainly due to technical challenges caused by the low expression level and easy degradation of RNA molecules. To tackle this issue, methods that are sensitive and specific are needed. Here, we present an RNA single-molecule chromogenic in situ hybridization assay based on DNA probe proximity ligation and rolling circle amplification. When the DNA probes hybridize into close proximity to the RNA molecules, they form a V-shape structure and mediate the circularization of circle probes. Thus, our method was termed vsmCISH. We successfully applied our method to assess HER2 mRNA expression status in invasive breast cancer tissue and investigated the utility of albumin mRNA ISH for differentiating primary from metastatic liver cancer. The promising results on clinical samples indicate that our method has great potential for application in diagnosing diseases using RNA biomarkers.
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Affiliation(s)
- Meng Jiang
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Kaipeng Wei
- Department of Pathology, The 910 Hospital, Quanzhou, Fujian, China
| | - Meiqing Li
- Department of Pathology, Women and Children's Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Chen Lin
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
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11
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Monné Rodríguez JM, Frisk AL, Kreutzer R, Lemarchand T, Lezmi S, Saravanan C, Stierstorfer B, Thuilliez C, Vezzali E, Wieczorek G, Yun SW, Schaudien D. European Society of Toxicologic Pathology (Pathology 2.0 Molecular Pathology Special Interest Group): Review of In Situ Hybridization Techniques for Drug Research and Development. Toxicol Pathol 2023; 51:92-111. [PMID: 37449403 PMCID: PMC10467011 DOI: 10.1177/01926233231178282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In situ hybridization (ISH) is used for the localization of specific nucleic acid sequences in cells or tissues by complementary binding of a nucleotide probe to a specific target nucleic acid sequence. In the last years, the specificity and sensitivity of ISH assays were improved by innovative techniques like synthetic nucleic acids and tandem oligonucleotide probes combined with signal amplification methods like branched DNA, hybridization chain reaction and tyramide signal amplification. These improvements increased the application spectrum for ISH on formalin-fixed paraffin-embedded tissues. ISH is a powerful tool to investigate DNA, mRNA transcripts, regulatory noncoding RNA, and therapeutic oligonucleotides. ISH can be used to obtain spatial information of a cell type, subcellular localization, or expression levels of targets. Since immunohistochemistry and ISH share similar workflows, their combination can address simultaneous transcriptomics and proteomics questions. The goal of this review paper is to revisit the current state of the scientific approaches in ISH and its application in drug research and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Seong-Wook Yun
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
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12
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Li Y, Huang D, Pei Y, Wu Y, Xu R, Quan F, Gao H, Zhang J, Hou H, Zhang K, Li J. CasSABER for Programmable In Situ Visualization of Low and Nonrepetitive Gene Loci. Anal Chem 2023; 95:2992-3001. [PMID: 36703533 DOI: 10.1021/acs.analchem.2c04867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Site-specific imaging of target genes using CRISPR probes is essential for understanding the molecular mechanisms of gene function and engineering tools to modulate its downstream pathways. Herein, we develop CRISPR/Cas9-mediated signal amplification by exchange reaction (CasSABER) for programmable in situ imaging of low and nonrepetitive regions of the target gene in the cell nucleus. The presynthesized primer-exchange reaction (PER) probe is able to hybridize multiple fluorophore-bearing imager strands to specifically light up dCas9/sgRNA target-bound gene loci, enabling in situ imaging of fixed cellular gene loci with high specificity and signal-to-noise ratio. In combination with a multiround branching strategy, we successfully detected nonrepetitive gene regions using a single sgRNA. As an intensity-codable and orthogonal probe system, CasSABER enables the adjustable amplification of local signals in fixed cells, resulting in the simultaneous visualization of multicopy and single-copy gene loci with similar fluorescence intensity. Owing to avoiding the complexity of controlling in situ mutistep enzymatic reactions, CasSABER shows good reliability, sensitivity, and ease of implementation, providing a rapid and cost-effective molecular toolkit for studying multigene interaction in fundamental research and gene diagnosis.
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Affiliation(s)
- Yanan Li
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Di Huang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Yiran Pei
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Yonghua Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Ru Xu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Fenglei Quan
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Hua Gao
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Junli Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou450001, China
- Beijing Institute of Life Science and Technology, Beijing100083, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing100084, China
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13
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Attar S, Browning VE, Liu Y, Nichols EK, Tsue AF, Shechner DM, Shendure J, Lieberman JA, Akilesh S, Beliveau BJ. Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526264. [PMID: 36778496 PMCID: PMC9915481 DOI: 10.1101/2023.01.30.526264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In situ hybridization (ISH) is a powerful tool for investigating the spatial arrangement of nucleic acid targets in fixed samples. ISH is typically visualized using fluorophores to allow high sensitivity and multiplexing or with colorimetric labels to facilitate co-visualization with histopathological stains. Both approaches benefit from signal amplification, which makes target detection effective, rapid, and compatible with a broad range of optical systems. Here, we introduce a unified technical platform, termed 'pSABER', for the amplification of ISH signals in cell and tissue systems. pSABER decorates the in situ target with concatemeric binding sites for a horseradish peroxidase-conjugated oligonucleotide which can then catalyze the massive localized deposition of fluorescent or colorimetric substrates. We demonstrate that pSABER effectively labels DNA and RNA targets, works robustly in cultured cells and challenging formalin fixed paraffin embedded (FFPE) specimens. Furthermore, pSABER can achieve 25-fold signal amplification over conventional signal amplification by exchange reaction (SABER) and can be serially multiplexed using solution exchange. Therefore, by linking nucleic acid detection to robust signal amplification capable of diverse readouts, pSABER will have broad utility in research and clinical settings.
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14
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Moissoglu K, Lockett SJ, Mili S. Visualizing and Quantifying mRNA Localization at the Invasive Front of 3D Cancer Spheroids. Methods Mol Biol 2023; 2608:263-280. [PMID: 36653713 PMCID: PMC10411857 DOI: 10.1007/978-1-0716-2887-4_16] [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] [Indexed: 01/20/2023]
Abstract
Localization of mRNAs at the front of migrating cells is a widely used mechanism that functionally supports efficient cell movement. It is observed in single cells on two-dimensional surfaces, as well as in multicellular three-dimensional (3D) structures and in tissue in vivo. 3D multicellular cultures can reveal how the topology of the extracellular matrix and cell-cell contacts influence subcellular mRNA distributions. Here we describe a method for mRNA imaging in an inducible system of collective cancer cell invasion. MDA-MB-231 cancer cell spheroids are embedded in Matrigel, induced to invade, and processed to image mRNAs with single-molecule sensitivity. An analysis algorithm is used to quantify and compare mRNA distributions at the front of invasive leader cells. The approach can be easily adapted and applied to analyze RNA distributions in additional settings where cells polarize along a linear axis.
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Affiliation(s)
- Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc. for the National Cancer Institute, NIH, Frederick, MD, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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15
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Martel R, Shen ML, DeCorwin-Martin P, de Araujo LO, Juncker D. Extracellular Vesicle Antibody Microarray for Multiplexed Inner and Outer Protein Analysis. ACS Sens 2022; 7:3817-3828. [PMID: 36515500 PMCID: PMC9791990 DOI: 10.1021/acssensors.2c01750] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins are found both outside and inside of extracellular vesicles (EVs) and govern the properties and functions of EVs, while also constituting a signature of the cell of origin and of biological function and disease. Outer proteins on EVs can be directly bound by antibodies to either enrich EVs, or probe the expression of a protein on EVs, including in a combinatorial manner. However, co-profiling of inner proteins remains challenging. Here, we present the high-throughput, multiplexed analysis of EV inner and outer proteins (EVPio). We describe the optimization of fixation and heat-induced protein epitope retrieval for EVs, along with oligo-barcoded antibodies and branched DNA signal amplification for sensitive, multiplexed, and high-throughput assays. We captured four subpopulations of EVs from colorectal cancer (CRC) cell lines HT29 and SW403 based on EpCAM, CD9, CD63, and CD81 expression, and quantified the co-expression of eight outer [integrins (ITGs) and tetraspanins] and four inner (heat shock, endosomal, and inner leaflet) proteins. The differences in co-expression patterns were consistent with the literature and known biological function. In conclusion, EVPio analysis can simultaneously detect multiple inner and outer proteins in EVs immobilized on a surface, opening the way to extensive combinatorial protein profiles for both discovery and clinical translation.
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Affiliation(s)
- Rosalie Martel
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada,McGill
Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Molly L. Shen
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada,McGill
Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Philippe DeCorwin-Martin
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada,McGill
Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Lorenna Oliveira
Fernandes de Araujo
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada,McGill
Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - David Juncker
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada,McGill
Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada,
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16
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Chiriboga L, Callis GM, Wang Y, Chlipala E. Guide for collecting and reporting metadata on protocol variables and parameters from slide-based histotechnology assays to enhance reproducibility. J Histotechnol 2022; 45:132-147. [DOI: 10.1080/01478885.2022.2134022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- NYULH Center for Biospecimen Research and Development, New York, NY, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas, MO, USA
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17
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Tsuneoka Y, Atsumi Y, Makanae A, Yashiro M, Funato H. Fluorescence quenching by high-power LEDs for highly sensitive fluorescence in situ hybridization. Front Mol Neurosci 2022; 15:976349. [PMID: 36117911 PMCID: PMC9479452 DOI: 10.3389/fnmol.2022.976349] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Recent technical advances have made fluorescent in situ hybridization (ISH) a pivotal method to analyze neural tissue. In a highly sensitive ISH, it is important to reduce tissue autofluorescence. We developed a photobleaching device using a light-emitting diode (LED) illuminator to quench autofluorescence in neural tissue. This device was equipped with 12 high-power LEDs (30 W per single LED) and an evaporative cooling system, and these features achieved highly efficient bleaching of autofluorescence and minimized tissue damage. Even after 60 min of photobleaching with evaporative cooling, the temperature gain of the tissue slide was suppressed almost completely. The autofluorescence of lipofuscin-like granules completely disappeared after 60 min of photobleaching, as did other background autofluorescence observed in the mouse cortex and hippocampus. In combination with the recently developed fluorescent ISH method using the hybridization chain reaction (HCR), high signal/noise ratio imaging was achieved without reduction of ISH sensitivity to visualize rare mRNA at single copy resolution by quenching autofluorescence. Photobleaching by the LED illuminator was also effective in quenching the fluorescent staining of ISH-HCR. We performed multiround ISH by repeating the cycle of HCR staining, confocal imaging, and photobleaching. In addition to the two-round ISH, fluorescent immunohistochemistry or fluorescent Nissl staining was conducted on the same tissue. This LED illuminator provides a quick and simple way to reduce autofluorescence and quench fluorescent dyes for multiround ISH with minimum tissue degradation.
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Affiliation(s)
- Yousuke Tsuneoka
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- *Correspondence: Yousuke Tsuneoka Hiromasa Funato
| | - Yusuke Atsumi
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- Center for Research and Product Development, Nepa Gene Co., Ltd., Chiba, Japan
| | - Aki Makanae
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- Center for Research and Product Development, Nepa Gene Co., Ltd., Chiba, Japan
| | - Mitsuru Yashiro
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- Center for Research and Product Development, Nepa Gene Co., Ltd., Chiba, Japan
| | - Hiromasa Funato
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- International Institutes for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki, Japan
- *Correspondence: Yousuke Tsuneoka Hiromasa Funato
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18
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Casadei L, Sarchet P, de Faria FCC, Calore F, Nigita G, Tahara S, Cascione L, Wabitsch M, Hornicek FJ, Grignol V, Croce CM, Pollock RE. In situ hybridization to detect DNA amplification in extracellular vesicles. J Extracell Vesicles 2022; 11:e12251. [PMID: 36043432 PMCID: PMC9428764 DOI: 10.1002/jev2.12251] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/07/2022] Open
Abstract
EVs have emerged as an important component in tumour initiation, progression and metastasis. Although notable progresses have been made, the detection of EV cargoes remain significantly challenging for researchers to practically use; faster and more convenient methods are required to validate the EV cargoes, especially as biomarkers. Here we show, the possibility of examining embedded EVs as substrates to be used for detecting DNA amplification through ultrasensitive in situ hybridization (ISH). This methodology allows the visualization of DNA targets in a more direct manner, without time consuming optimization steps or particular expertise. Additionally, formalin‐fixed paraffin‐embedded (FFPE) blocks of EVs allows long‐term preservation of samples, permitting future studies. We report here: (i) the successful isolation of EVs from liposarcoma tissues; (ii) the EV embedding in FFPE blocks (iii) the successful selective, specific ultrasensitive ISH examination of EVs derived from tissues, cell line, and sera; (iv) and the detection of MDM2 DNA amplification in EVs from liposarcoma tissues, cell lines and sera. Ultrasensitive ISH on EVs would enable cargo study while the application of ISH to serum EVs, could represent a possible novel methodology for diagnostic confirmation. Modification of probes may enable researchers to detect targets and specific DNA alterations directly in tumour EVs, thereby facilitating detection, diagnosis, and improved understanding of tumour biology relevant to many cancer types.
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Affiliation(s)
- Lucia Casadei
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Patricia Sarchet
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | | | - Federica Calore
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
| | - Giovanni Nigita
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
| | - Sayumi Tahara
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Luciano Cascione
- Institute of Oncology Research (IOR), Faculty of Biomedical SciencesUniversità della Svizzera italiana (USI), Bellinzona, Switzerland, Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine Division of Paediatric Endocrinology and Diabetes Centre for Hormonal Disorders in Children and AdolescentsUlm University HospitalUlmGermany
| | - Francis J. Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedics, Sylvester Comprehensive Cancer Centerand the University of Miami Miller School of MedicineMiamiFloridaUSA
| | - Valerie Grignol
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Carlo M. Croce
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
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19
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Conrad T, Altmüller J. Single cell- and spatial 'Omics revolutionize physiology. Acta Physiol (Oxf) 2022; 235:e13848. [PMID: 35656634 DOI: 10.1111/apha.13848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/24/2022] [Accepted: 05/27/2022] [Indexed: 11/29/2022]
Abstract
Single cell multi- 'Omics and Spatial Transcriptomics are prominent technological highlights of recent years, and both fields still witness a ceaseless firework of novel approaches for high resolution profiling of additional omics layers. As all life processes in organs and organisms are based on the functions of their fundamental building blocks, the individual cells and their interactions, these methods are of utmost worth for the study of physiology in health and disease. Recent discoveries on embryonic development, tumor immunology, the detailed cellular composition and function of complex tissues like for example the kidney or the brain, different roles of the same cell type in different organs, the oncogenic program of individual tumor entities, or the architecture of immunopathology in infected tissue are based on single cell and spatial transcriptomics experiments. In this review, we will give a broad overview of technological concepts for single cell and spatial analysis, showing both advantages and limitations, and illustrate their impact with some particularly impressive case studies.
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Affiliation(s)
- Thomas Conrad
- Genomics Technology Platform Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany
| | - Janine Altmüller
- Genomics Technology Platform Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany
- Core Facility Genomics Berlin Institute of Health at Charité ‐ Universitätsmedizin Berlin Berlin Germany
- Center for Molecular Medicine Cologne (CMMC) Cologne Germany
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20
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Lidin E, Sköld MK, Angéria M, Davidsson J, Risling M. Hippocampal Expression of Cytochrome P450 1B1 in Penetrating Traumatic Brain Injury. Int J Mol Sci 2022; 23:722. [PMID: 35054909 PMCID: PMC8775891 DOI: 10.3390/ijms23020722] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/04/2023] Open
Abstract
Hippocampal dysfunction contributes to multiple traumatic brain injury sequala. Female rodents' outcome is superior to male which has been ascribed the neuroprotective sex hormones 17β-estradiol and progesterone. Cytochrome P450 1B1 (CYP1B1) is an oxidative enzyme influencing the neuroinflammatory response by creating inflammatory mediators and metabolizing neuroprotective 17β-estradiol and progesterone. In this study, we aimed to describe hippocampal CYP1B1 mRNA expression, protein presence of CYP1B1 and its key redox partner Cytochrome P450 reductase (CPR) in both sexes, as well as the effect of penetrating traumatic brain injury (pTBI). A total 64 adult Sprague Dawley rats divided by sex received pTBI or sham-surgery and were assigned survival times of 1-, 3-, 5- or 7 days. CYP1B1 mRNA was quantified using in-situ hybridization and immunohistochemistry performed to verify protein colocalization. CYP1B1 mRNA expression was present in all subregions but greatest in CA2 irrespective of sex, survival time or intervention. At 3-, 5- and 7 days post-injury, expression in CA2 was reduced in male rats subjected to pTBI compared to sham-surgery. Females subjected to pTBI instead exhibited increased expression in all CA subregions 3 days post-injury, the only time point expression in CA2 was greater in females than in males. Immunohistochemical analysis confirmed neuronal CYP1B1 protein in all hippocampal subregions, while CPR was limited to CA1 and CA2. CYP1B1 mRNA is constitutively expressed in both sexes. In response to pTBI, females displayed a more urgent but brief regulatory response than males. This indicates there may be sex-dependent differences in CYP1B1 activity, possibly influencing inflammation and neuroprotection in pTBI.
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Affiliation(s)
- Erik Lidin
- Experimental Traumatology Unit, Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden; (M.K.S.); (M.A.); (M.R.)
| | - Mattias K. Sköld
- Experimental Traumatology Unit, Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden; (M.K.S.); (M.A.); (M.R.)
- Section of Neurosurgery, Department of Neuroscience, Uppsala University, 751 85 Uppsala, Sweden
| | - Maria Angéria
- Experimental Traumatology Unit, Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden; (M.K.S.); (M.A.); (M.R.)
| | - Johan Davidsson
- Department of Mechanics and Maritime Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | - Mårten Risling
- Experimental Traumatology Unit, Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden; (M.K.S.); (M.A.); (M.R.)
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21
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Dubé M, Kaufmann DE. Single-Cell Multiparametric Analysis of Rare HIV-Infected Cells Identified by Duplexed RNAflow-FISH. Methods Mol Biol 2022; 2407:291-313. [PMID: 34985672 DOI: 10.1007/978-1-0716-1871-4_20] [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] [Indexed: 06/14/2023]
Abstract
HIV-infected cells are difficult to characterize in vivo because of their great paucity and their diversity. This chapter describes a duplexed flow cytometry method that enables detection, quantification and phenotyping of these rare cells at single-cell resolution. Primary CD4+ T cells are enriched from PBMCs, stained for surface and intracellular proteins and then subjected to fluorescent in situ hybridization to label viral RNA before acquisition on a flow cytometer. Technical and analytical advices are provided to improve the quality of the data. This flow cytometric RNA fluorescent in situ hybridization (RNAflow-FISH) procedure can be applied to the characterization of both HIV-infected cells from viremic people living with HIV and reactivated viral reservoirs from virally suppressed individuals on therapy.
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Affiliation(s)
- Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.
- Université de Montréal, Montreal, QC, Canada.
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22
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Steimel JP, Hu X. Visualization of RNA Transcripts in Western Corn Rootworm (Diabrotica virgifera virgifera) and Plants by In Situ Hybridization. Methods Mol Biol 2022; 2360:59-74. [PMID: 34495507 DOI: 10.1007/978-1-0716-1633-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In situ hybridization (ISH) is a methodology by which nucleic acids are detected within fixed tissue samples. Recent advances in detection technology and target recovery have greatly enhanced the technique's ability to detect single mRNA molecules. Here we detail the fixation, paraffin embedding, sectioning, target recovery, and chromogenic detection of an mRNA (DvSSJ1), encoding for a membrane protein associated with the smooth septate junction (SSJ) in Western corn rootworm [Diabrotica virgifera (Dv)]. Further, we demonstrate, the expression of dsRNA of DvSSJ1 in maize root tissues using signal amplification and background suppression technology.
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Affiliation(s)
| | - Xu Hu
- Corteva Agriscience, Johnston, IA, USA.
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23
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Ravn Warncke S, Rohde Knudsen C. Detection methods targeting the positive- and negative-sense RNA transcripts from plus-stranded RNA viruses. APMIS 2021; 130:284-292. [PMID: 34939239 PMCID: PMC9306919 DOI: 10.1111/apm.13202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 11/27/2022]
Abstract
The largest group of viruses in the Baltimore classification system comprises viruses with a positive-sense, single-stranded RNA genome. Once the viral genome is released into the cytoplasm of a specific host cell following virus entry, it functions directly as a mRNA and the virus-encoded proteins that are essential for genome replication, are produced by the translation apparatus of the host cell. The positive-sense genome is replicated in two stages, initially the positive strand is copied to make a negative-sense RNA, which then functions as the template for transcription of many new positive-sense genomes. Virus infections can be detected at different stages throughout the infection cycle for diagnostic and scientific purposes. Here, the advantages and disadvantages of some of the relevant methods for genome detection will be briefly reviewed with special emphasis on techniques allowing strand-specific RNA detection. Furthermore, tools of the future are considered.
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Affiliation(s)
- Signe Ravn Warncke
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
| | - Charlotte Rohde Knudsen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
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24
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Savulescu AF, Bouilhol E, Beaume N, Nikolski M. Prediction of RNA subcellular localization: Learning from heterogeneous data sources. iScience 2021; 24:103298. [PMID: 34765919 PMCID: PMC8571491 DOI: 10.1016/j.isci.2021.103298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA subcellular localization has recently emerged as a widespread phenomenon, which may apply to the majority of RNAs. The two main sources of data for characterization of RNA localization are sequence features and microscopy images, such as obtained from single-molecule fluorescent in situ hybridization-based techniques. Although such imaging data are ideal for characterization of RNA distribution, these techniques remain costly, time-consuming, and technically challenging. Given these limitations, imaging data exist only for a limited number of RNAs. We argue that the field of RNA localization would greatly benefit from complementary techniques able to characterize location of RNA. Here we discuss the importance of RNA localization and the current methodology in the field, followed by an introduction on prediction of location of molecules. We then suggest a machine learning approach based on the integration between imaging localization data and sequence-based data to assist in characterization of RNA localization on a transcriptome level.
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Affiliation(s)
- Anca Flavia Savulescu
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925 Cape Town, South Africa
| | - Emmanuel Bouilhol
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Nicolas Beaume
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town,7925 Cape Town, South Africa
| | - Macha Nikolski
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
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25
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Schwarzkopf M, Liu MC, Schulte SJ, Ives R, Husain N, Choi HMT, Pierce NA. Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization. Development 2021; 148:dev199847. [PMID: 35020875 PMCID: PMC8645210 DOI: 10.1242/dev.199847] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022]
Abstract
RNA in situ hybridization based on the mechanism of the hybridization chain reaction (HCR) enables multiplexed, quantitative, high-resolution RNA imaging in highly autofluorescent samples, including whole-mount vertebrate embryos, thick brain slices and formalin-fixed paraffin-embedded tissue sections. Here, we extend the benefits of one-step, multiplexed, quantitative, isothermal, enzyme-free HCR signal amplification to immunohistochemistry, enabling accurate and precise protein relative quantitation with subcellular resolution in an anatomical context. Moreover, we provide a unified framework for simultaneous quantitative protein and RNA imaging with one-step HCR signal amplification performed for all target proteins and RNAs simultaneously.
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Affiliation(s)
- Maayan Schwarzkopf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mike C. Liu
- Molecular Instruments, Los Angeles, CA 90041, USA
| | - Samuel J. Schulte
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rachel Ives
- Molecular Instruments, Los Angeles, CA 90041, USA
| | - Naeem Husain
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Niles A. Pierce
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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26
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Rombouts S, Nollmann M. RNA imaging in bacteria. FEMS Microbiol Rev 2021; 45:5917984. [PMID: 33016325 DOI: 10.1093/femsre/fuaa051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/01/2020] [Indexed: 12/25/2022] Open
Abstract
The spatiotemporal regulation of gene expression plays an essential role in many biological processes. Recently, several imaging-based RNA labeling and detection methods, both in fixed and live cells, were developed and now enable the study of transcript abundance, localization and dynamics. Here, we review the main single-cell techniques for RNA visualization with fluorescence microscopy and describe their applications in bacteria.
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Affiliation(s)
- Sara Rombouts
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 Rue de Navacelles, 34090, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 Rue de Navacelles, 34090, Montpellier, France
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27
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Soheili M, Keyvani H, Soheili M, Nasseri S. Human papilloma virus: A review study of epidemiology, carcinogenesis, diagnostic methods, and treatment of all HPV-related cancers. Med J Islam Repub Iran 2021; 35:65. [PMID: 34277502 PMCID: PMC8278030 DOI: 10.47176/mjiri.35.65] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Human papillomavirus (HPV) infection is considered as the most common viral sexually transmitted infection worldwide. This poses an increasingly interdisciplinary medical challenge. Since there is vast scattered information in databases about HPV and the correlated diseases, we decided to collect useful data so that the experts can get a more comprehensive view of HPV. Methods: In this article, HPV-associated diseases, prevalence, prevention, and new treatments are discussed. The retrieved articles reporting the latest data about the required information for our review were selected through searching in Web of Science, Scopus, Medline (PubMed), EMBASE, Cochrane Library, Ovid, and CINHAL with language limitations of English and German. Results: There are 2 groups of HPVs: (1) low-risk HPV types that can lead to genital warts, and (2) high-risk HPV types that are involved in HPV-associated oncogenesis. About 70% of all sexually active women are infected and most of these infections heal within many weeks or months. In the case of HPV-persistence, a risk of preneoplasia or carcinoma exists. These types of viruses are responsible for the existence of genitoanal, gastrointestinal, urinary tract, and head and neck tumors. There is still no definite successful treatment. The detection of HPV-related condylomata occurs macroscopically in women and men, and the diagnosis of the precursors of cervical carcinoma in women is possible by Pap smear. Conclusion: For extragenital manifestations, there is no structured early detection program. Meanwhile, studies on HPV vaccines confirm that they should be used for the primary prevention of HPV-dependent diseases. However, we need more research to find out the real advantages and disadvantages of vaccines.
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Affiliation(s)
- Maryam Soheili
- School of Kinesiology and Health Science, York University, Toronto, Canada
| | - Hossein Keyvani
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Gastrointestinal and Liver Disease Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Soheili
- Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Human Revivification Society of Congress 60, Tehran, Iran
| | - Sherko Nasseri
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Department of Molecular Medicine and Medical Genetics, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
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28
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Ma J, Tran G, Wan AMD, Young EWK, Kumacheva E, Iscove NN, Zandstra PW. Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection. Sci Rep 2021; 11:6777. [PMID: 33762663 PMCID: PMC7990930 DOI: 10.1038/s41598-021-86087-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost. Here, we present a novel microdroplet-based, one-step reverse-transcriptase polymerase chain reaction (RT-PCR) platform and demonstrate the detection of three targets simultaneously in over 100,000 single cells in a single experiment with a rapid read-out. Our customized reagent cocktail incorporates the bacteriophage T7 gene 2.5 protein to overcome cell lysate-mediated inhibition and allows for one-step RT-PCR of single cells encapsulated in nanoliter droplets. Fluorescent signals indicative of gene expressions are analyzed using a probabilistic deconvolution method to account for ambient RNA and cell doublets and produce single-cell gene signature profiles, as well as predict cell frequencies within heterogeneous samples. We also developed a simulation model to guide experimental design and optimize the accuracy and precision of the assay. Using mixtures of in vitro transcripts and murine cell lines, we demonstrated the detection of single RNA molecules and rare cell populations at a frequency of 0.1%. This low cost, sensitive, and adaptable technique will provide an accessible platform for high throughput single-cell analysis and enable a wide range of research and clinical applications.
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Affiliation(s)
- Jennifer Ma
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Gary Tran
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alwin M D Wan
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Edmond W K Young
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Eugenia Kumacheva
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Norman N Iscove
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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29
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Gao R, Liao X, Zhao X, Liu D, Ding T. The diagnostic tools for viable but nonculturable pathogens in the food industry: Current status and future prospects. Compr Rev Food Sci Food Saf 2021; 20:2146-2175. [PMID: 33484068 DOI: 10.1111/1541-4337.12695] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022]
Abstract
Viable but nonculturable (VBNC) microorganisms have been recognized as pathogenic contaminants in foods and environments. The failure of VBNC cells to form the visible colonies hinders the ability to use conventional media for their detection. Efficient and rapid detection of pathogens in the VBNC state is a prerequisite to ensure the food safety and public health. Despite their nonculturability, VBNC cells have distinct characteristics, such as morphology, metabolism, chemical composition, and gene and protein expression, that have been used as the basis for the development of abundant diagnostic tools. This review covers the current status and advances in various approaches for examining microorganisms in the VBNC state, including but not limited to the methodological aspects, advantages, and drawbacks of each technique. Existing methods, such as direct viable count, SYTO/PI dual staining, and propidium monoazide quantitative polymerase chain reaction (PCR), as well as some techniques with potential to be applied in the future, such as digital PCR, enhanced-surface Raman spectroscopy, and impedance-based techniques, are summarized in depth. Finally, future prospects for the one-step detection of VBNC bacteria are proposed and discussed. We believe that this review can provide more optional methods for researchers and promote the development of rapid, accurate detecting methods, and for inspectors, the diagnostic tools can provide data to undertake risk analysis of VBNC cells.
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Affiliation(s)
- Rui Gao
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyu Liao
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Donghong Liu
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tian Ding
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
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30
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[RNA in situ hybridization: technology, potential, and fields of application]. DER PATHOLOGE 2021; 41:563-573. [PMID: 32997158 DOI: 10.1007/s00292-020-00839-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Significant improvements in the technology of RNA in situ hybridization (RNA-ISH) in the past five decades have opened up novel fields of its application as a valuable and an attractive adjunct to the portfolio of pathologist's daily routine diagnostic practice.In contrast to the former methodology, the current bDNA-based technology is not only easier to handle but also considerably more sensitive, enabling single-target molecule detection in formalin-fixed and paraffin-embedded tissue specimens without significant effort by both the lab and the evaluating pathologist, as assays can be run on standard automated staining devices and evaluated by light microscopy. Compared to molecular methods like RT-PCR and whole-genome analysis, RNA-ISH maintains tissue integrity thus offering the invaluable advantage of localization of target cells especially in relation to secreted proteins and expression of the target sequence in multiple cell types. The first clinical trials implementing RNA-ISH for patient stratification and selection are in progress and already led to the first drug approvals based on its use as a CDx test.In addition to its role as a complementary method for the establishment of novel IHC procedures or as an addition or replacement to IHC in the standard routine portfolio, RNA-ISH has gained special importance for its capacity to detect noncoding RNA species or mutation or splice variants, where no alternative procedures are available. This more complex application requires development of standardized procedures and involvement of the pathologist during assay establishment and for routine specimen evaluation.The present article reviews the development of RNA-ISH from its early uses to its current applications in research and diagnostics based on the authors' considerable experience of applying it as tool in a biopharmaceutical research organization.
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31
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Ultrasensitive RNAscope In Situ Hybridization System on Embryonic and Adult Mouse Retinas. Methods Mol Biol 2020; 2092:147-158. [PMID: 31786787 DOI: 10.1007/978-1-0716-0175-4_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In situ hybridization (ISH) techniques provide important information regarding gene expression in cells and tissues. Especially, ISH details complex spatial RNA expression in highly heterogeneous tissues, such as developing and mature central nervous systems, where rare genes involved in many fundamental developmental or biological events are expressed. Although several techniques have been developed to detect low levels of RNA expression, there are still problematic issues caused by a low signal-to-noise ratio after signal amplification. RNAscope is a recently developed ISH technique with high sensitivity and low background. RNAscope utilizes a unique probe system (double Z probe) to amplify signal from rare RNAs. Additionally, the double Z probe enables a significant reduction in nonspecific signal amplification. Here we report detailed procedures of the brown-color RNAscope ISH on embryonic and adult mouse retinas.
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32
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Brion C, Lutz SM, Albert FW. Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation. eLife 2020; 9:60645. [PMID: 33191917 PMCID: PMC7707838 DOI: 10.7554/elife.60645] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/14/2020] [Indexed: 01/27/2023] Open
Abstract
Trans-acting DNA variants may specifically affect mRNA or protein levels of genes located throughout the genome. However, prior work compared trans-acting loci mapped in separate studies, many of which had limited statistical power. Here, we developed a CRISPR-based system for simultaneous quantification of mRNA and protein of a given gene via dual fluorescent reporters in single, live cells of the yeast Saccharomyces cerevisiae. In large populations of recombinant cells from a cross between two genetically divergent strains, we mapped 86 trans-acting loci affecting the expression of ten genes. Less than 20% of these loci had concordant effects on mRNA and protein of the same gene. Most loci influenced protein but not mRNA of a given gene. One locus harbored a premature stop variant in the YAK1 kinase gene that had specific effects on protein or mRNA of dozens of genes. These results demonstrate complex, post-transcriptional genetic effects on gene expression.
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Affiliation(s)
- Christian Brion
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Sheila M Lutz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Frank Wolfgang Albert
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
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33
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Shah R, Lan S, Puray-Chavez MN, Liu D, Tedbury PR, Sarafianos SG. Single-cell Multiplexed Fluorescence Imaging to Visualize Viral Nucleic Acids and Proteins and Monitor HIV, HTLV, HBV, HCV, Zika Virus, and Influenza Infection. J Vis Exp 2020. [PMID: 33191939 DOI: 10.3791/61843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Capturing the dynamic replication and assembly processes of viruses has been hindered by the lack of robust in situ hybridization (ISH) technologies that enable sensitive and simultaneous labeling of viral nucleic acid and protein. Conventional DNA fluorescence in situ hybridization (FISH) methods are often not compatible with immunostaining. We have therefore developed an imaging approach, MICDDRP (multiplex immunofluorescent cell-based detection of DNA, RNA and protein), which enables simultaneous single-cell visualization of DNA, RNA, and protein. Compared to conventional DNA FISH, MICDDRP utilizes branched DNA (bDNA) ISH technology, which dramatically improves oligonucleotide probe sensitivity and detection. Small modifications of MICDDRP enable imaging of viral proteins concomitantly with nucleic acids (RNA or DNA) of different strandedness. We have applied these protocols to study the life cycles of multiple viral pathogens, including human immunodeficiency virus (HIV)-1, human T-lymphotropic virus (HTLV)-1, hepatitis B virus (HBV), hepatitis C virus (HCV), Zika virus (ZKV), and influenza A virus (IAV). We demonstrated that we can efficiently label viral nucleic acids and proteins across a diverse range of viruses. These studies can provide us with improved mechanistic understanding of multiple viral systems, and in addition, serve as a template for application of multiplexed fluorescence imaging of DNA, RNA, and protein across a broad spectrum of cellular systems.
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Affiliation(s)
- Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine
| | - Shuiyun Lan
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine
| | - Maritza N Puray-Chavez
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine
| | - Dandan Liu
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine;
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34
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Dou HH, Mallari R, Pipathsouk A, Das A, Lo MC. An Automated High-Throughput Fluorescence In Situ Hybridization (FISH) Assay Platform for Use in the Identification and Optimization of siRNA-Based Therapeutics. SLAS DISCOVERY 2020; 26:281-291. [PMID: 33016168 DOI: 10.1177/2472555220960045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Since the revolutionary discovery of RNA interference (RNAi) more than 20 years ago, synthetic small interfering RNAs (siRNAs) have held great promise as therapeutic agents for treating human diseases by the specific knockdown of disease-causing gene products. To facilitate the development of siRNA therapeutics, a robust, high-throughput in vitro assay for measuring gene silencing is imperative during the initial siRNA lead sequence identification and, later, during the lead optimization with chemically modified siRNAs. There are several potential assays for measuring gene expression. Quantitative reverse transcription PCR (qRT-PCR) has been widely used to quantitate messenger RNA (mRNA). This method has a few disadvantages, however, such as the requirement for RNA isolation, complementary DNA (cDNA) generation, and PCR reaction, which are labor-intensive, limit the assay throughput, and introduce variability. We chose a high-content imaging assay, bDNA FISH, that combines the branched DNA (bDNA) technology with fluorescence in situ hybridization (FISH) to measure gene silencing by siRNAs because it is sensitive and robust with a short reagent procurement and assay development time. We also built a fully automated liquid-handling platform for executing bDNA FISH assays to increase throughput, and the system has a capacity of generating 192 concentration-response curves in a single run. We have successfully developed and executed the bDNA FISH assays for multiple targets using this automated platform to identify and optimize siRNA candidate molecules. Examples of the bDNA FISH assay for selected targets are presented.
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Affiliation(s)
- Hui H Dou
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA
| | - Rommel Mallari
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA
| | - Andrew Pipathsouk
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA
| | - Amrita Das
- Cardiometabolic Disorders, Amgen Research, South San Francisco, CA, USA
| | - Mei-Chu Lo
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA
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35
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Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, Beliveau BJ, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT. 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nat Methods 2020; 17:822-832. [PMID: 32719531 PMCID: PMC7537785 DOI: 10.1038/s41592-020-0890-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/08/2020] [Indexed: 12/31/2022]
Abstract
There is a need for methods that can image chromosomes with genome-wide coverage, as well as greater genomic and optical resolution. We introduce OligoFISSEQ, a suite of three methods that leverage fluorescence in situ sequencing (FISSEQ) of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. Applying OligoFISSEQ to human diploid fibroblast cells, we show how four rounds of sequencing are sufficient to produce 3D maps of 36 genomic targets across six chromosomes in hundreds to thousands of cells, implying a potential to image thousands of targets in only five to eight rounds of sequencing. We also use OligoFISSEQ to trace chromosomes at finer resolution, following the path of the X chromosome through 46 regions, with separate studies showing compatibility of OligoFISSEQ with immunocytochemistry. Finally, we combined OligoFISSEQ with OligoSTORM, laying the foundation for accelerated single-molecule super-resolution imaging of large swaths of, if not entire, human genomes.
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Affiliation(s)
- Huy Q Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard Medical School, Boston, MA, USA
| | | | - Elliot A Hershberg
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Paul L Reginato
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard Medical School, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mohammed Hannan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard Medical School, Boston, MA, USA
| | - Evan R Daugharthy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- ReadCoor, Cambridge, MA, USA
- ReadCoor, Cambridge, MA, USA
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- CRG, BIST, Barcelona, Spain.
- Pompeu Fabra University, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute, Harvard Medical School, Boston, MA, USA.
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36
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Tavakoli S, Liu Y, Potts JL, Rouhanifard SH. Click chemistry-based amplification and detection of endogenous RNA and DNA molecules in situ using clampFISH probes. Methods Enzymol 2020; 641:459-476. [PMID: 32713535 DOI: 10.1016/bs.mie.2020.04.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Direct labeling and measurement of gene expression in single cells show the tremendous variability otherwise hidden in bulk measurements. Single-molecule RNA fluorescence in situ hybridization (FISH) has become a mainstay in laboratories worldwide for measuring gene expression with precision. However, this method remains relatively low throughput because the total fluorescent signal produced is weak and requires long exposure times and high magnification microscopy, which limits the total number of cells sampled in each image. As such, it is experimentally difficult and time-consuming to sample a large enough population of cells to visualize and quantify specific gene expression of rare cells directly. Several FISH-based tools were recently developed that retain single-molecule sensitivity and specificity while greatly amplifying the fluorescent signal, thus making FISH-based analysis possible using standard microscopes with low magnification objectives. These tools have also enabled the detection of smaller and more specific targets like splice junctions or single nucleotide polymorphisms. Here we will describe one such tool, clampFISH, an oligonucleotide-based fluorescence amplification strategy for visualizing genomic loci and individual RNA transcripts in fixed cells. ClampFISH maintains specificity while amplifying fluorescent signals, making it amenable to high throughput assays such as low magnification microscopy, spatial transcriptomics, and flow sorting. The clampFISH technique involves probing the target RNA or DNA using a series of C-shaped oligonucleotide probes, each with a 3' azide and a 5' alkyne. Hybridization of the probe with the target nucleic acid brings the azide and the alkyne in close proximity, allowing for ligation via bioorthogonal click chemistry (CuAAC). As a result, the probe forms a closed loop around the target sequence, thus enabling stringent washes to remove nonspecific binding in further rounds of amplification and retention of signal throughout liquid handling steps. Iterative rounds of hybridization with C-shaped, fluorescently labeled probes exponentially amplify the fluorescent signal. ClampFISH is simple to implement and expands the utility of in situ hybridization for multiple high throughput techniques such as low magnification microscopy, flow cytometry, and sorting based on RNA expression levels.
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Affiliation(s)
- Sepideh Tavakoli
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Yifang Liu
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Jacob L Potts
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Sara H Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, MA, United States.
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Nicotinic Receptor Subunit Distribution in Auditory Cortex: Impact of Aging on Receptor Number and Function. J Neurosci 2020; 40:5724-5739. [PMID: 32541068 DOI: 10.1523/jneurosci.0093-20.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 01/08/2023] Open
Abstract
The presence of novel or degraded communication sounds likely results in activation of basal forebrain cholinergic neurons increasing release of ACh onto presynaptic and postsynaptic nAChRs in primary auditory cortex (A1). nAChR subtypes include high-affinity heteromeric nAChRs commonly composed of α4 and β2 subunits and low-affinity homomeric nAChRs composed of α7 subunits. In young male FBN rats, we detail the following: (1) the distribution/expression of nAChR subunit transcripts in excitatory (VGluT1) and inhibitory (VGAT) neurons across A1 layers; (2) heteromeric nAChR binding across A1 layers; and (3) nAChR excitability in A1 layer (L) 5 cells. In aged rats, we detailed the impact of aging on A1 nAChR subunit expression across layers, heteromeric nAChR receptor binding, and nAChR excitability of A1 L5 cells. A majority of A1 cells coexpressed transcripts for β2 and α4 with or without α7, while dispersed subpopulations expressed β2 and α7 or α7 alone. nAChR subunit transcripts were expressed in young excitatory and inhibitory neurons across L2-L6. Transcript abundance varied across layers, and was highest for β2 and α4. Significant age-related decreases in nAChR subunit transcript expression (message) and receptor binding (protein) were observed in L2-6, most pronounced in infragranular layers. In vitro patch-clamp recordings from L5B pyramidal output neurons showed age-related nAChR subunit-selective reductions in postsynaptic responses to ACh. Age-related losses of nAChR subunits likely impact ways in which A1 neurons respond to ACh release. While the elderly require additional resources to disambiguate degraded speech codes, resources mediated by nAChRs may be compromised with aging.SIGNIFICANCE STATEMENT When attention is required, cholinergic basal forebrain neurons may trigger increased release of ACh onto auditory neurons in primary auditory cortex (A1). Laminar and phenotypic differences in neuronal nAChR expression determine ways in which A1 neurons respond to release of ACh in challenging acoustic environments. This study detailed the distribution and expression of nAChR subunit transcript and protein across A1 layers in young and aged rats. Results showed a differential distribution of nAChR subunits across A1 layers. Age-related decreases in transcript/protein expression were reflected in age-related subunit specific functional loss of nAChR signaling to ACh application in A1 layer 5. Together, these findings could reflect the age-related decline in selective attention observed in the elderly.
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McKinley KL, Castillo-Azofeifa D, Klein OD. Tools and Concepts for Interrogating and Defining Cellular Identity. Cell Stem Cell 2020; 26:632-656. [PMID: 32386555 PMCID: PMC7250495 DOI: 10.1016/j.stem.2020.03.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Defining the mechanisms that generate specialized cell types and coordinate their functions is critical for understanding organ development and renewal. New tools and discoveries are challenging and refining our definitions of a cell type. A rapidly growing toolkit for single-cell analyses has expanded the number of markers that can be assigned to a cell simultaneously, revealing heterogeneity within cell types that were previously regarded as homogeneous populations. Additionally, cell types defined by specific molecular markers can exhibit distinct, context-dependent functions; for example, between tissues in homeostasis and those responding to damage. Here we review the current technologies used to identify and characterize cells, and we discuss how experimental and pathological perturbations are adding increasing complexity to our definitions of cell identity.
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Affiliation(s)
- Kara L McKinley
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - David Castillo-Azofeifa
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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39
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Lee EJ, Chiang WCJ, Kroeger H, Bi CX, Chao DL, Skowronska-Krawczyk D, Mastey RR, Tsang SH, Chea L, Kim K, Lambert SR, Grandjean JM, Baumann B, Audo I, Kohl S, Moore AT, Wiseman RL, Carroll J, Lin JH. Multiexon deletion alleles of ATF6 linked to achromatopsia. JCI Insight 2020; 5:136041. [PMID: 32271167 PMCID: PMC7205249 DOI: 10.1172/jci.insight.136041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
Achromatopsia (ACHM) is an autosomal recessive disease that results in severe visual loss. Symptoms of ACHM include impaired visual acuity, nystagmus, and photoaversion starting from infancy; furthermore, ACHM is associated with bilateral foveal hypoplasia and absent or severely reduced cone photoreceptor function on electroretinography. Here, we performed genetic sequencing in 3 patients from 2 families with ACHM, identifying and functionally characterizing 2 mutations in the activating transcription factor 6 (ATF6) gene. We identified a homozygous deletion covering exons 8-14 of the ATF6 gene from 2 siblings from the same family. In another patient from a different family, we identified a heterozygous deletion covering exons 2 and 3 of the ATF6 gene found in trans with a previously identified ATF6 c.970C>T (p.Arg324Cys) ACHM disease allele. Recombinant ATF6 proteins bearing these exon deletions showed markedly impaired transcriptional activity by qPCR and RNA-Seq analysis compared with WT-ATF6. Finally, RNAscope revealed that ATF6 and the related ATF6B transcripts were expressed in cones as well as in all retinal layers in normal human retina. Overall, our data identify loss-of-function ATF6 disease alleles that cause human foveal disease.
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Affiliation(s)
- Eun-Jin Lee
- Department of Ophthalmology, Shiley Eye Institute, and
- Department of Pathology, UCSD, San Diego, California, USA
- Department of Ophthalmology, Stanford University, Stanford, California, USA
| | - Wei-Chieh Jerry Chiang
- Department of Pathology, UCSD, San Diego, California, USA
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Heike Kroeger
- Department of Pathology, UCSD, San Diego, California, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | | | | | | | - Rebecca R. Mastey
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Stephen H. Tsang
- Departments of Ophthalmology and Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Leon Chea
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Kyle Kim
- Department of Pathology, UCSD, San Diego, California, USA
| | - Scott R. Lambert
- Department of Ophthalmology, Stanford University, Stanford, California, USA
| | - Julia M.D. Grandjean
- Department of Molecular Medicine, The Scripps Research Institute, San Diego, California, USA
| | - Britta Baumann
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC1423, Paris, France
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Anthony T. Moore
- Department of Ophthalmology, UCSF, San Francisco, California, USA
| | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, San Diego, California, USA
| | - Joseph Carroll
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jonathan H. Lin
- Department of Ophthalmology, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University, Stanford, California, USA
- VA Palo Alto Healthcare System, Palo Alto, California, USA
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40
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MYCN RNA levels determined by quantitative in situ hybridization is better than MYCN gene dosages in predicting the prognosis of neuroblastoma patients. Mod Pathol 2020; 33:531-540. [PMID: 31695155 DOI: 10.1038/s41379-019-0410-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023]
Abstract
The aim of this study was to investigate the prognostic role of MYCN RNA expression by quantitative RNA in situ hybridization and its association with MYCN amplification in neuroblastoma. MYCN RNA expression in 69 neuroblastoma tumors was evaluated by an ultrasensitive quantitative RNA in situ hybridization technique, RNAscope. The correlations between MYCN RNA expression, MYCN amplification, and other clinicopathologic variables of neuroblastoma were analyzed. High expression levels of MYCN RNA were detected 30 of 69 (43%) of neuroblastomas, mainly in those with undifferentiated or poorly differentiated histology. High expression of MYCN RNA was significantly associated with MYCN amplification (P < 0.001) and other adversely prognostic factors, including older age at diagnosis (>18 months, P = 0.017), advanced clinical stage (International Neuroblastoma Staging System stage 3, 4, P = 0.002), unfavorable International Neuroblastoma Pathology Classification tumor histology (P < 0.001), and high-risk Children's Oncology Group risk group (P = 0.001). In Kaplan-Meier analysis, MYCN RNA levels determined by quantitative in situ hybridization were better than MYCN gene dosages determined by chromogenic in situ hybridization in discriminating good and poor prognostic groups of neuroblastoma patients. In multivariate analysis, we further confirmed that high expression of MYCN RNA was an independent adverse prognostic factor for event-free and overall survival. Furthermore, high expression of MYCN RNA predicted unfavorable survival outcomes for neuroblastoma patients with MYCN non-amplification or high-risk Children's Oncology Group risk group. In conclusion, our study is the first report to show the application of MYCN RNA in situ hybridization in neuroblastoma and established that high expression of MYCN RNA could be a better biomarker than MYCN amplification for predicting poor prognosis of neuroblastoma patients.
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41
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Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 2020; 8:e8806. [PMID: 32219032 PMCID: PMC7085896 DOI: 10.7717/peerj.8806] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual targets. Taken together, this information will guide the methods development process for investigators that seek to perform FISH in organisms that lack documented or optimized protocols.
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Affiliation(s)
- Alexander P Young
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| | - Daniel J Jackson
- Department of Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
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42
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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43
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Voith von Voithenberg L, Fomitcheva Khartchenko A, Huber D, Schraml P, Kaigala GV. Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity. Nucleic Acids Res 2020; 48:e17. [PMID: 31853536 PMCID: PMC7026647 DOI: 10.1093/nar/gkz1151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/20/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases.
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Affiliation(s)
| | | | - Deborah Huber
- IBM Research Zürich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| | - Peter Schraml
- University Hospital Zurich, Department of Pathology and Molecular Pathology, Schmelzbergstr. 12, CH-8091 Zurich, Switzerland
| | - Govind V Kaigala
- IBM Research Zürich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
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44
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Lauter G, Söll I, Hauptmann G. Sensitive Multiplexed Fluorescent In Situ Hybridization Using Enhanced Tyramide Signal Amplification and Its Combination with Immunofluorescent Protein Visualization in Zebrafish. Methods Mol Biol 2020; 2047:397-409. [PMID: 31552667 DOI: 10.1007/978-1-4939-9732-9_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fluorescent in situ hybridization (FISH) provides sensitive detection and visualization of RNA transcripts in tissues and cells with high resolution. We present here a multiplex RNA FISH method using enhanced tyramide signal amplification (TSA) for colocalization analysis of three different transcripts in intact zebrafish brains. To achieve enhancement of fluorescent signals, essential steps of the FISH procedure are optimized including embryo permeability, hybridization efficacy, and fluorogenic TSA-reaction conditions. Critical to this protocol, the enzymatic peroxidase (PO) reactivity is significantly improved by the application of viscosity-increasing polymers, PO accelerators, and highly effective bench-made tyramide substrates. These advancements lead to an optimized TSA-FISH protocol with dramatically increased signal intensity and signal-to-background ratio allowing for visualization of three mRNA transcript patterns simultaneously. The TSA-FISH procedure can be combined with immunofluorescence (IF) to compare mRNA transcript and protein expression patterns.
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Affiliation(s)
- Gilbert Lauter
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
| | - Iris Söll
- Department of Molecular Biosciences, The Wenner-Gren Institute, MBW, Stockholm University, Stockholm, Sweden
| | - Giselbert Hauptmann
- Department of Molecular Biosciences, The Wenner-Gren Institute, MBW, Stockholm University, Stockholm, Sweden.
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45
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Nielsen BS, Møller T, Kjems J. Automated One-Double-Z Pair BaseScope™ for CircRNA In Situ Hybridization. Methods Mol Biol 2020; 2148:379-388. [PMID: 32394395 DOI: 10.1007/978-1-0716-0623-0_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Circular RNAs (circRNAs) are single-stranded RNA, typically exons, connected head to tail by back-splicing. The functions of circRNAs include binding of microRNA, regulation of transcription, regulation of alternative splicing, and modulation of immune response. As for other RNA transcripts their levels vary during development and may also become deregulated during disease progression. Different from linear RNAs, the circRNAs are not susceptible to traditional exonuclease activity and therefore more stable in tissues and blood. This makes the circRNAs an attractive new group of potential biomarkers. Specific detection of circRNAs in situ is challenged by the need to discriminate bona fide circRNAs from the linear precursor forms and splice variants that contain largely overlapping sequences. Knowing the sequence around the splice junction site makes the branched DNA probe technology, BaseScope, suitable for selective detection of unique circRNAs. Here, we present the automated application of BaseScope with a one-double-Z pair probe set designed for the junction of circHIPK3.
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Affiliation(s)
| | - Trine Møller
- Molecular Histology, Bioneer A/S, Hørsholm, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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46
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Abstract
The premise of this book is the importance of the tumor microenvironment (TME). Until recently, most research on and clinical attention to cancer biology, diagnosis, and prognosis were focused on the malignant (or premalignant) cellular compartment that could be readily appreciated using standard morphology-based imaging.
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47
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Abstract
As RNA in situ hybridization (ISH) moves into the mainstream lab and increasingly into clinical adoption and additional multiplexing techniques are developed to enable further RNA ISH identification, a set of guidelines on the validation of ISH is required. These guidelines include choice of methods, appropriate controls, and protocol optimization as well as a central core message of understanding the target, understanding the ISH technique, and using the most appropriate controlling mechanisms to enable reproducible and trustworthy data to be obtained.
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48
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Visualization of Positive and Negative Sense Viral RNA for Probing the Mechanism of Direct-Acting Antivirals against Hepatitis C Virus. Viruses 2019; 11:v11111039. [PMID: 31717338 PMCID: PMC6893808 DOI: 10.3390/v11111039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
RNA viruses are highly successful pathogens and are the causative agents for many important diseases. To fully understand the replication of these viruses it is necessary to address the roles of both positive-strand RNA ((+)RNA) and negative-strand RNA ((−)RNA), and their interplay with viral and host proteins. Here we used branched DNA (bDNA) fluorescence in situ hybridization (FISH) to stain both the abundant (+)RNA and the far less abundant (−)RNA in both hepatitis C virus (HCV)- and Zika virus-infected cells, and combined these analyses with visualization of viral proteins through confocal imaging. We were able to phenotypically examine HCV-infected cells in the presence of uninfected cells and revealed the effect of direct-acting antivirals on HCV (+)RNA, (−)RNA, and protein, within hours of commencing treatment. Herein, we demonstrate that bDNA FISH is a powerful tool for the study of RNA viruses that can provide insights into drug efficacy and mechanism of action.
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49
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Soares RJ, Maglieri G, Gutschner T, Diederichs S, Lund AH, Nielsen BS, Holmstrøm K. Evaluation of fluorescence in situ hybridization techniques to study long non-coding RNA expression in cultured cells. Nucleic Acids Res 2019; 46:e4. [PMID: 29059327 PMCID: PMC5758870 DOI: 10.1093/nar/gkx946] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/04/2017] [Indexed: 02/06/2023] Open
Abstract
Deciphering the functions of long non-coding RNAs (lncRNAs) is facilitated by visualization of their subcellular localization using in situ hybridization (ISH) techniques. We evaluated four different ISH methods for detection of MALAT1 and CYTOR in cultured cells: a multiple probe detection approach with or without enzymatic signal amplification, a branched-DNA (bDNA) probe and an LNA-modified probe with enzymatic signal amplification. All four methods adequately stained MALAT1 in the nucleus in all of three cell lines investigated, HeLa, NHDF and T47D, and three of the methods detected the less expressed CYTOR. The sensitivity of the four ISH methods was evaluated by image analysis. In all three cell lines, the two methods involving enzymatic amplification gave the most intense MALAT1 signal, but the signal-to-background ratios were not different. CYTOR was best detected using the bDNA method. All four ISH methods showed significantly reduced MALAT1 signal in knock-out cells, and siRNA-induced knock-down of CYTOR resulted in significantly reduced CYTOR ISH signal, indicating good specificity of the probe designs and detection systems. Our data suggest that the ISH methods allow detection of both abundant and less abundantly expressed lncRNAs, although the latter required the use of the most specific and sensitive probe detection system.
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Affiliation(s)
| | - Giulia Maglieri
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Tony Gutschner
- Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany.,Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK), Partner Site Freiburg, D-79106 Freiburg, Germany
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Kim Holmstrøm
- Bioneer A/S, Kogle Allé 2, DK-2970 Hørsholm, Denmark
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50
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Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P. SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat Methods 2019; 16:533-544. [PMID: 31110282 PMCID: PMC6544483 DOI: 10.1038/s41592-019-0404-0] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 04/03/2019] [Indexed: 12/24/2022]
Abstract
Fluorescence in situ hybridization (FISH) reveals the abundance and positioning of nucleic acid sequences in fixed samples. Despite recent advances in multiplexed amplification of FISH signals, it remains challenging to achieve high levels of simultaneous amplification and sequential detection with high sampling efficiency and simple workflows. Here we introduce signal amplification by exchange reaction (SABER), which endows oligonucleotide-based FISH probes with long, single-stranded DNA concatemers that aggregate a multitude of short complementary fluorescent imager strands. We show that SABER amplified RNA and DNA FISH signals (5- to 450-fold) in fixed cells and tissues. We also applied 17 orthogonal amplifiers against chromosomal targets simultaneously and detected mRNAs with high efficiency. We then used 10-plex SABER-FISH to identify in vivo introduced enhancers with cell-type-specific activity in the mouse retina. SABER represents a simple and versatile molecular toolkit for rapid and cost-effective multiplexed imaging of nucleic acid targets.
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Affiliation(s)
- Jocelyn Y Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sylvain W Lapan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brian J Beliveau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Allen Zhu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Hiroshi M Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Constance L Cepko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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