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Mu X, Ma C, Mei X, Liao J, Bojar R, Kuang S, Rong Q, Yao J, Zhang YS. On-demand expansion fluorescence and photoacoustic microscopy (ExFLPAM). PHOTOACOUSTICS 2024; 38:100610. [PMID: 38726025 PMCID: PMC11079527 DOI: 10.1016/j.pacs.2024.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 03/04/2024] [Accepted: 04/21/2024] [Indexed: 05/12/2024]
Abstract
Expansion microscopy (ExM) is a promising technology that enables nanoscale imaging on conventional optical microscopes by physically magnifying the specimens. Here, we report the development of a strategy that enables i) on-demand labeling of subcellular organelles in live cells for ExM through transfection of fluorescent proteins that are well-retained during the expansion procedure; and ii) non-fluorescent chromogenic color-development towards efficient bright-field and photoacoustic imaging in both planar and volumetric formats, which is applicable to both cultured cells and biological tissues. Compared to the conventional ExM methods, our strategy provides an expanded toolkit, which we term as expansion fluorescence and photoacoustic microscopy (ExFLPAM), by allowing on-demand fluorescent protein labeling of cultured cells, as well as non-fluorescent absorption contrast-imaging of biological samples.
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Affiliation(s)
- Xuan Mu
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Xuan Mei
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Junlong Liao
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Rebecca Bojar
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
- Barnard College, Columbia University, New York, NY 10027, USA
| | - Sizhe Kuang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Qiangzhou Rong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
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2
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Wu X, Xu W, Deng L, Li Y, Wang Z, Sun L, Gao A, Wang H, Yang X, Wu C, Zou Y, Yan K, Liu Z, Zhang L, Du G, Yang L, Lin D, Yue J, Wang P, Han Y, Fu Z, Dai J, Cao G. Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing. Nat Biomed Eng 2024:10.1038/s41551-024-01205-7. [PMID: 38745110 DOI: 10.1038/s41551-024-01205-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/01/2024] [Indexed: 05/16/2024]
Abstract
Technology for spatial multi-omics aids the discovery of new insights into cellular functions and disease mechanisms. Here we report the development and applicability of multi-omics in situ pairwise sequencing (MiP-seq), a method for the simultaneous detection of DNAs, RNAs, proteins and biomolecules at subcellular resolution. Compared with other in situ sequencing methods, MiP-seq enhances decoding capacity and reduces sequencing and imaging costs while maintaining the efficacy of detection of gene mutations, allele-specific expression and RNA modifications. MiP-seq can be integrated with in vivo calcium imaging and Raman imaging, which enabled us to generate a spatial multi-omics atlas of mouse brain tissues and to correlate gene expression with neuronal activity and cellular biochemical fingerprints. We also report a sequential dilution strategy for resolving optically crowded signals during in situ sequencing. High-throughput in situ pairwise sequencing may facilitate the multidimensional analysis of molecular and functional maps of tissues.
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Affiliation(s)
- Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lulu Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yue Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhongchao Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Leqiang Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Anran Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haoqi Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaodan Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yanyan Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Keji Yan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhixiang Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lingkai Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Guohua Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liyao Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Junqiu Yue
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Wang
- Britton Chance Centre for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Centre for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Yunyun Han
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhenfang Fu
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jinxia Dai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
- Faculty of Life and Health Sciences, and Shenzhen-Hong Kong Institute of Brain Science and The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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3
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White-Mathieu BM, Baskin JM. Super-Resolution Imaging of Clickable Lipids With Lipid Expansion Microscopy (LExM). Curr Protoc 2024; 4:e1051. [PMID: 38779885 PMCID: PMC11125533 DOI: 10.1002/cpz1.1051] [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: 05/25/2024]
Abstract
Fluorescent imaging of cellular membranes is challenged by the size of lipid bilayers, which are smaller than the diffraction limit of light. Recently, expansion microscopy (ExM) has emerged as an approachable super-resolution method that requires only widely accessible confocal microscopes. In this method, biomolecules of interest are anchored to hydrogel-based, polymeric networks that are expanded through osmosis to physically separate and resolve features smaller than the diffraction limit of light. Whereas ExM has been employed for super-resolution imaging of proteins, DNA, RNA, and glycans, the application of this method to the study of lipids is challenged by the requirement of permeabilization procedures that remove lipids and compromise the integrity of the membrane. Here, we describe our recently developed protocols for lipid expansion microscopy (LExM), a method that enables ExM of membranes without permeabilization. These detailed protocols and accompanying commentary sections aim to make LExM accessible to any experimentalist interested in imaging membranes with super-resolution. © 2024 Wiley Periodicals LLC. Basic Protocol 1: LExM of alkyne-choline lipids Basic Protocol 2: LExM of IMPACT-labeled lipids Basic Protocol 3: LExM of clickable cholesterol Basic Protocol 4: Determining the expansion factor.
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Affiliation(s)
- Brittany M. White-Mathieu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A. Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife 2024; 12:RP91357. [PMID: 38577979 PMCID: PMC10997330 DOI: 10.7554/elife.91357] [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: 04/06/2024] Open
Abstract
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
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Affiliation(s)
- Allison Coté
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Aoife O'Farrell
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Ian Dardani
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Margaret Dunagin
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Chris Coté
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Yihan Wan
- School of Life Sciences, Westlake UniversityHangzhouChina
| | - Sareh Bayatpour
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Heather L Drexler
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Katherine A Alexander
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Fei Chen
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Asmamaw T Wassie
- Department of Cell and Molecular Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Rohan Patel
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Kenneth Pham
- Department of Cell and Molecular Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Edward S Boyden
- Departments of Biological Engineering and Brain and Cognitive Sciences, Media Lab and McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Shelly Berger
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | | | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Arjun Raj
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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5
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Hümpfer N, Thielhorn R, Ewers H. Expanding boundaries - a cell biologist's guide to expansion microscopy. J Cell Sci 2024; 137:jcs260765. [PMID: 38629499 PMCID: PMC11058692 DOI: 10.1242/jcs.260765] [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: 04/19/2024] Open
Abstract
Expansion microscopy (ExM) is a revolutionary novel approach to increase resolution in light microscopy. In contrast to super-resolution microscopy methods that rely on sophisticated technological advances, including novel instrumentation, ExM instead is entirely based on sample preparation. In ExM, labeled target molecules in fixed cells are anchored in a hydrogel, which is then physically enlarged by osmotic swelling. The isotropic swelling of the hydrogel pulls the labels apart from one another, and their relative organization can thus be resolved using conventional microscopes even if it was below the diffraction limit of light beforehand. As ExM can additionally benefit from the technical resolution enhancements achieved by super-resolution microscopy, it can reach into the nanometer range of resolution with an astoundingly low degree of error induced by distortion during the physical expansion process. Because the underlying chemistry is well understood and the technique is based on a relatively simple procedure, ExM is easily reproducible in non-expert laboratories and has quickly been adopted to address an ever-expanding spectrum of problems across the life sciences. In this Review, we provide an overview of this rapidly expanding new field, summarize the most important insights gained so far and attempt to offer an outlook on future developments.
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Affiliation(s)
- Nadja Hümpfer
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ria Thielhorn
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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6
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Liffner B, Absalon S. Expansion microscopy of apicomplexan parasites. Mol Microbiol 2024; 121:619-635. [PMID: 37571814 DOI: 10.1111/mmi.15135] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023]
Abstract
Apicomplexan parasites comprise significant pathogens of humans, livestock and wildlife, but also represent a diverse group of eukaryotes with interesting and unique cell biology. The study of cell biology in apicomplexan parasites is complicated by their small size, and historically this has required the application of cutting-edge microscopy techniques to investigate fundamental processes like mitosis or cell division in these organisms. Recently, a technique called expansion microscopy has been developed, which rather than increasing instrument resolution like most imaging modalities, physically expands a biological sample. In only a few years since its development, a derivative of expansion microscopy known as ultrastructure-expansion microscopy (U-ExM) has been widely adopted and proven extremely useful for studying cell biology of Apicomplexa. Here, we review the insights into apicomplexan cell biology that have been enabled through the use of U-ExM, with a specific focus on Plasmodium, Toxoplasma and Cryptosporidium. Further, we summarize emerging expansion microscopy modifications and modalities and forecast how these may influence the field of parasite cell biology in future.
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Affiliation(s)
- Benjamin Liffner
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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7
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Woodworth MA, Lakadamyali M. Toward a comprehensive view of gene architecture during transcription. Curr Opin Genet Dev 2024; 85:102154. [PMID: 38309073 PMCID: PMC10989512 DOI: 10.1016/j.gde.2024.102154] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
The activation of genes within the nucleus of eukaryotic cells is a tightly regulated process, orchestrated by a complex interplay of various physical properties and interacting factors. Studying the multitude of components and features that collectively contribute to gene activation has proven challenging due to the complexities of simultaneously visualizing the dynamic and transiently interacting elements that coalesce within the small space occupied by each individual gene. However, various labeling and imaging advances are now starting to overcome this challenge, enabling visualization of gene activation at different lengths and timescales. In this review, we aim to highlight these microscopy-based advances and suggest how they can be combined to provide a comprehensive view of the mechanisms regulating gene activation.
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Affiliation(s)
- Marcus A Woodworth
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Tišma M, Bock FP, Kerssemakers J, Antar H, Japaridze A, Gruber S, Dekker C. Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells. Nat Commun 2024; 15:2737. [PMID: 38548820 PMCID: PMC10979009 DOI: 10.1038/s41467-024-47094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Bacterial chromosomes are folded into tightly regulated three-dimensional structures to ensure proper transcription, replication, and segregation of the genetic information. Direct visualization of chromosomal shape within bacterial cells is hampered by cell-wall confinement and the optical diffraction limit. Here, we combine cell-shape manipulation strategies, high-resolution fluorescence microscopy techniques, and genetic engineering to visualize the shape of unconfined bacterial chromosome in real-time in live Bacillus subtilis cells that are expanded in volume. We show that the chromosomes predominantly exhibit crescent shapes with a non-uniform DNA density that is increased near the origin of replication (oriC). Additionally, we localized ParB and BsSMC proteins - the key drivers of chromosomal organization - along the contour of the crescent chromosome, showing the highest density near oriC. Opening of the BsSMC ring complex disrupted the crescent chromosome shape and instead yielded a torus shape. These findings help to understand the threedimensional organization of the chromosome and the main protein complexes that underlie its structure.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Florian Patrick Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jacob Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
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9
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Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K. Mapping human tissues with highly multiplexed RNA in situ hybridization. Nat Commun 2024; 15:2511. [PMID: 38509069 PMCID: PMC10954689 DOI: 10.1038/s41467-024-46437-y] [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: 08/16/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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Affiliation(s)
- Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Chien-Ju Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Ho Suk Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Electrical Engineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mahsa Nafisi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yixu Yuan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jinghui Song
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Blue B Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, 98103, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Altos Labs, San Diego, CA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | | | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Altos Labs, San Diego, CA, USA.
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10
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Pesce L, Ricci P, Sportelli G, Belcari N, Sancataldo G. Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging. SMALL METHODS 2024:e2301715. [PMID: 38461540 DOI: 10.1002/smtd.202301715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/10/2024] [Indexed: 03/12/2024]
Abstract
Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.
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Affiliation(s)
- Luca Pesce
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Pietro Ricci
- Department of Applied Physics, University of Barcelona, C/Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Giancarlo Sportelli
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Nicola Belcari
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Giuseppe Sancataldo
- Department of Physics - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, Palermo, 90128, Italy
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11
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Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES. Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583776. [PMID: 38496681 PMCID: PMC10942445 DOI: 10.1101/2024.03.07.583776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines a novel membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validated the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supported the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrated the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yielded ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.
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Affiliation(s)
- Tay Won Shin
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hao Wang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Picower Inst. for Learning and Memory, Cambridge
| | - Chi Zhang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Bobae An
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Yangning Lu
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Elizabeth Zhang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Xiaotang Lu
- Department of Cellular and Molecular Biology, Harvard University, Cambridge, MA, United States
| | | | - Jeong Seuk Kang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Amauche Emenari
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Panagiotis Symvoulidis
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Shoh Asano
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Leanne Lin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Emma K. Costa
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Adam H. Marblestone
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- present address: Convergent Research
| | - Narayanan Kasthuri
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Picower Inst. for Learning and Memory, Cambridge
| | - Edward S. Boyden
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- K. Lisa Yang Center for Bionics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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12
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Shi Y, Huang L, Dong H, Yang M, Ding W, Zhou X, Lu T, Liu Z, Zhou X, Wang M, Zeng B, Sun Y, Zhong S, Wang B, Wang W, Yin C, Wang X, Wu Q. Decoding the spatiotemporal regulation of transcription factors during human spinal cord development. Cell Res 2024; 34:193-213. [PMID: 38177242 PMCID: PMC10907391 DOI: 10.1038/s41422-023-00897-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/02/2023] [Indexed: 01/06/2024] Open
Abstract
The spinal cord is a crucial component of the central nervous system that facilitates sensory processing and motor performance. Despite its importance, the spatiotemporal codes underlying human spinal cord development have remained elusive. In this study, we have introduced an image-based single-cell transcription factor (TF) expression decoding spatial transcriptome method (TF-seqFISH) to investigate the spatial expression and regulation of TFs during human spinal cord development. By combining spatial transcriptomic data from TF-seqFISH and single-cell RNA-sequencing data, we uncovered the spatial distribution of neural progenitor cells characterized by combinatorial TFs along the dorsoventral axis, as well as the molecular and spatial features governing neuronal generation, migration, and differentiation along the mediolateral axis. Notably, we observed a sandwich-like organization of excitatory and inhibitory interneurons transiently appearing in the dorsal horns of the developing human spinal cord. In addition, we integrated data from 10× Visium to identify early and late waves of neurogenesis in the dorsal horn, revealing the formation of laminas in the dorsal horns. Our study also illuminated the spatial differences and molecular cues underlying motor neuron (MN) diversification, and the enrichment of Amyotrophic Lateral Sclerosis (ALS) risk genes in MNs and microglia. Interestingly, we detected disease-associated microglia (DAM)-like microglia groups in the developing human spinal cord, which are predicted to be vulnerable to ALS and engaged in the TYROBP causal network and response to unfolded proteins. These findings provide spatiotemporal transcriptomic resources on the developing human spinal cord and potential strategies for spinal cord injury repair and ALS treatment.
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Affiliation(s)
- Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, China.
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Yang
- Changping Laboratory, Beijing, China
| | - Wenyu Ding
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Xiang Zhou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xin Zhou
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Changping Laboratory, Beijing, China
| | - Yinuo Sun
- Changping Laboratory, Beijing, China
| | - Suijuan Zhong
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
| | - Qian Wu
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
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13
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Baghdasaryan O, Khan S, Lin JC, Lee-Kin J, Hsu CY, Hu CMJ, Tan C. Synthetic control of living cells by intracellular polymerization. Trends Biotechnol 2024; 42:241-252. [PMID: 37743158 PMCID: PMC11132853 DOI: 10.1016/j.tibtech.2023.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
An emerging cellular engineering method creates synthetic polymer matrices inside cells. By contrast with classical genetic, enzymatic, or radioactive techniques, this materials-based approach introduces non-natural polymers inside cells, thus modifying cellular states and functionalities. Here, we cover various materials and chemistries that have been exploited to create intracellular polymer matrices. In addition, we discuss emergent cellular properties due to the intracellular polymerization, including nonreplicating but active metabolism, maintenance of membrane integrity, and resistance to environmental stressors. We also discuss past work and future opportunities for developing and applying synthetic cells that contain intracellular polymers. The materials-based approach will usher in new applications of synthetic cells for broad biotechnological applications.
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Affiliation(s)
- Ofelya Baghdasaryan
- Biomedical Engineering, University of California Davis, Davis, CA 95616-5270, USA
| | - Shahid Khan
- Biomedical Engineering, University of California Davis, Davis, CA 95616-5270, USA
| | - Jung-Chen Lin
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Jared Lee-Kin
- Biomedical Engineering, University of California Davis, Davis, CA 95616-5270, USA
| | - Chung-Yao Hsu
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Che-Ming Jack Hu
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Cheemeng Tan
- Biomedical Engineering, University of California Davis, Davis, CA 95616-5270, USA.
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14
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Valdes PA, Yu CC(J, Aronson J, Ghosh D, Zhao Y, An B, Bernstock JD, Bhere D, Felicella MM, Viapiano MS, Shah K, Chiocca EA, Boyden ES. Improved immunostaining of nanostructures and cells in human brain specimens through expansion-mediated protein decrowding. Sci Transl Med 2024; 16:eabo0049. [PMID: 38295184 PMCID: PMC10911838 DOI: 10.1126/scitranslmed.abo0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Proteins are densely packed in cells and tissues, where they form complex nanostructures. Expansion microscopy (ExM) variants have been used to separate proteins from each other in preserved biospecimens, improving antibody access to epitopes. Here, we present an ExM variant, decrowding expansion pathology (dExPath), that can expand proteins away from each other in human brain pathology specimens, including formalin-fixed paraffin-embedded (FFPE) clinical specimens. Immunostaining of dExPath-expanded specimens reveals, with nanoscale precision, previously unobserved cellular structures, as well as more continuous patterns of staining. This enhanced molecular staining results in observation of previously invisible disease marker-positive cell populations in human glioma specimens, with potential implications for tumor aggressiveness. dExPath results in improved fluorescence signals even as it eliminates lipofuscin-associated autofluorescence. Thus, this form of expansion-mediated protein decrowding may, through improved epitope access for antibodies, render immunohistochemistry more powerful in clinical science and, perhaps, diagnosis.
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Affiliation(s)
- Pablo A. Valdes
- Department of Neurosurgery, University of Texas Medical Branch, Galveston, TX, 77555
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
| | - Chih-Chieh (Jay) Yu
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Jenna Aronson
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Debarati Ghosh
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
| | - Yongxin Zhao
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA, 15213
| | - Bobae An
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Koch Institute, MIT, Cambridge, MA, USA, 02139
| | - Deepak Bhere
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Department of Pathology, Microbiology and Immunology, School of Medicine Columbia, University of South Carolina, Columbia, SC, USA, 29209
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - Michelle M. Felicella
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA, 77555
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA, 13210
| | - Khalid Shah
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Edward S. Boyden
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
- Koch Institute, MIT, Cambridge, MA, USA, 02139
- MIT Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics, MIT, Cambridge, MA, USA, 02139
- Howard Hughes Medical Institute, Cambridge, MA, USA, 02139
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15
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Haak A, Lesslich HM, Dietzel ID. Visualization of the membrane surface and cytoskeleton of oligodendrocyte progenitor cell growth cones using a combination of scanning ion conductance and four times expansion microscopy. Biol Chem 2024; 405:31-41. [PMID: 37950644 DOI: 10.1515/hsz-2023-0217] [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: 05/16/2023] [Accepted: 10/17/2023] [Indexed: 11/13/2023]
Abstract
Growth cones of oligodendrocyte progenitor cells (OPCs) are challenging to investigate with conventional light microscopy due to their small size. Especially substructures such as filopodia, lamellipodia and their underlying cytoskeleton are difficult to resolve with diffraction limited microscopy. Light microscopy techniques, which surpass the diffraction limit such as stimulated emission depletion microscopy, often require expensive setups and specially trained personnel rendering them inaccessible to smaller research groups. Lately, the invention of expansion microscopy (ExM) has enabled super-resolution imaging with any light microscope without the need for additional equipment. Apart from the necessary resolution, investigating OPC growth cones comes with another challenge: Imaging the topography of membranes, especially label- and contact-free, is only possible with very few microscopy techniques one of them being scanning ion conductance microscopy (SICM). We here present a new imaging workflow combining SICM and ExM, which enables the visualization of OPC growth cone nanostructures. We correlated SICM recordings and ExM images of OPC growth cones captured with a conventional widefield microscope. This enabled the visualization of the growth cones' membrane topography as well as their underlying actin and tubulin cytoskeleton.
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Affiliation(s)
- Annika Haak
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Heiko M Lesslich
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Irmgard D Dietzel
- Department of Biochemistry II, Electrobiochemistry of Neural Cells, Ruhr-Universität Bochum, D-44801 Bochum, Germany
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16
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Park S, Shi X. Expansion Microscopy of Ciliary Proteins. Methods Mol Biol 2024; 2725:79-88. [PMID: 37856018 DOI: 10.1007/978-1-0716-3507-0_4] [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: 10/20/2023]
Abstract
Label-retention expansion microscopy (LR-ExM) is a sample preparation technique, which embeds the cells or tissues in a swellable hydrogel and expands the sample so that one can achieve a high resolution with any conventional fluorescence microscopes. Fluorescence loss during polymerization and protein denaturation have been a major limitation of standard expansion microscopy. To minimize fluorescence loss, LR-ExM uses trifunctional anchors, which can survive from polymerization and denaturation, and then introduce fluorophores after expansion. By using LR-ExM, one can study the structure of primary cilia at molecular-scale resolution with a much higher signal-to-noise ratio, compared with previously introduced expansion microscopy methods. In this chapter, we describe a detailed procedure showing how LR-ExM is used to study ciliary proteins.
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Affiliation(s)
- Sohyeon Park
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA
| | - Xiaoyu Shi
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
- Department of Chemistry, University of California Irvine, Irvine, CA, USA.
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17
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Ciolli Mattioli C, Avraham R. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in Bacteria. Methods Mol Biol 2024; 2784:3-23. [PMID: 38502475 DOI: 10.1007/978-1-0716-3766-1_1] [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: 03/21/2024]
Abstract
In this chapter, we describe in detail how to perform a successful smFISH experiment and how to quantify mRNA transcripts in bacterial cells. The flexibility of the method allows for straightforward adaptation to different bacterial species and experimental conditions. Thanks to the feasibility of the approach, the method can easily be adapted by other laboratories. Finally, we believe that this method has a great potential to generate insights into the complicated life of bacteria.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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18
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Zhuang Y, Shi X. Label-Retention Expansion Microscopy (LR-ExM) for Enhanced Fluorescent Signals using Trifunctional Probes. Curr Protoc 2024; 4:e973. [PMID: 38265180 DOI: 10.1002/cpz1.973] [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: 01/25/2024]
Abstract
Expansion microscopy (ExM) is a super-resolution imaging technique that bypasses the diffraction limit of conventional optical microscopy (∼250 nm) by enlarging samples with a swellable hydrogel. Combined with various light microscopes, ExM enables an effective resolution ranging from 5 to 70 nm. ExM has now been successfully applied to cell, tissue, and whole-organism samples, providing biologists with a low-cost strategy to visualize samples at the molecular level. However, fluorescence signal loss easily happens for beginners and with early versions of ExM protocols. Here, we describe a protocol called label-retention expansion microscopy (LR-ExM), which can preserve and enhance the signal of ExM imaging via a series of trifunctional probes. These trifunctional probes are antibody-based and easy to prepare, and thus suit the needs of most laboratories. © 2024 Wiley Periodicals LLC. Basic Protocol: LR-ExM using trifunctional probes for enhanced fluorescent signals.
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Affiliation(s)
- Yinyin Zhuang
- Department of Developmental and Cell Biology, University of California, Irvine, California
| | - Xiaoyu Shi
- Department of Developmental and Cell Biology, University of California, Irvine, California
- Department of Chemistry, University of California, Irvine, California
- Department of Biomedical Engineering, University of California, Irvine, California
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19
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Valdivieso González D, Jara J, Almendro-Vedia VG, Orgaz B, López-Montero I. Expansion microscopy applied to mono- and dual-species biofilms. NPJ Biofilms Microbiomes 2023; 9:92. [PMID: 38049404 PMCID: PMC10696089 DOI: 10.1038/s41522-023-00460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
Expansion microscopy (ExM) is a new super-resolution technique based on embedding the biological sample within a hydrogel and its physical expansion after swelling. This allows increasing its size by several times while preserving its structural details. Applied to prokaryotic cells, ExM requires digestion steps for efficient expansion as bacteria are surrounded by a rigid cell wall. Furthermore, bacteria can live in social groups forming biofilms, where cells are protected from environmental stresses by a self-produced matrix. The extracellular matrix represents an additional impenetrable barrier for ExM. Here we optimize the current protocols of ExM and apply them to mono- and dual-species biofilms formed by clinical isolates of Limosilactobacillus reuteri, Enterococcus faecalis, Serratia marcescens and Staphylococcus aureus. Using scanning electron microscopy for comparison, our results demonstrate that embedded bacteria expanded 3-fold. Moreover, ExM allowed visualizing the three-dimensional architecture of the biofilm and identifying the distribution of different microbial species and their interactions. We also detected the presence of the extracellular matrix after expansion with a specific stain of the polysaccharide component. The potential applications of ExM in biofilms will improve our understanding of these complex communities and have far-reaching implications for industrial and clinical research.
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Affiliation(s)
- David Valdivieso González
- Dto. Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain
| | - Josué Jara
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Víctor G Almendro-Vedia
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain
| | - Belén Orgaz
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
| | - Iván López-Montero
- Dto. Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain.
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain.
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain.
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20
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Bandeira PT, Ortiz SFDN, Benchimol M, de Souza W. Expansion Microscopy of trichomonads. Exp Parasitol 2023; 255:108629. [PMID: 37802179 DOI: 10.1016/j.exppara.2023.108629] [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: 07/14/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
Light microscopy has significantly advanced in recent decades, especially concerning the increased resolution obtained in fluorescence images. Here we present the Expansion Microscopy (ExM) technique in two parasites, Trichomonas vaginalis and Tritrichomonas foetus, which significantly improved the localization of distinct proteins closely associated with cytoskeleton by immunofluorescence microscopy. The ExM techniques have been used in various cell types, tissues and other protist parasites. It requires the embedment of the samples in a swellable gel that is highly hydrophilic. As a result, cells are expanded 4.5 times in an isotropic manner, offering a spatial resolution of ∼70 nm. We used this new methodology not only to observe the structural organization of protozoa in more detail but also to increase the resolution by immunofluorescence microscopy of two major proteins such as tubulin, found in structures formed by microtubules, and costain 1, the only protein identified until now in the T. foetus's costa, a unique rod-shaped like structure. The individualized microtubules of the axostyle were seen for the first time in fluorescence microscopy and several other details are presented after this technique.
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Affiliation(s)
- Paula Terra Bandeira
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Sharmila Fiama das Neves Ortiz
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Marlene Benchimol
- BIOTRANS-CAXIAS, Universidade do Grande Rio. UNIGRANRIO, Rio de Janeiro, 96200-000, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil.
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
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21
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Wen G, Lycas MD, Jia Y, Leen V, Sauer M, Hofkens J. Trifunctional Linkers Enable Improved Visualization of Actin by Expansion Microscopy. ACS NANO 2023; 17:20589-20600. [PMID: 37787755 DOI: 10.1021/acsnano.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Expansion microscopy (ExM) revolutionized the field of super-resolution microscopy by allowing for subdiffraction resolution fluorescence imaging on standard fluorescence microscopes. However, it has been found that it is hard to visualize actin filaments efficiently using ExM. To improve actin imaging, multifunctional molecules have been designed with moderate success. Here, we present optimized methods for phalloidin conjugate grafting that have a high efficiency for both cellular and tissue samples. Our optimized strategy improves anchoring and signal retention by ∼10 times. We demonstrate the potential of optimized trifunctional linkers (TRITON) for actin imaging in combination with immunolabeling using different ExM protocols. 10X ExM of actin labeled with optimized TRITON enabled us to visualize the periodicity of actin rings in cultured hippocampal neurons and brain slices by Airyscan confocal microscopy. Thus, TRITON linkers provide an efficient grafting method, especially in cases in which the concentration of target-bound monomers is insufficient for high-quality ExM.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthew Domenic Lycas
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Yuqing Jia
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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22
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Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo EF, Brown KM, Milman T, Wang Y, Gallagher BR, Lagree K, Jena BP, Pulido JS, Filler SG, Mitchell AP, Hiller NL, Lacy‐Hulbert A, Zhao Y. MicroMagnify: A Multiplexed Expansion Microscopy Method for Pathogens and Infected Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302249. [PMID: 37658522 PMCID: PMC10602566 DOI: 10.1002/advs.202302249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/29/2023] [Indexed: 09/03/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. MicroMagnify (µMagnify) is developed, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. The combination of heat denaturation and enzyme cocktails essential is found for robust cell wall digestion and expansion of microbial cells and infected tissues without distortion. µMagnify efficiently retains biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. It demonstrates up to eightfold expansion with µMagnify on a broad range of pathogen-containing specimens, including bacterial and fungal biofilms, infected culture cells, fungus-infected mouse tone, and formalin-fixed paraffin-embedded human cornea infected by various pathogens. Additionally, an associated virtual reality tool is developed to facilitate the visualization and navigation of complex 3D images generated by this method in an immersive environment allowing collaborative exploration among researchers worldwide. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables the development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
- Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Caroline Stefani
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | | | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Aramchan Lee
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Emma F. DiBernardo
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Karina Mueller Brown
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Tatyana Milman
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Yuhong Wang
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Brendan R. Gallagher
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Katherine Lagree
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Bhanu P. Jena
- Viron Molecular Medicine Institute201 Washington StreetBostonMA02201USA
- Department of PhysiologyWayne State University42 W Warren AveDetroitMI48202USA
- NanoBioScience InstituteWayne State University42 W Warren AveDetroitMI48202USA
- Center for Molecular Medicine & GeneticsSchool of MedicineWayne State University42 W Warren AveDetroitMI48202USA
| | - Jose S. Pulido
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Scott G. Filler
- Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical Center1124 W Carson StTorranceCA90502USA
- David Geffen School of Medicine at UCLA10833 Le Conte AveLos AngelesCA90095USA
| | - Aaron P. Mitchell
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Department of MicrobiologyUniversity of Georgia210 S Jackson streetAthensGA30602USA
| | - N. Luisa Hiller
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Adam Lacy‐Hulbert
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
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23
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Eilts J, Reinhard S, Michetschläger N, Werner C, Sauer M. Enhanced synaptic protein visualization by multicolor super-resolution expansion microscopy. NEUROPHOTONICS 2023; 10:044412. [PMID: 37886043 PMCID: PMC10599331 DOI: 10.1117/1.nph.10.4.044412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/28/2023]
Abstract
Significance Understanding the organization of biomolecules into complexes and their dynamics is crucial for comprehending cellular functions and dysfunctions, particularly in neuronal networks connected by synapses. In the last two decades, various powerful super-resolution (SR) microscopy techniques have been developed that produced stunning images of synapses and their molecular organization. However, current SR microscopy methods do not permit multicolor fluorescence imaging with 20 to 30 nm spatial resolution. Aim We developed a method that enables 4-color fluorescence imaging of synaptic proteins in neurons with 20 to 30 nm lateral resolution. Approach We used post-expansion immunolabeling of eightfold expanded hippocampal neurons in combination with Airyscan and structured illumination microscopy (SIM). Results We demonstrate that post-expansion immunolabeling of approximately eightfold expanded hippocampal neurons enables efficient labeling of synaptic proteins in crowded compartments with minimal linkage error and enables in combination with Airyscan and SIM four-color three-dimensional fluorescence imaging with 20 to 30 nm lateral resolution. Using immunolabeling of Synaptobrevin 2 as an efficient marker of the vesicle pool allowed us to identify individual synaptic vesicles colocalized with Rab3-interacting molecule 1 and 2 (RIM1/2), a marker of pre-synaptic fusion sites. Conclusions Our optimized expansion microscopy approach improves the visualization and location of pre- and post-synaptic proteins and can thus provide invaluable insights into the spatial organization of proteins at synapses.
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Affiliation(s)
- Janna Eilts
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Sebastian Reinhard
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Nikolas Michetschläger
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Christian Werner
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Markus Sauer
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
- University of Würzburg, Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, Würzburg, Germany
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24
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Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol 2023; 24:695-713. [PMID: 37280296 PMCID: PMC10242609 DOI: 10.1038/s41580-023-00615-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/08/2023]
Abstract
Single-cell multi-omics technologies and methods characterize cell states and activities by simultaneously integrating various single-modality omics methods that profile the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and other (emerging) omics. Collectively, these methods are revolutionizing molecular cell biology research. In this comprehensive Review, we discuss established multi-omics technologies as well as cutting-edge and state-of-the-art methods in the field. We discuss how multi-omics technologies have been adapted and improved over the past decade using a framework characterized by optimization of throughput and resolution, modality integration, uniqueness and accuracy, and we also discuss multi-omics limitations. We highlight the impact that single-cell multi-omics technologies have had in cell lineage tracing, tissue-specific and cell-specific atlas production, tumour immunology and cancer genetics, and in mapping of cellular spatial information in fundamental and translational research. Finally, we discuss bioinformatics tools that have been developed to link different omics modalities and elucidate functionality through the use of better mathematical modelling and computational methods.
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Affiliation(s)
- Alev Baysoy
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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25
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Cui Y, Yang G, Goodwin DR, O’Flanagan CH, Sinha A, Zhang C, Kitko KE, Shin TW, Park D, Aparicio S, Boyden ES. Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAs. PLoS One 2023; 18:e0291506. [PMID: 37729182 PMCID: PMC10511132 DOI: 10.1371/journal.pone.0291506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
Expansion microscopy (ExM), by physically enlarging specimens in an isotropic fashion, enables nanoimaging on standard light microscopes. Key to existing ExM protocols is the equipping of different kinds of molecules, with different kinds of anchoring moieties, so they can all be pulled apart from each other by polymer swelling. Here we present a multifunctional anchor, an acrylate epoxide, that enables proteins and RNAs to be equipped with anchors in a single experimental step. This reagent simplifies ExM protocols and reduces cost (by 2-10-fold for a typical multiplexed ExM experiment) compared to previous strategies for equipping RNAs with anchors. We show that this united ExM (uniExM) protocol can be used to preserve and visualize RNA transcripts, proteins in biologically relevant ultrastructures, and sets of RNA transcripts in patient-derived xenograft (PDX) cancer tissues and may support the visualization of other kinds of biomolecular species as well. uniExM may find many uses in the simple, multimodal nanoscale analysis of cells and tissues.
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Affiliation(s)
- Yi Cui
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Gaojie Yang
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Daniel R. Goodwin
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Ciara H. O’Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Anubhav Sinha
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, Massachusetts, United States of America
| | - Chi Zhang
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Kristina E. Kitko
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Tay Won Shin
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Demian Park
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Edward S. Boyden
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, United States of America
- Koch Institute for Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, MIT, Cambridge, Massachusetts, United States of America
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26
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Jang MJ, Coughlin GM, Jackson CR, Chen X, Chuapoco MR, Vendemiatti JL, Wang AZ, Gradinaru V. Spatial transcriptomics for profiling the tropism of viral vectors in tissues. Nat Biotechnol 2023; 41:1272-1286. [PMID: 36702899 PMCID: PMC10443732 DOI: 10.1038/s41587-022-01648-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/15/2022] [Indexed: 01/27/2023]
Abstract
A barrier to advancing engineered adeno-associated viral vectors (AAVs) for precision access to cell subtypes is a lack of high-throughput, high-resolution assays to characterize in vivo transduction profiles. In this study, we developed an ultrasensitive, sequential fluorescence in situ hybridization (USeqFISH) method for spatial transcriptomic profiling of endogenous and viral RNA with a short barcode in intact tissue volumes by integrating hydrogel-based tissue clearing, enhanced signal amplification and multiplexing using sequential labeling. Using USeqFISH, we investigated the transduction and cell subtype tropisms across mouse brain regions of six systemic AAVs, including AAV-PHP.AX, a new variant that transduces robustly and efficiently across neurons and astrocytes. Here we reveal distinct cell subtype biases of each AAV variant, including a bias of AAV-PHP.N toward excitatory neurons. USeqFISH also enables profiling of pooled regulatory cargos, as we show for a 13-variant pool of microRNA target sites in AAV genomes. Lastly, we demonstrate potential applications of USeqFISH for in situ AAV profiling and multimodal single-cell analysis in non-human primates.
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Affiliation(s)
- Min J Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gerard M Coughlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Cameron R Jackson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Miguel R Chuapoco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julia L Vendemiatti
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexander Z Wang
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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27
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Kraft N, Muenz TS, Reinhard S, Werner C, Sauer M, Groh C, Rössler W. Expansion microscopy in honeybee brains for high-resolution neuroanatomical analyses in social insects. Cell Tissue Res 2023; 393:489-506. [PMID: 37421435 PMCID: PMC10484815 DOI: 10.1007/s00441-023-03803-4] [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: 01/27/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
The diffraction limit of light microscopy poses a problem that is frequently faced in structural analyses of social insect brains. With the introduction of expansion microscopy (ExM), a tool became available to overcome this limitation by isotropic physical expansion of preserved specimens. Our analyses focus on synaptic microcircuits (microglomeruli, MG) in the mushroom body (MB) of social insects, high-order brain centers for sensory integration, learning, and memory. MG undergo significant structural reorganizations with age, sensory experience, and during long-term memory formation. However, the changes in subcellular architecture involved in this plasticity have only partially been accessed yet. Using the western honeybee Apis mellifera as an experimental model, we established ExM for the first time in a social insect species and applied it to investigate plasticity in synaptic microcircuits within MG of the MB calyces. Using combinations of antibody staining and neuronal tracing, we demonstrate that this technique enables quantitative and qualitative analyses of structural neuronal plasticity at high resolution in a social insect brain.
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Affiliation(s)
- Nadine Kraft
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany.
| | - Thomas S Muenz
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Claudia Groh
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Wolfgang Rössler
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
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28
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Xie J, Han D, Xu S, Zhang H, Li Y, Zhang M, Deng Z, Tian J, Ye Q. An Image-Based High-Throughput and High-Content Drug Screening Method Based on Microarray and Expansion Microscopy. ACS NANO 2023; 17:15516-15528. [PMID: 37548636 DOI: 10.1021/acsnano.3c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
A high-efficiency drug screening method is urgently needed due to the expanding number of potential targets and the extremely long time required to assess them. To date, high throughput and high content have not been successfully combined in image-based drug screening, which is the main obstacle to improve the efficiency. Here, we establish a high-throughput and high-content drug screening method by preparing a superhydrophobic microwell array plate (SMAP) and combining it with protein-retention expansion microscopy (proExM). Primarily, we described a flexible method to prepare the SMAP based on photolithography. Cells were cultured in the SMAP and treated with different drugs using a microcolumn-microwell sandwiching technology. After drug treatment, proExM was applied to realize super-resolution imaging. As a demonstration, a 7 × 7 image array of microtubules was successfully collected within 3 h with 68 nm resolution using this method. Qualitative and quantitative analyses of microtubule and mitochondria morphological changes after drug treatment suggested that more details were revealed after applying proExM, demonstrating the successful combination of high throughput and high content.
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Affiliation(s)
- Junfang Xie
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Daobo Han
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Shuai Xu
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Haitong Zhang
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Yonghe Li
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Mingshan Zhang
- Institute of Modern Optics, Nankai University, Tianjin 300350, China
| | - Zhichao Deng
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
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29
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Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer C, Yuan Y, Zhang Y, Song J, Knoten A, Lake BB, Gaut JP, Keene D, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K. Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553610. [PMID: 37645998 PMCID: PMC10462101 DOI: 10.1101/2023.08.16.553610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. Recently there has been a surge of multiplexed RNA in situ techniques but their application to human tissues and clinical biopsies has been limited due to their large size, general lower tissue quality and high background autofluorescence. Here we report DART-FISH, a versatile padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections at cellular resolution. We introduced an omni-cell type cytoplasmic stain, dubbed RiboSoma that substantially improves the segmentation of cell bodies. We developed a computational decoding-by-deconvolution workflow to extract gene spots even in the presence of optical crowding. Our enzyme-free isothermal decoding procedure allowed us to image 121 genes in a large section from the human neocortex in less than 10 hours, where we successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. Additionally, we demonstrated the detection of transcripts as short as 461 nucleotides, including neuropeptides and discovered new cortical layer markers. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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Affiliation(s)
- Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally
| | - Chien-Ju Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally
| | - Ho Suk Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Electrical Engineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mahsa Nafisi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carter Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yixu Yuan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jinghui Song
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Joseph P. Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St
| | - Dirk Keene
- University of Washington School of Medicine, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA Louis, MO, USA
| | - Peter V. Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St
| | | | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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30
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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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31
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Zhuang Y, Shi X. Expansion microscopy: A chemical approach for super-resolution microscopy. Curr Opin Struct Biol 2023; 81:102614. [PMID: 37253290 PMCID: PMC11103276 DOI: 10.1016/j.sbi.2023.102614] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/13/2023] [Accepted: 05/01/2023] [Indexed: 06/01/2023]
Abstract
Super-resolution microscopy is a series of imaging techniques that bypass the diffraction limit of resolution. Since the 1990s, optical approaches, such as single-molecular localization microscopy, have allowed us to visualize biological samples from the sub-organelle to the molecular level. Recently, a chemical approach called expansion microscopy emerged as a new trend in super-resolution microscopy. It physically enlarges cells and tissues, which leads to an increase in the effective resolution of any microscope by the length expansion factor. Compared with optical approaches, expansion microscopy has a lower cost and higher imaging depth but requires a more complex procedure. The integration of expansion microscopy and advanced microscopes significantly pushed forward the boundary of super-resolution microscopy. This review covers the current state of the art in expansion microscopy, including the latest methods and their applications, as well as challenges and opportunities for future research.
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Affiliation(s)
- Yinyin Zhuang
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA. https://twitter.com/YinyinZhuang
| | - Xiaoyu Shi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
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32
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Klimas A, Gallagher BR, DiBernardo E, Cheng Z, Zhao Y. 11-fold Expansion Microscopy with Universal Molecular Retention Using Magnify. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:999-1001. [PMID: 37613623 DOI: 10.1093/micmic/ozad067.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Aleksandra Klimas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Emma DiBernardo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Zhangyu Cheng
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
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33
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Wang X, Yu S, Lou E, Tan YL, Tan ZJ. RNA 3D Structure Prediction: Progress and Perspective. Molecules 2023; 28:5532. [PMID: 37513407 PMCID: PMC10386116 DOI: 10.3390/molecules28145532] [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: 06/14/2023] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled to their structures or proper structure changes, and RNA structure prediction has been paid much attention in the last two decades. Some computational models have been developed to predict RNA three-dimensional (3D) structures in silico, and these models are generally composed of predicting RNA 3D structure ensemble, evaluating near-native RNAs from the structure ensemble, and refining the identified RNAs. In this review, we will make a comprehensive overview of the recent advances in RNA 3D structure modeling, including structure ensemble prediction, evaluation, and refinement. Finally, we will emphasize some insights and perspectives in modeling RNA 3D structures.
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Affiliation(s)
- Xunxun Wang
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Shixiong Yu
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - En Lou
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- School of Bioengineering and Health, Wuhan Textile University, Wuhan 430200, China
- Research Center of Nonlinear Science, School of Mathematical and Physical Sciences, Wuhan Textile University, Wuhan 430200, China
| | - Zhi-Jie Tan
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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34
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [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: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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35
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Glaser A, Chandrashekar J, Vasquez J, Arshadi C, Ouellette N, Jiang X, Baka J, Kovacs G, Woodard M, Seshamani S, Cao K, Clack N, Recknagel A, Grim A, Balaram P, Turschak E, Liddell A, Rohde J, Hellevik A, Takasaki K, Barner LE, Logsdon M, Chronopoulos C, de Vries S, Ting J, Perlmutter S, Kalmbach B, Dembrow N, Reid RC, Feng D, Svoboda K. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544277. [PMID: 37425699 PMCID: PMC10327101 DOI: 10.1101/2023.06.08.544277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher imaging throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with diffraction-limited and aberration-free performance over a large field of view (85 mm 2 ) and working distance (35 mm). Combined with new tissue clearing and expansion methods, the microscope allows nanoscale imaging of centimeter-scale samples, including entire mouse brains, with diffraction-limited resolutions and high contrast without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and tracing axons in human white matter.
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36
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Zhang Y, Miller JA, Park J, Lelieveldt BP, Long B, Abdelaal T, Aevermann BD, Biancalani T, Comiter C, Dzyubachyk O, Eggermont J, Langseth CM, Petukhov V, Scalia G, Vaishnav ED, Zhao Y, Lein ES, Scheuermann RH. Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain. Sci Rep 2023; 13:9567. [PMID: 37311768 DOI: 10.1038/s41598-023-36638-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Abstract
With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and gene expression information about cells in tissue sections at single cell resolution. Cell type classification of these spatially-resolved cells can be inferred by matching the spatial transcriptomics data to reference atlases derived from single cell RNA-sequencing (scRNA-seq) in which cell types are defined by differences in their gene expression profiles. However, robust cell type matching of the spatially-resolved cells to reference scRNA-seq atlases is challenging due to the intrinsic differences in resolution between the spatial and scRNA-seq data. In this study, we systematically evaluated six computational algorithms for cell type matching across four image-based spatial transcriptomics experimental protocols (MERFISH, smFISH, BaristaSeq, and ExSeq) conducted on the same mouse primary visual cortex (VISp) brain region. We find that many cells are assigned as the same type by multiple cell type matching algorithms and are present in spatial patterns previously reported from scRNA-seq studies in VISp. Furthermore, by combining the results of individual matching strategies into consensus cell type assignments, we see even greater alignment with biological expectations. We present two ensemble meta-analysis strategies used in this study and share the consensus cell type matching results in the Cytosplore Viewer ( https://viewer.cytosplore.org ) for interactive visualization and data exploration. The consensus matching can also guide spatial data analysis using SSAM, allowing segmentation-free cell type assignment.
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Affiliation(s)
- Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Jeongbin Park
- School of Biomedical Convergence Engineering, Pusan National University, Busan, Korea
| | - Boudewijn P Lelieveldt
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, The Netherlands
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tamim Abdelaal
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, The Netherlands
| | - Brian D Aevermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Tommaso Biancalani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Oleh Dzyubachyk
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Eggermont
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Viktor Petukhov
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gabriele Scalia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Yilin Zhao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA.
- Department of Pathology, University of California, San Diego, CA, USA.
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.
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37
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Grodner B, Shi H, Farchione O, Vill AC, Ntekas I, Diebold PJ, Zipfel WR, Brito IL, Vlaminck ID. Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544291. [PMID: 37333098 PMCID: PMC10274929 DOI: 10.1101/2023.06.09.544291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.
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Affiliation(s)
- Benjamin Grodner
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Hao Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Owen Farchione
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Albert C Vill
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ioannis Ntekas
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Warren R Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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38
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Tang M, Han Y, Jia D, Yang Q, Cheng JX. Far-field super-resolution chemical microscopy. LIGHT, SCIENCE & APPLICATIONS 2023; 12:137. [PMID: 37277396 DOI: 10.1038/s41377-023-01182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
Far-field chemical microscopy providing molecular electronic or vibrational fingerprint information opens a new window for the study of three-dimensional biological, material, and chemical systems. Chemical microscopy provides a nondestructive way of chemical identification without exterior labels. However, the diffraction limit of optics hindered it from discovering more details under the resolution limit. Recent development of super-resolution techniques gives enlightenment to open this door behind far-field chemical microscopy. Here, we review recent advances that have pushed the boundary of far-field chemical microscopy in terms of spatial resolution. We further highlight applications in biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.
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Affiliation(s)
- Mingwei Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Yubing Han
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Danchen Jia
- Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Photonics Center, Boston University, Boston, MA, 02459, USA
| | - Qing Yang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Photonics Center, Boston University, Boston, MA, 02459, USA.
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39
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Flores V, Farabella I, Nir G. Genome-wide tracing to decipher nuclear organization. Curr Opin Cell Biol 2023; 82:102175. [PMID: 37263058 DOI: 10.1016/j.ceb.2023.102175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]
Abstract
Nuclear organization impacts gene expression activity and cell phenotype. Our current understanding is mainly derived from ensemble-level sequencing studies that reflect the 3D genome structure of millions of cells. These approaches have provided invaluable details on the 3D organizations of the genome and their relation to other nuclear landmarks. However, they mostly lack the ability to provide multimodal information simultaneously at the single-cell level. In recent years, cutting-edge imaging technologies have risen to the challenge of simultaneously describing multiple components of the nuclear space at the single-cell level, paving the way for a deeper understanding of the genome structure-function relationship. This review will focus on the development and utilization of such technologies to gain a multi-component view of the nucleus at single-cell resolution, dissecting the complexity and heterogeneity of nuclear organization.
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Affiliation(s)
- Victoria Flores
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Irene Farabella
- Integrative Nuclear Architecture Laboratory, Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy.
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
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40
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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41
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Klimas A, Gallagher BR, Wijesekara P, Fekir S, DiBernardo EF, Cheng Z, Stolz DB, Cambi F, Watkins SC, Brody SL, Horani A, Barth AL, Moore CI, Ren X, Zhao Y. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nat Biotechnol 2023; 41:858-869. [PMID: 36593399 PMCID: PMC10264239 DOI: 10.1038/s41587-022-01546-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/05/2022] [Indexed: 01/03/2023]
Abstract
Expansion microscopy enables nanoimaging with conventional microscopes by physically and isotropically magnifying preserved biological specimens embedded in a crosslinked water-swellable hydrogel. Current expansion microscopy protocols require prior treatment with reactive anchoring chemicals to link specific labels and biomolecule classes to the gel. We describe a strategy called Magnify, which uses a mechanically sturdy gel that retains nucleic acids, proteins and lipids without the need for a separate anchoring step. Magnify expands biological specimens up to 11 times and facilitates imaging of cells and tissues with effectively around 25-nm resolution using a diffraction-limited objective lens of about 280 nm on conventional optical microscopes or with around 15 nm effective resolution if combined with super-resolution optical fluctuation imaging. We demonstrate Magnify on a broad range of biological specimens, providing insight into nanoscopic subcellular structures, including synaptic proteins from mouse brain, podocyte foot processes in formalin-fixed paraffin-embedded human kidney and defects in cilia and basal bodies in drug-treated human lung organoids.
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Affiliation(s)
- Aleksandra Klimas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Piyumi Wijesekara
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sinda Fekir
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Emma F DiBernardo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhangyu Cheng
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Donna B Stolz
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Franca Cambi
- Veterans Administration Pittsburgh, Pittsburgh, PA, USA
- Department of Neurology/PIND, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison L Barth
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Christopher I Moore
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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42
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Tian L, Chen F, Macosko EZ. The expanding vistas of spatial transcriptomics. Nat Biotechnol 2023; 41:773-782. [PMID: 36192637 PMCID: PMC10091579 DOI: 10.1038/s41587-022-01448-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The formation and maintenance of tissue integrity requires complex, coordinated activities by thousands of genes and their encoded products. Until recently, transcript levels could only be quantified for a few genes in tissues, but advances in DNA sequencing, oligonucleotide synthesis and fluorescence microscopy have enabled the invention of a suite of spatial transcriptomics technologies capable of measuring the expression of many, or all, genes in situ. These technologies have evolved rapidly in sensitivity, multiplexing and throughput. As such, they have enabled the determination of the cell-type architecture of tissues, the querying of cell-cell interactions and the monitoring of molecular interactions between tissue components. The rapidly evolving spatial genomics landscape will enable generalized high-throughput genomic measurements and perturbations to be performed in the context of tissues. These advances will empower hypothesis generation and biological discovery and bridge the worlds of tissue biology and genomics.
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Affiliation(s)
- Luyi Tian
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Stem Cell and Regenerative Biology, Cambridge, MA, USA.
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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43
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Park H, Jo SH, Lee RH, Macks CP, Ku T, Park J, Lee CW, Hur JK, Sohn CH. Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206939. [PMID: 37026425 PMCID: PMC10238226 DOI: 10.1002/advs.202206939] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/10/2023] [Indexed: 06/04/2023]
Abstract
Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional biological studies to "in situ" biology, spatial transcriptomics can provide transcriptome-scale spatial information. Currently, the ability to simultaneously characterize gene expression profiles of cells and relevant cellular environment is a paradigm shift for biological studies. In this review, recent progress in spatial transcriptomics and its applications in neuroscience and cancer studies are highlighted. Technical aspects of existing technologies and future directions of new developments (as of March 2023), computational analysis of spatial transcriptome data, application notes in neuroscience and cancer studies, and discussions regarding future directions of spatial multi-omics and their expanding roles in biomedical applications are emphasized.
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Affiliation(s)
- Han‐Eol Park
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
- School of Biological SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Song Hyun Jo
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Rosalind H. Lee
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Christian P. Macks
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jihwan Park
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Chung Whan Lee
- Department of ChemistryGachon UniversitySeongnamGyeonggi‐do13120Republic of Korea
| | - Junho K. Hur
- Department of GeneticsCollege of MedicineHanyang UniversitySeoul04763Republic of Korea
| | - Chang Ho Sohn
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
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44
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Günay KA, Chang TL, Skillin NP, Rao VV, Macdougall LJ, Cutler AA, Silver JS, Brown TE, Zhang C, Yu CCJ, Olwin BB, Boyden ES, Anseth KS. Photo-expansion microscopy enables super-resolution imaging of cells embedded in 3D hydrogels. NATURE MATERIALS 2023; 22:777-785. [PMID: 37217701 PMCID: PMC10590656 DOI: 10.1038/s41563-023-01558-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Hydrogels are extensively used as tunable, biomimetic three-dimensional cell culture matrices, but optically deep, high-resolution images are often difficult to obtain, limiting nanoscale quantification of cell-matrix interactions and outside-in signalling. Here we present photopolymerized hydrogels for expansion microscopy that enable optical clearance and tunable ×4.6-6.7 homogeneous expansion of not only monolayer cell cultures and tissue sections, but cells embedded within hydrogels. The photopolymerized hydrogels for expansion microscopy formulation relies on a rapid photoinitiated thiol/acrylate mixed-mode polymerization that is not inhibited by oxygen and decouples monomer diffusion from polymerization, which is particularly beneficial when expanding cells embedded within hydrogels. Using this technology, we visualize human mesenchymal stem cells and their interactions with nascently deposited proteins at <120 nm resolution when cultured in proteolytically degradable synthetic polyethylene glycol hydrogels. Results support the notion that focal adhesion maturation requires cellular fibronectin deposition; nuclear deformation precedes cellular spreading; and human mesenchymal stem cells display cell-surface metalloproteinases for matrix remodelling.
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Affiliation(s)
- Kemal Arda Günay
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Tze-Ling Chang
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Nathaniel P Skillin
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Varsha V Rao
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Laura J Macdougall
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Alicia A Cutler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Jason S Silver
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Tobin E Brown
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Chi Zhang
- McGovern Institute, MIT, Cambridge, MA, USA
- HHMI, Cambridge, MA, USA
- Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, MIT, Cambridge, MA, USA
| | - Chih-Chieh Jay Yu
- McGovern Institute, MIT, Cambridge, MA, USA
- HHMI, Cambridge, MA, USA
- Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, MIT, Cambridge, MA, USA
| | - Bradley B Olwin
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Edward S Boyden
- McGovern Institute, MIT, Cambridge, MA, USA
- HHMI, Cambridge, MA, USA
- Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, MIT, Cambridge, MA, USA
| | - Kristi S Anseth
- Department of Chemical and Biological Engineering and the BioFrontiers Institute, University of Colorado, Boulder, CO, USA.
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45
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Parveen S, Jones NW, Millerschultz I, Paré AC. Using Expansion Microscopy to Physically Enlarge Whole-Mount Drosophila Embryos for Super-Resolution Imaging. J Vis Exp 2023:10.3791/64662. [PMID: 37184263 PMCID: PMC11081397 DOI: 10.3791/64662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The workhorse of developmental biology is the confocal microscope, which allows researchers to determine the three-dimensional localization of tagged molecules within complex biological samples. While traditional confocal microscopes allow one to resolve two adjacent fluorescent point sources located a few hundred nanometers apart, observing the finer details of subcellular biology requires the ability to resolve signals in the order of tens of nanometers. Numerous hardware-based methods for super-resolution microscopy have been developed to allow researchers to sidestep such resolution limits, although these methods require specialized microscopes that are not available to all researchers. An alternative method for increasing resolving power is to isotropically enlarge the sample itself through a process known as expansion microscopy (ExM), which was first described by the Boyden group in 2015. ExM is not a type of microscopy per se but is rather a method for swelling a sample while preserving the relative spatial organization of its constituent molecules. The expanded sample can then be observed at an effectively increased resolution using a traditional confocal microscope. Here, we describe a protocol for implementing ExM in whole-mount Drosophila embryos, which is used to examine the localization of Par-3, myosin II, and mitochondria within the surface epithelial cells. This protocol yields an approximately four-fold increase in sample size, allowing for the detection of subcellular details that are not visible with conventional confocal microscopy. As proof of principle, an anti-GFP antibody is used to distinguish distinct pools of myosin-GFP between adjacent cell cortices, and fluorescently labeled streptavidin is used to detect endogenous biotinylated molecules to reveal the fine details of the mitochondrial network architecture. This protocol utilizes common antibodies and reagents for fluorescence labeling, and it should be compatible with many existing immunofluorescence protocols.
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Affiliation(s)
- Samia Parveen
- Department of Biological Sciences, University of Arkansas
| | | | | | - Adam C Paré
- Department of Biological Sciences, University of Arkansas;
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46
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Ghosh S, Sapkota BS, Rao RS, Patil S, Rajkumar C, Lakshminarayan S. Expansion microscopy: A revolution in diagnostic pathology. J Microsc 2023; 290:3-9. [PMID: 36641735 DOI: 10.1111/jmi.13170] [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: 11/20/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/16/2023]
Abstract
Expansion microscopy (ExM) is a recent discovery in diagnostic pathology and microbiology that promotes a physical magnification of the tissue specimen instead of optical magnification. It not only improves the resolution of the specimen but also enhances the diagnostic precision, and permits nanoscale imaging of the specimen. Optical microscopy is routinely used in histopathology and microbiology for ages. Due to its simplicity, compatibility with different types of specimens, and ease of operation it is accepted by pathologists. ExM and its variants have been widely tested in different types of tissue specimens and microbiological specimens and yielded brilliant results.
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Affiliation(s)
- Snehashish Ghosh
- Department of Oral Pathology, College of Medical Sciences, Bharatpur, Nepal
| | | | - Roopa S Rao
- Faculty of Dental Sciences, Department of Oral Pathology, Ramaiah University of Applied Sciences, Bangalore, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, Utah
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Chandini Rajkumar
- Department of Oral Pathology and Microbiology, Sathyabama Dental College and Hospital, Chennai, India
| | - Surendra Lakshminarayan
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
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47
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Chang TJB, Hsu JCC, Yang TT. Single-molecule localization microscopy reveals the ultrastructural constitution of distal appendages in expanded mammalian centrioles. Nat Commun 2023; 14:1688. [PMID: 36973278 PMCID: PMC10043031 DOI: 10.1038/s41467-023-37342-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Distal appendages (DAPs) are vital in cilia formation, mediating vesicular and ciliary docking to the plasma membrane during early ciliogenesis. Although numerous DAP proteins arranging a nine-fold symmetry have been studied using superresolution microscopy analyses, the extensive ultrastructural understanding of the DAP structure developing from the centriole wall remains elusive owing to insufficient resolution. Here, we proposed a pragmatic imaging strategy for two-color single-molecule localization microscopy of expanded mammalian DAP. Importantly, our imaging workflow enables us to push the resolution limit of a light microscope well close to a molecular level, thus achieving an unprecedented mapping resolution inside intact cells. Upon this workflow, we unravel the ultra-resolved higher-order protein complexes of the DAP and its associated proteins. Intriguingly, our images show that C2CD3, microtubule triplet, MNR, CEP90, OFD1, and ODF2 jointly constitute a unique molecular configuration at the DAP base. Moreover, our finding suggests that ODF2 plays an auxiliary role in coordinating and maintaining DAP nine-fold symmetry. Together, we develop an organelle-based drift correction protocol and a two-color solution with minimum crosstalk, allowing a robust localization microscopy imaging of expanded DAP structures deep into the gel-specimen composites.
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Affiliation(s)
- Ting-Jui Ben Chang
- Department of Physics, National Taiwan University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | | | - T Tony Yang
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
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48
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Wen G, Leen V, Rohand T, Sauer M, Hofkens J. Current Progress in Expansion Microscopy: Chemical Strategies and Applications. Chem Rev 2023; 123:3299-3323. [PMID: 36881995 DOI: 10.1021/acs.chemrev.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Taoufik Rohand
- Laboratory of Analytical and Molecular Chemistry, Faculty Polydisciplinaire of Safi, University Cadi Ayyad Marrakech, BP 4162, 46000 Safi, Morocco
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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49
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Cao Z, Zuo W, Wang L, Chen J, Qu Z, Jin F, Dai L. Spatial profiling of microbial communities by sequential FISH with error-robust encoding. Nat Commun 2023; 14:1477. [PMID: 36932092 PMCID: PMC10023729 DOI: 10.1038/s41467-023-37188-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.
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Affiliation(s)
- Zhaohui Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junyu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zepeng Qu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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50
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Zhao Y, Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo E, Mueller Brown K, Milman T, Gallagher B, Lagree K, Jena B, Pulido J, Filler S, Mitchell A, Hiller L, Lacy-Hulbert A. MicroMagnify: a multiplexed expansion microscopy method for pathogens and infected tissues. RESEARCH SQUARE 2023:rs.3.rs-2637060. [PMID: 36945526 PMCID: PMC10029075 DOI: 10.21203/rs.3.rs-2637060/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. We developed µMagnify, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. We formulated an enzyme cocktail specifically designed for robust cell wall digestion and expansion of microbial cells without distortion while efficiently retaining biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. Additionally, we developed an associated virtual reality tool to facilitate the visualization and navigation of complex three-dimensional images generated by this method in an immersive environment allowing collaborative exploration among researchers around the world. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bhanu Jena
- Wayne State University School of Medicine
| | - Jose Pulido
- Wills Eye Hospital and Jefferson University Hospital
| | - Scott Filler
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
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