1
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Song M, Wang J, Hou J, Fu T, Feng Y, Lv W, Ge F, Peng R, Han D, Tan W. Multiplexed In Situ Imaging of Site-Specific m6A Methylation with Proximity Hybridization Followed by Primer Exchange Amplification (m6A-PHPEA). ACS NANO 2024. [PMID: 39331796 DOI: 10.1021/acsnano.4c08407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2024]
Abstract
Post-transcriptional modification of N6-methyladenosine (m6A) is crucial for ribonucleic acid (RNA) metabolism and cellular function. The ability to visualize site-specific m6A methylation at the single-cell level would markedly enhance our understanding of its pivotal regulatory functions in the field of epitranscriptomics. Despite this, current in situ imaging techniques for site-specific m6A are constrained, posing a significant barrier to epitranscriptomic studies and pathological diagnostics. Capitalizing on the precise targeting capability of deoxyribonucleic acid (DNA) hybridization and the high specificity of the m6A antibody, we present a method, termed proximity hybridization followed by primer exchange amplification (m6A-PHPEA), for the site-specific imaging of m6A methylation within cells. This approach enables high-resolution, single-cell imaging of m6A methylation across various RNA molecules coupled with efficient signal amplification. We successfully imaged three distinct m6A methylation sites concurrently in multiple cell types, revealing cell-to-cell variability in expression levels. This method promises to illuminate the dynamics of m6A-modified RNAs, potentially revolutionizing epitranscriptomic research and the development of advanced pathological diagnosis for chemical modifications.
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Affiliation(s)
- Minghui Song
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, P. R. China
- Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Junyan Wang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Jianing Hou
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ting Fu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Yawei Feng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Wenyi Lv
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Feng Ge
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Ruizi Peng
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Da Han
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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2
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Kurikawa Y, Koyama-Honda I, Tamura N, Koike S, Mizushima N. Organelle landscape analysis using a multiparametric particle-based method. PLoS Biol 2024; 22:e3002777. [PMID: 39288101 PMCID: PMC11407678 DOI: 10.1371/journal.pbio.3002777] [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: 01/25/2024] [Accepted: 07/30/2024] [Indexed: 09/19/2024] Open
Abstract
Organelles have unique structures and molecular compositions for their functions and have been classified accordingly. However, many organelles are heterogeneous and in the process of maturation and differentiation. Because traditional methods have a limited number of parameters and spatial resolution, they struggle to capture the heterogeneous landscapes of organelles. Here, we present a method for multiparametric particle-based analysis of organelles. After disrupting cells, fluorescence microscopy images of organelle particles labeled with 6 to 8 different organelle markers were obtained, and their multidimensional data were represented in two-dimensional uniform manifold approximation and projection (UMAP) spaces. This method enabled visualization of landscapes of 7 major organelles as well as the transitional states of endocytic organelles directed to the recycling and degradation pathways. Furthermore, endoplasmic reticulum-mitochondria contact sites were detected in these maps. Our proposed method successfully detects a wide array of organelles simultaneously, enabling the analysis of heterogeneous organelle landscapes.
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Affiliation(s)
- Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Norito Tamura
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seiichi Koike
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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3
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Wang Y, Liu X, Zeng Y, Saka S, Xie W, Goldaracena I, Kohman R, Yin P, Church G. Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res 2024; 52:e71. [PMID: 38966983 PMCID: PMC11347153 DOI: 10.1093/nar/gkae592] [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: 07/25/2023] [Revised: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.
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Affiliation(s)
- Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Xiaoyu Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yitian Zeng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxin Xie
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richie E Kohman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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4
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Chang TJ, Yang TT. Multiplexed Nanoscopy via Buffer Exchange. ACS NANO 2024; 18:23445-23456. [PMID: 39143924 PMCID: PMC11363122 DOI: 10.1021/acsnano.4c06829] [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: 05/22/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024]
Abstract
Understanding cellular functions, particularly in their intricate complexity, can greatly benefit from the spatial mapping of diverse molecules through multitarget single-molecule localization microscopy (SMLM). Existing methodologies, primarily restricting the encoding dimensions to color and lifetime or requiring cyclic staining, often involve broad chromatic detection, specialized optical configurations, or sophisticated labeling techniques. Here, we propose a simple approach called buffer-exchange stochastic optical reconstruction microscopy (beSTORM), which introduces an additional dimension to differentiate between single molecules irrespective of their spectral properties. This method leverages the distinguishable photoblinking responses to distinct buffer conditions, offering a straightforward yet effective means of fluorophore discrimination. Through buffer exchanges, beSTORM achieves multitarget SMLM imaging with minimal crosstalk. Direct integration with expansion microscopy (ExM) demonstrates its capability to resolve up to six proteins at the molecular level within a single emission color without chromatic aberration. Overall, beSTORM presents a highly compatible imaging platform, promising significant advancements in highly multiplexed nanoscopy for exploring multiple targets in biological systems with nanoscale precision.
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Affiliation(s)
- Ting-Jui
Ben Chang
- Department
of Electrical Engineering, National Taiwan
University, Taipei 10617, Taiwan
- Graduate
Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
- Department
of Physics, National Taiwan University, Taipei 10617, Taiwan
- Nano
Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - T. Tony Yang
- Department
of Electrical Engineering, National Taiwan
University, Taipei 10617, Taiwan
- Graduate
Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
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5
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Garate X, Gómez-García PA, Merino MF, Angles MC, Zhu C, Castells-García A, Ed-Daoui I, Martin L, Ochiai H, Neguembor MV, Cosma MP. The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition. Nucleic Acids Res 2024; 52:8146-8164. [PMID: 38850157 DOI: 10.1093/nar/gkae476] [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: 04/03/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
During early development, gene expression is tightly regulated. However, how genome organization controls gene expression during the transition from naïve embryonic stem cells to epiblast stem cells is still poorly understood. Using single-molecule microscopy approaches to reach nanoscale resolution, we show that genome remodeling affects gene transcription during pluripotency transition. Specifically, after exit from the naïve pluripotency state, chromatin becomes less compacted, and the OCT4 transcription factor has lower mobility and is more bound to its cognate sites. In epiblast cells, the active transcription hallmark, H3K9ac, decreases within the Oct4 locus, correlating with reduced accessibility of OCT4 and, in turn, with reduced expression of Oct4 nascent RNAs. Despite the high variability in the distances between active pluripotency genes, distances between Nodal and Oct4 decrease during epiblast specification. In particular, highly expressed Oct4 alleles are closer to nuclear speckles during all stages of the pluripotency transition, while only a distinct group of highly expressed Nodal alleles are in close proximity to Oct4 when associated with a nuclear speckle in epiblast cells. Overall, our results provide new insights into the role of the spatiotemporal genome remodeling during mouse pluripotency transition and its correlation with the expression of key pluripotency genes.
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Affiliation(s)
- Ximena Garate
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Manuel Fernández Merino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marta Cadevall Angles
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chenggan Zhu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Alvaro Castells-García
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu district, 510080 Guangzhou, China
| | - Ilyas Ed-Daoui
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu district, 510080 Guangzhou, China
| | - Laura Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu district, 510080 Guangzhou, China
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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6
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Lycas MD, Manley S. DNA-PAINT adaptors make for efficient multiplexing. CELL REPORTS METHODS 2024; 4:100801. [PMID: 38889688 PMCID: PMC11228366 DOI: 10.1016/j.crmeth.2024.100801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024]
Abstract
Multiplexed super-resolution imaging offers a route to spatial proteomics; however, time-efficient mapping of many protein species has been challenging. Two recent works in Cell highlight SUM-PAINT and FLASH-PAINT, methods that leverage adaptor DNA strand design to combine advances in multiplexing with increases in speed of label exchange. These advances permit unbiased omics-style analyses to advance biological insights from super-resolution images.
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Affiliation(s)
- Matthew D Lycas
- Laboratory of Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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7
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Rocha Tapia A, Abgottspon F, Nilvebrant J, Nygren PÅ, Duclos Ivetich S, Bello Hernandez AJ, Thanasi IA, Szijj PA, Sekkat G, Cuenot FM, Chudasama V, Aceto N, deMello AJ, Richards DA. Site-directed conjugation of single-stranded DNA to affinity proteins: quantifying the importance of conjugation strategy. Chem Sci 2024; 15:8982-8992. [PMID: 38873052 PMCID: PMC11168188 DOI: 10.1039/d4sc01838a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/27/2024] [Indexed: 06/15/2024] Open
Abstract
Affinity protein-oligonucleotide conjugates are increasingly being explored as diagnostic and therapeutic tools. Despite growing interest, these probes are typically constructed using outdated, non-selective chemistries, and little has been done to investigate how conjugation to oligonucleotides influences the function of affinity proteins. Herein, we report a novel site-selective conjugation method for furnishing affinity protein-oligonucleotide conjugates in a 93% yield within fifteen minutes. Using SPR, we explore how the choice of affinity protein, conjugation strategy, and DNA length impact target binding and reveal the deleterious effects of non-specific conjugation methods. Furthermore, we show that these adverse effects can be minimised by employing our site-selective conjugation strategy, leading to improved performance in an immuno-PCR assay. Finally, we investigate the interactions between affinity protein-oligonucleotide conjugates and live cells, demonstrating the benefits of site-selective conjugation. This work provides critical insight into the importance of conjugation strategy when constructing affinity protein-oligonucleotide conjugates.
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Affiliation(s)
- Andres Rocha Tapia
- Institute for Chemical and Bioengineering, ETH Zurich Vladimir-Prelog-Weg 1 8093 Zürich Switzerland
| | - Fabrice Abgottspon
- Institute for Chemical and Bioengineering, ETH Zurich Vladimir-Prelog-Weg 1 8093 Zürich Switzerland
| | - Johan Nilvebrant
- Department of Protein Science, KTH Royal Institute of Technology, AlbaNova University Center 106 91 Stockholm Sweden
| | - Per-Åke Nygren
- Department of Protein Science, KTH Royal Institute of Technology, AlbaNova University Center 106 91 Stockholm Sweden
| | - Sarah Duclos Ivetich
- Institute for Chemical and Bioengineering, ETH Zurich Vladimir-Prelog-Weg 1 8093 Zürich Switzerland
| | | | - Ioanna A Thanasi
- Department of Chemistry, University College London 20 Gordon Street WC1H 0AJ London UK
| | - Peter A Szijj
- Department of Chemistry, University College London 20 Gordon Street WC1H 0AJ London UK
| | - Ghali Sekkat
- Institute for Chemical and Bioengineering, ETH Zurich Vladimir-Prelog-Weg 1 8093 Zürich Switzerland
| | - François M Cuenot
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich Otto-Stern-Weg 7 8093 Zürich Switzerland
| | - Vijay Chudasama
- Department of Chemistry, University College London 20 Gordon Street WC1H 0AJ London UK
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich Otto-Stern-Weg 7 8093 Zürich Switzerland
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, ETH Zurich Vladimir-Prelog-Weg 1 8093 Zürich Switzerland
| | - Daniel A Richards
- Institute for Chemical and Bioengineering, ETH Zurich Vladimir-Prelog-Weg 1 8093 Zürich Switzerland
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8
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Hoffmann ES, De Pascali MC, Neu L, Domnick C, Soldà A, Kath-Schorr S. Reverse transcription as key step in RNA in vitro evolution with unnatural base pairs. RSC Chem Biol 2024; 5:556-566. [PMID: 38846072 PMCID: PMC11151862 DOI: 10.1039/d4cb00084f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/23/2024] [Indexed: 06/09/2024] Open
Abstract
Unnatural base pairs (UBPs) augment the chemical diversity of artificial nucleic acids and can thus enable the generation of new aptamers and catalytic nucleic acids by in vitro selection. However, owing to a lack of methodologies, the reverse transcription of UBPs, a key step in RNA aptamer selection, has not been sufficiently characterized. Here, we present a series of versatile assays to investigate the reverse transcription of the TPT3:NaM base pair as a representative for hydrophobic unnatural base pairs. We determine the fidelity and retention of the UBP for four different reverse transcriptases (RT) in the context of RNA in vitro evolution. The retention of the TPT3:NaM pair during the RNA in vitro selection process was investigated using a novel click-chemistry based electromobility shift assay. Real-time monitoring of reverse transcription kinetics revealed considerable differences in polymerase activity processing the TPT3:NaM base pair. Our findings identified SuperScript IV RT as the most efficient RT for processing the TPT3:NaM pair. Our approach can be applied universally to study newly developed UBPs, not only at the reverse transcription level, but also during PCR and in vitro transcription.
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Affiliation(s)
- Eva S Hoffmann
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Mareike C De Pascali
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience Garching 85748 Germany
- Dynamic Biosensors GmbH Perchtinger Str. 8/10 Munich 81379 Germany
| | - Lukas Neu
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Christof Domnick
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Alice Soldà
- Dynamic Biosensors GmbH Perchtinger Str. 8/10 Munich 81379 Germany
| | - Stephanie Kath-Schorr
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
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9
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Xia Y, Ma J, Yang X, Liu D, Zhu Y, Zhao Y, Fei X, Xu D, Dai J. Identifying the Spatial Architecture That Restricts the Proximity of CD8 + T Cells to Tumor Cells in Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2024; 16:1434. [PMID: 38611111 PMCID: PMC11010991 DOI: 10.3390/cancers16071434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
The anti-tumor function of CD8+ T cells is dependent on their proximity to tumor cells. Current studies have focused on the infiltration level of CD8+ T cells in the tumor microenvironment, while further spatial information, such as spatial localization and inter-cellular communication, have not been defined. In this study, co-detection by indexing (CODEX) was designed to characterize PDAC tissue regions with seven protein markers in order to identify the spatial architecture that regulates CD8+ T cells in human pancreatic ductal adenocarcinoma (PDAC). The cellular neighborhood algorithm was used to identify a total of six conserved and distinct cellular neighborhoods. Among these, one unique spatial architecture of CD8+ T and CD4+ T cell-enriched neighborhoods enriched the majority of CD8+ T cells, but heralded a poor prognosis. The proximity analysis revealed that the CD8+ T cells in this spatial architecture were significantly closer to themselves and the CD4+ T cells than to the tumor cells. Collectively, we identified a unique spatial architecture that restricted the proximity of CD8+ T cells to tumor cells in the tumor microenvironment, indicating a novel immune evasion mechanism of pancreatic ductal adenocarcinoma in a topologically regulated manner and providing new insights into the biology of PDAC.
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Affiliation(s)
- Yihan Xia
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Junrui Ma
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaobao Yang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danping Liu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yujie Zhu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanan Zhao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xuefeng Fei
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dakang Xu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Dai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; (Y.X.); (J.M.); (X.Y.); (D.L.); (Y.Z.); (Y.Z.); (X.F.)
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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10
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Schueder F, Rivera-Molina F, Su M, Marin Z, Kidd P, Rothman JE, Toomre D, Bewersdorf J. Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging. Cell 2024; 187:1769-1784.e18. [PMID: 38552613 DOI: 10.1016/j.cell.2024.02.033] [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: 05/17/2023] [Revised: 12/22/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Mapping the intricate spatial relationships between the many different molecules inside a cell is essential to understanding cellular functions in all their complexity. Super-resolution fluorescence microscopy offers the required spatial resolution but struggles to reveal more than four different targets simultaneously. Exchanging labels in subsequent imaging rounds for multiplexed imaging extends this number but is limited by its low throughput. Here, we present a method for rapid multiplexed super-resolution microscopy that can, in principle, be applied to a nearly unlimited number of molecular targets by leveraging fluorogenic labeling in conjunction with transient adapter-mediated switching for high-throughput DNA-PAINT (FLASH-PAINT). We demonstrate the versatility of FLASH-PAINT with four applications: mapping nine proteins in a single mammalian cell, elucidating the functional organization of primary cilia by nine-target imaging, revealing the changes in proximity of thirteen different targets in unperturbed and dissociated Golgi stacks, and investigating and quantifying inter-organelle contacts at 3D super-resolution.
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Affiliation(s)
- Florian Schueder
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
| | | | - Maohan Su
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - James E Rothman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Derek Toomre
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA; Department of Physics, Yale University, New Haven, CT, USA.
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11
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Scheuermann S, Kristmann B, Engelmann F, Nuernbergk A, Scheuermann D, Koloseus M, Abed T, Solass W, Seitz CM. Unveiling spatial complexity in solid tumor immune microenvironments through multiplexed imaging. Front Immunol 2024; 15:1383932. [PMID: 38566984 PMCID: PMC10985204 DOI: 10.3389/fimmu.2024.1383932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Deciphering cellular components and the spatial interaction network of the tumor immune microenvironment (TIME) of solid tumors is pivotal for understanding biologically relevant cross-talks and, ultimately, advancing therapies. Multiplexed tissue imaging provides a powerful tool to elucidate spatial complexity in a holistic manner. We established and cross-validated a comprehensive immunophenotyping panel comprising over 121 markers for multiplexed tissue imaging using MACSima™ imaging cyclic staining (MICS) alongside an end-to-end analysis workflow. Applying this panel and workflow to primary cancer tissues, we characterized tumor heterogeneity, investigated potential therapeutical targets, conducted in-depth profiling of cell types and states, sub-phenotyped T cells within the TIME, and scrutinized cellular neighborhoods of diverse T cell subsets. Our findings highlight the advantage of spatial profiling, revealing immunosuppressive molecular signatures of tumor-associated myeloid cells interacting with neighboring exhausted, PD1high T cells in the TIME of hepatocellular carcinoma (HCC). This study establishes a robust framework for spatial exploration of TIMEs in solid tumors and underscores the potency of multiplexed tissue imaging and ultra-deep cell phenotyping in unraveling clinically relevant tumor components.
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Affiliation(s)
- Sophia Scheuermann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 ‘Image-Guided and Functionally Instructed Tumor Therapies’, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Tuebingen, Tuebingen, Germany
| | - Beate Kristmann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Fabienne Engelmann
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Alice Nuernbergk
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - David Scheuermann
- School of Business and Economics, Faculty of Economics and Social Sciences, University of Tuebingen, Tuebingen, Germany
| | - Marie Koloseus
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Tayeb Abed
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Wiebke Solass
- Institute of Tissue Medicine and Pathology (ITMP), University of Bern, Bern, Switzerland
| | - Christian M. Seitz
- Department of Haematology, Oncology, Gastroenterology, Nephrology, Rheumatology, University Children’s Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 ‘Image-Guided and Functionally Instructed Tumor Therapies’, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen, a partnership between German Cancer Research Center (DKFZ) and University Hospital Tuebingen, Tuebingen, Germany
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12
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Lv Y, Fu Q, Xu Y, Shi P. Sequentially-Activated Antibodies Based on Programmable DNA Tags for Rapid Multiplexed Protein Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306638. [PMID: 37922530 DOI: 10.1002/smll.202306638] [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: 08/03/2023] [Revised: 10/08/2023] [Indexed: 11/07/2023]
Abstract
The achievement of rapid multiplexed protein imaging is limited by the use of stimulating reagents, extensive incubating and washing steps, and the low fluorescence intensity of targets. In this study, sequentially-activated DNA tags are developed and combined them with primary antibodies using signal enhancement strategies to create sequentially-activated antibodies (SAAs). These SAAs enable rapid, wash-free sequential imaging of different protein targets. The samples are pre-processed to label all targets of interest with SAAs simultaneously, and the signal is turned ON for only one target in each stage. The sequential imaging of multiple targets is achieved through wash-free strand displacement reactions that exhibit rapid kinetics with t1/2 < 10 s in a cellular context. Remarkably, this method successfully demonstrates sequential imaging of nine different protein targets within just a few minutes. This all-in-one platform for multiplexed protein imaging holds great promise for diverse applications in immunofluorescence imaging.
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Affiliation(s)
- Yuheng Lv
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, P. R. China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Qin Fu
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, P. R. China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Yi Xu
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, P. R. China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Peng Shi
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, P. R. China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, P. R. China
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13
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Seabury AG, Khodabocus AJ, Kogan IM, Hoy GR, DeSalvo GA, Wustholz KL. Blinking characteristics of organic fluorophores for blink-based multiplexing. Commun Chem 2024; 7:18. [PMID: 38280979 PMCID: PMC10821931 DOI: 10.1038/s42004-024-01106-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.
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Affiliation(s)
| | | | | | - Grayson R Hoy
- Chemistry Department, William & Mary, Williamsburg, VA, USA
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14
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Schueder F, Jungmann R. In Situ Imaging of Proteins Using DNA-PAINT Super-Resolution Microscopy. Methods Mol Biol 2024; 2800:103-113. [PMID: 38709481 DOI: 10.1007/978-1-0716-3834-7_9] [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: 05/07/2024]
Abstract
The spatial resolution of conventional light microscopy is restricted by the diffraction limit to hundreds of nanometers. Super-resolution microscopy enables single digit nanometer resolution by circumventing the diffraction limit of conventional light microscopy. DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) belongs to the family of single-molecule localization super-resolution approaches. Unique features of DNA-PAINT are that it allows for sub-nanometer resolution, spectrally unlimited multiplexing, proximity detection, and quantitative counting of target molecules. Here, we describe prerequisites for efficient DNA-PAINT microscopy.
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Affiliation(s)
- Florian Schueder
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany.
- Max Planck Institute of Biochemistry, Planegg, Germany.
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15
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Ortiz-Perez A, Zhang M, Fitzpatrick LW, Izquierdo-Lozano C, Albertazzi L. Advanced optical imaging for the rational design of nanomedicines. Adv Drug Deliv Rev 2024; 204:115138. [PMID: 37980951 DOI: 10.1016/j.addr.2023.115138] [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: 06/09/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
Despite the enormous potential of nanomedicines to shape the future of medicine, their clinical translation remains suboptimal. Translational challenges are present in every step of the development pipeline, from a lack of understanding of patient heterogeneity to insufficient insights on nanoparticle properties and their impact on material-cell interactions. Here, we discuss how the adoption of advanced optical microscopy techniques, such as super-resolution optical microscopies, correlative techniques, and high-content modalities, could aid the rational design of nanocarriers, by characterizing the cell, the nanomaterial, and their interaction with unprecedented spatial and/or temporal detail. In this nanomedicine arena, we will discuss how the implementation of these techniques, with their versatility and specificity, can yield high volumes of multi-parametric data; and how machine learning can aid the rapid advances in microscopy: from image acquisition to data interpretation.
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Affiliation(s)
- Ana Ortiz-Perez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Miao Zhang
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Laurence W Fitzpatrick
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Cristina Izquierdo-Lozano
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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16
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Rames M, Kenison JP, Heineck D, Civitci F, Szczepaniak M, Zheng T, Shangguan J, Zhang Y, Tao K, Esener S, Nan X. Multiplexed and Millimeter-Scale Fluorescence Nanoscopy of Cells and Tissue Sections via Prism-Illumination and Microfluidics-Enhanced DNA-PAINT. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:817-830. [PMID: 38155726 PMCID: PMC10751790 DOI: 10.1021/cbmi.3c00060] [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: 05/19/2023] [Revised: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 12/30/2023]
Abstract
Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it has historically afforded a small field-of-view (FOV) of around 50 μm × 50 μm at once and more recently up to ∼200 μm × 200 μm. Efforts to further increase the FOV in fluorescence nanoscopy have thus far relied on the use of fabricated waveguide substrates, adding cost and sample constraints to the applications. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for multiplexed fluorescence nanoscopy across millimeter-scale FOVs. Built upon the well-established prism-type total internal reflection microscopy, PRIME-PAINT achieves robust single-molecule localization with up to ∼520 μm × 520 μm single FOVs and 25-40 nm lateral resolutions. Through stitching, nanoscopic imaging over mm2 sample areas can be completed in as little as 40 min per target. An on-stage microfluidics chamber facilitates probe exchange for multiplexing and enhances image quality, particularly for formalin-fixed paraffin-embedded (FFPE) tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ∼106 caveolae structures in ∼1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. By imaging from nanometers to millimeters with multiplexity and broad sample compatibility, PRIME-PAINT will be useful for building multiscale, Google-Earth-like views of biological systems.
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Affiliation(s)
- Matthew
J. Rames
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - John P. Kenison
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Daniel Heineck
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Fehmi Civitci
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Malwina Szczepaniak
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Ting Zheng
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Julia Shangguan
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Yujia Zhang
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Kai Tao
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Sadik Esener
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Xiaolin Nan
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
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17
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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18
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Queiroz Zetune Villa Real K, Mougios N, Rehm R, Sograte-Idrissi S, Albert L, Rahimi AM, Maidorn M, Hentze J, Martínez-Carranza M, Hosseini H, Saal KA, Oleksiievets N, Prigge M, Tsukanov R, Stenmark P, Fornasiero EF, Opazo F. A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy. SMALL METHODS 2023; 7:e2300218. [PMID: 37421204 DOI: 10.1002/smtd.202300218] [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: 02/21/2023] [Revised: 06/09/2023] [Indexed: 07/10/2023]
Abstract
Imaging of living synapses has relied for over two decades on the overexpression of synaptic proteins fused to fluorescent reporters. This strategy alters the stoichiometry of synaptic components and ultimately affects synapse physiology. To overcome these limitations, here a nanobody is presented that binds the calcium sensor synaptotagmin-1 (NbSyt1). This nanobody functions as an intrabody (iNbSyt1) in living neurons and is minimally invasive, leaving synaptic transmission almost unaffected, as suggested by the crystal structure of the NbSyt1 bound to Synaptotagmin-1 and by the physiological data. Its single-domain nature enables the generation of protein-based fluorescent reporters, as showcased here by measuring spatially localized presynaptic Ca2+ with a NbSyt1- jGCaMP8 chimera. Moreover, the small size of NbSyt1 makes it ideal for various super-resolution imaging methods. Overall, NbSyt1 is a versatile binder that will enable imaging in cellular and molecular neuroscience with unprecedented precision across multiple spatiotemporal scales.
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Affiliation(s)
- Karine Queiroz Zetune Villa Real
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Nikolaos Mougios
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Ronja Rehm
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - László Albert
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Amir Mohammad Rahimi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Manuel Maidorn
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jannik Hentze
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Markel Martínez-Carranza
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm, SE-10691, Sweden
| | - Hassan Hosseini
- Research Group Neuromodulatory Networks, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Kim-Ann Saal
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Nazar Oleksiievets
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Matthias Prigge
- Research Group Neuromodulatory Networks, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39118, Magdeburg, Germany
| | - Roman Tsukanov
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm, SE-10691, Sweden
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
- NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany
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19
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Friedl K, Mau A, Boroni-Rueda F, Caorsi V, Bourg N, Lévêque-Fort S, Leterrier C. Assessing crosstalk in simultaneous multicolor single-molecule localization microscopy. CELL REPORTS METHODS 2023; 3:100571. [PMID: 37751691 PMCID: PMC10545913 DOI: 10.1016/j.crmeth.2023.100571] [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: 01/23/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023]
Abstract
Single-molecule localization microscopy (SMLM) can reach sub-50 nm resolution using techniques such as stochastic optical reconstruction microscopy (STORM) or DNA-point accumulation for imaging in nanoscale topography (PAINT). Here we implement two approaches for faster multicolor SMLM by splitting the emitted fluorescence toward two cameras: simultaneous two-color DNA-PAINT (S2C-DNA-PAINT) that images spectrally separated red and far-red imager strands on each camera, and spectral demixing dSTORM (SD-dSTORM) where spectrally close far-red fluorophores appear on both cameras before being identified by demixing. Using S2C-DNA-PAINT as a reference for low crosstalk, we evaluate SD-dSTORM crosstalk using three types of samples: DNA origami nanorulers of different sizes, single-target labeled cells, or cells labeled for multiple targets. We then assess if crosstalk can affect the detection of biologically relevant subdiffraction patterns. Extending these approaches to three-dimensional acquisition and SD-dSTORM to three-color imaging, we show that spectral demixing is an attractive option for robust and versatile multicolor SMLM investigations.
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Affiliation(s)
- Karoline Friedl
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France; Abbelight, 191 Avenue Aristide Briand, 94230 Cachan, France
| | - Adrien Mau
- Abbelight, 191 Avenue Aristide Briand, 94230 Cachan, France; Université Paris Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Fanny Boroni-Rueda
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France
| | | | - Nicolas Bourg
- Abbelight, 191 Avenue Aristide Briand, 94230 Cachan, France
| | - Sandrine Lévêque-Fort
- Université Paris Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Christophe Leterrier
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France.
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20
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Wei W, Zhang Y, Yang F, Zhou L, Zhang Y, Wang Y, Yang S, Li J, Dong H. Orthometric multicolor encoded hybridization chain reaction amplifiers for multiplexed microRNA profiling in living cells. Chem Sci 2023; 14:5503-5509. [PMID: 37234881 PMCID: PMC10208064 DOI: 10.1039/d3sc00563a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Multiplexed microRNA (miRNA) profiling of more than four types in living cells is challenging due to fluorescent spectral overlap, representing a significant limitation in studying the complex interactions related to the occurrence and development of diseases. Herein, we report a multiplexed fluorescent imaging strategy based on an orthometric multicolor encoded hybridization chain reaction amplifier named multi-HCR. The targeting miRNA can trigger this multi-HCR strategy due to the specific sequence recognition, and then its self-assembly to amplify the programmability signals. We take the four-colored chain amplifiers, showing that the multi-HCR can form 15 combinations simultaneously. In a living process of hypoxia-induced apoptosis and autophagy under complicated mitochondria and endoplasmic reticulum stress, the multi-HCR demonstrates excellent performance in detecting eight different miRNA changes. The multi-HCR provides a robust strategy for simultaneously profiling multiplexed miRNA biomarkers in studying complicated cellular processes.
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Affiliation(s)
- Wei Wei
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Beijing Yaogen Biotechnology Co. Ltd 26 Yongwangxi Road 102609 Beijing China
| | - Yiyi Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yufan Zhang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yeyu Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Beijing Yaogen Biotechnology Co. Ltd 26 Yongwangxi Road 102609 Beijing China
| | - Shuangshuang Yang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Jinze Li
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Haifeng Dong
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
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21
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Takei Y, Yang Y, White J, Yun J, Prasad M, Ombelets LJ, Schindler S, Cai L. High-resolution spatial multi-omics reveals cell-type specific nuclear compartments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539762. [PMID: 37214923 PMCID: PMC10197539 DOI: 10.1101/2023.05.07.539762] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1-3. Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yujing Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Meera Prasad
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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22
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Reinhardt SCM, Masullo LA, Baudrexel I, Steen PR, Kowalewski R, Eklund AS, Strauss S, Unterauer EM, Schlichthaerle T, Strauss MT, Klein C, Jungmann R. Ångström-resolution fluorescence microscopy. Nature 2023; 617:711-716. [PMID: 37225882 PMCID: PMC10208979 DOI: 10.1038/s41586-023-05925-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/07/2023] [Indexed: 05/26/2023]
Abstract
Fluorescence microscopy, with its molecular specificity, is one of the major characterization methods used in the life sciences to understand complex biological systems. Super-resolution approaches1-6 can achieve resolution in cells in the range of 15 to 20 nm, but interactions between individual biomolecules occur at length scales below 10 nm and characterization of intramolecular structure requires Ångström resolution. State-of-the-art super-resolution implementations7-14 have demonstrated spatial resolutions down to 5 nm and localization precisions of 1 nm under certain in vitro conditions. However, such resolutions do not directly translate to experiments in cells, and Ångström resolution has not been demonstrated to date. Here we introdue a DNA-barcoding method, resolution enhancement by sequential imaging (RESI), that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents. By sequentially imaging sparse target subsets at moderate spatial resolutions of >15 nm, we demonstrate that single-protein resolution can be achieved for biomolecules in whole intact cells. Furthermore, we experimentally resolve the DNA backbone distance of single bases in DNA origami with Ångström resolution. We use our method in a proof-of-principle demonstration to map the molecular arrangement of the immunotherapy target CD20 in situ in untreated and drug-treated cells, which opens possibilities for assessing the molecular mechanisms of targeted immunotherapy. These observations demonstrate that, by enabling intramolecular imaging under ambient conditions in whole intact cells, RESI closes the gap between super-resolution microscopy and structural biology studies and thus delivers information key to understanding complex biological systems.
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Affiliation(s)
- Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | | | - Isabelle Baudrexel
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Philipp R Steen
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Alexandra S Eklund
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Thomas Schlichthaerle
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Maximilian T Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Christian Klein
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
- Roche Innovation Center Zurich, Roche Pharma Research and Early Development, Schlieren, Switzerland
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany.
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany.
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23
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Banerjee A, Anand M, Ganji M. Labeling approaches for DNA-PAINT super-resolution imaging. NANOSCALE 2023; 15:6563-6580. [PMID: 36942769 DOI: 10.1039/d2nr06541j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
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24
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Kocabey S, Chiarelli G, Acuna GP, Ruegg C. Ultrasensitive and multiplexed miRNA detection system with DNA-PAINT. Biosens Bioelectron 2023; 224:115053. [PMID: 36608362 DOI: 10.1016/j.bios.2022.115053] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
MiRNAs hold great potential as biomarkers for the early detection and monitoring of diseases based on their differential expression profiles. Therefore, the sensitive, specific and accurate detection of miRNAs represents an emerging new tool to improve diagnosis and treatment of several diseases, cancer in particular. DNA origami-based miRNA detection is particularly advantageous as it allows to incorporate multiple attachment sites to capture different target miRNAs at the nanoscale. In this work, we present a DNA origami nanoarray system providing distance-dependent recognition of miRNAs by applying super-resolution microscopy technique; DNA-PAINT (point accumulation for imaging in nanoscale topography). The sensor can detect up to 4 miRNAs either separately or in combination based on the relative distance to the boundary markers on the structure using a single imager strand. The detection is highly sensitive, with a limit of detection down to the low femtomolar range (11 fM - 388 fM) and has a large dynamic range up to 10 nM without need for amplification. Moreover, our detection system can discriminate single base mismatches with low false positive rates. Using our strategy, we demonstrate the detection of endogenous miRNAs from cell extracts of cancer cell lines and plasma from breast cancer patients. Overall, we developed an ultrasensitive and amplification-free, DNA-PAINT imaging-based miRNA detection method using DNA origami nanoarray system for the detection of breast-cancer associated miRNAs which potentially provides a sensitive and accurate alternative to the current multiplexed diagnostic technologies.
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Affiliation(s)
- Samet Kocabey
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland.
| | - Germán Chiarelli
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700, Fribourg, Switzerland
| | - Guillermo P Acuna
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700, Fribourg, Switzerland
| | - Curzio Ruegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland
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25
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Jeong JE, Sutton JJ, Ryu HS, Kang M, Tay EJ, Nguyen TL, Gordon KC, Shim SH, Woo HY. Resonant Raman-Active Polymer Dot Barcodes for Multiplex Cell Mapping. ACS NANO 2023; 17:4800-4812. [PMID: 36863001 DOI: 10.1021/acsnano.2c11240] [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: 06/18/2023]
Abstract
Resonance Raman spectroscopy is an efficient tool for multiplex imaging because of the narrow bandwidth of the electronically enhanced vibrational signals. However, Raman signals are often overwhelmed by concurrent fluorescence. In this study, we synthesized a series of truxene-based conjugated Raman probes to show structure-specific Raman fingerprint patterns with a common 532 nm light source. The subsequent polymer dot (Pdot) formation of the Raman probes efficiently suppressed fluorescence via aggregation-induced quenching and improved the dispersion stability of particles without leakage of Raman probes or particle agglomeration for more than 1 year. Additionally, the Raman signal amplified by electronic resonance and increased probe concentration exhibited over 103 times higher relative Raman intensities versus 5-ethynyl-2'-deoxyuridine, enabling successful Raman imaging. Finally, multiplex Raman mapping was demonstrated with a single 532 nm laser using six Raman-active and biocompatible Pdots as barcodes for live cells. Resonant Raman-active Pdots may suggest a simple, robust, and efficient way for multiplex Raman imaging using a standard Raman spectrometer, suggesting the broad applicability of our strategy.
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Affiliation(s)
- Ji-Eun Jeong
- Department of Specialty Chemicals, Division of Specialty and Bio-based Chemicals Technology, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44412, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Joshua J Sutton
- Department of Chemistry, University of Otago, Dunedin and MacDiarmid Institute, Dunedin 9016, New Zealand
| | - Hwa Sook Ryu
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minsu Kang
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Elliot J Tay
- Department of Chemistry, University of Otago, Dunedin and MacDiarmid Institute, Dunedin 9016, New Zealand
| | - Thanh Luan Nguyen
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Keith C Gordon
- Department of Chemistry, University of Otago, Dunedin and MacDiarmid Institute, Dunedin 9016, New Zealand
| | - Sang-Hee Shim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Han Young Woo
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
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26
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Schueder F, Mangeol P, Chan EH, Rees R, Schünemann J, Jungmann R, Görlich D, Schnorrer F. Nanobodies combined with DNA-PAINT super-resolution reveal a staggered titin nanoarchitecture in flight muscles. eLife 2023; 12:e79344. [PMID: 36645127 PMCID: PMC9886278 DOI: 10.7554/elife.79344] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 11/22/2022] [Indexed: 01/17/2023] Open
Abstract
Sarcomeres are the force-producing units of all striated muscles. Their nanoarchitecture critically depends on the large titin protein, which in vertebrates spans from the sarcomeric Z-disc to the M-band and hence links actin and myosin filaments stably together. This ensures sarcomeric integrity and determines the length of vertebrate sarcomeres. However, the instructive role of titins for sarcomeric architecture outside of vertebrates is not as well understood. Here, we used a series of nanobodies, the Drosophila titin nanobody toolbox, recognising specific domains of the two Drosophila titin homologs Sallimus and Projectin to determine their precise location in intact flight muscles. By combining nanobodies with DNA-PAINT super-resolution microscopy, we found that, similar to vertebrate titin, Sallimus bridges across the flight muscle I-band, whereas Projectin is located at the beginning of the A-band. Interestingly, the ends of both proteins overlap at the I-band/A-band border, revealing a staggered organisation of the two Drosophila titin homologs. This architecture may help to stably anchor Sallimus at the myosin filament and hence ensure efficient force transduction during flight.
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Affiliation(s)
- Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian UniversityMunichGermany
- Max Planck Institute of BiochemistryMartinsriedGermany
| | - Pierre Mangeol
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living SystemsMarseilleFrance
| | - Eunice HoYee Chan
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living SystemsMarseilleFrance
| | - Renate Rees
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | | | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian UniversityMunichGermany
- Max Planck Institute of BiochemistryMartinsriedGermany
| | - Dirk Görlich
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Frank Schnorrer
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living SystemsMarseilleFrance
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27
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Scinto SL, Reagle TR, Fox JM. Affinity Bioorthogonal Chemistry (ABC) Tags for Site-Selective Conjugation, On-Resin Protein-Protein Coupling, and Purification of Protein Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207661. [PMID: 36058881 PMCID: PMC10029600 DOI: 10.1002/anie.202207661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 11/12/2022]
Abstract
The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the nickel-iminodiacetate (Ni-IDA) resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity-based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC-tagging works with a range of site-selective bioconjugation methods with proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions to provide protein-protein conjugates.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Tyler R Reagle
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
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28
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Koester AM, Szczepaniak M, Nan X. Fast and Multiplexed Super Resolution Imaging of Fixed and Immunostained Cells with DNA-PAINT-ERS. Curr Protoc 2022; 2:e618. [PMID: 36426921 PMCID: PMC9708096 DOI: 10.1002/cpz1.618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recent advances in super resolution microscopy have enabled imaging at the 10-20 nm scale on a light microscope, providing unprecedented details of native biological structures and processes in intact and hydrated samples. Of the existing strategies, DNA points accumulation in imaging nanoscale topography (DNA-PAINT) affords convenient multiplexing, an important feature in interrogating complex biological systems. A practical limitation of DNA-PAINT, however, has been the slow imaging speed. In its original form, DNA-PAINT imaging of each target takes tens of minutes to hours to complete. To address this challenge, several improved implementations have been introduced. These include DNA-PAINT-ERS (where E = ethylene carbonate; R = repeat sequence; S = spacer), a set of strategies that leads to both accelerated DNA-PAINT imaging speed and improved image quality. With DNA-PAINT-ERS, imaging of typical cellular targets such as microtubules takes only 5-10 min. Importantly, DNA-PAINT-ERS also facilitates multiplexing and can be easily integrated into current workflows for fluorescence staining of biological samples. Here, we provide a detailed, step-by-step guide for fast and multiplexed DNA-PAINT-ERS imaging of fixed and immunostained cells grown on glass substrates as adherent monolayers. The protocol should be readily extended to biological samples of a different format (for example tissue sections) or staining mechanisms (for example using nanobodies). © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of probes for DNA-PAINT-ERS Basic Protocol 2: Sample preparation for imaging membrane targets with DNA-PAINT-ERS in fixed cells Alternate Protocol: Immunostaining of extracted U2OS cells Basic Protocol 3: Super resolution image acquisition and analysis.
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Affiliation(s)
- Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
| | - Malwina Szczepaniak
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
| | - Xiaolin Nan
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA
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29
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Conze C, Trushina NI, Holtmannspötter M, Rierola M, Attanasio S, Bakota L, Piehler J, Brandt R. Super-resolution imaging and quantitative analysis of microtubule arrays in model neurons show that epothilone D increases the density but decreases the length and straightness of microtubules in axon-like processes. Brain Res Bull 2022; 190:234-243. [PMID: 36244582 PMCID: PMC9634454 DOI: 10.1016/j.brainresbull.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Microtubules are essential for the development of neurons and the regulation of their structural plasticity. Microtubules also provide the structural basis for the long-distance transport of cargo. Various factors influence the organization and dynamics of neuronal microtubules, and disturbance of microtubule regulation is thought to play a central role in neurodegenerative diseases. However, imaging and quantitative assessment of the microtubule organization in the densely packed neuronal processes is challenging. The development of super-resolution techniques combined with the use of nanobodies offers new possibilities to visualize microtubules in neurites in high resolution. In combination with recently developed computational analysis tools, this allows automated quantification of neuronal microtubule organization with high precision. Here we have implemented three-dimensional DNA-PAINT (Point Accumulation in Nanoscale Topography), a single-molecule localization microscopy (SMLM) technique, which allows us to acquire 3D arrays of the microtubule lattice in axons of model neurons (neuronally differentiated PC12 cells) and dendrites of primary neurons. For the quantitative analysis of the microtubule organization, we used the open-source software package SMLM image filament extractor (SIFNE). We found that treatment with nanomolar concentrations of the microtubule-targeting drug epothilone D (EpoD) increased microtubule density in axon-like processes of model neurons and shifted the microtubule length distribution to shorter ones, with a mean microtubule length of 2.39 µm (without EpoD) and 1.98 µm (with EpoD). We also observed a significant decrease in microtubule straightness after EpoD treatment. The changes in microtubule density were consistent with live-cell imaging measurements of ensemble microtubule dynamics using a previously established Fluorescence Decay After Photoactivation (FDAP) assay. For comparison, we determined the organization of the microtubule array in dendrites of primary hippocampal neurons. We observed that dendritic microtubules have a very similar length distribution and straightness compared to microtubules in axon-like processes of a neuronal cell line. Our data show that super-resolution imaging of microtubules followed by algorithm-based image analysis represents a powerful tool to quantitatively assess changes in microtubule organization in neuronal processes, useful to determine the effect of microtubule-modulating conditions. We also provide evidence that the approach is robust and can be applied to neuronal cell lines or primary neurons, both after incorporation of labeled tubulin and by anti-tubulin antibody staining.
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Affiliation(s)
- Christian Conze
- Department of Neurobiology, Osnabrück University, Osnabrück, Germany
| | | | | | - Marina Rierola
- Department of Neurobiology, Osnabrück University, Osnabrück, Germany
| | - Simone Attanasio
- Department of Neurobiology, Osnabrück University, Osnabrück, Germany
| | - Lidia Bakota
- Department of Neurobiology, Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany; Division of Biophysics, Osnabrück University, Osnabrück, Germany
| | - Roland Brandt
- Department of Neurobiology, Osnabrück University, Osnabrück, Germany; Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany; Institute of Cognitive Science, Osnabrück University, Osnabrück, Germany.
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30
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Hu B, Sajid M, Lv R, Liu L, Sun C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front Immunol 2022; 13:996721. [PMID: 36389765 PMCID: PMC9659855 DOI: 10.3389/fimmu.2022.996721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/17/2022] [Indexed: 08/13/2023] Open
Abstract
Interpreting the mechanisms and principles that govern gene activity and how these genes work according to -their cellular distribution in organisms has profound implications for cancer research. The latest technological advancements, such as imaging-based approaches and next-generation single-cell sequencing technologies, have established a platform for spatial transcriptomics to systematically quantify the expression of all or most genes in the entire tumor microenvironment and explore an array of disease milieus, particularly in tumors. Spatial profiling technologies permit the study of transcriptional activity at the spatial or single-cell level. This multidimensional classification of the transcriptomic and proteomic signatures of tumors, especially the associated immune and stromal cells, facilitates evaluation of tumor heterogeneity, details of the evolutionary trajectory of each tumor, and multifaceted interactions between each tumor cell and its microenvironment. Therefore, spatial profiling technologies may provide abundant and high-resolution information required for the description of clinical-related features in immuno-oncology. From this perspective, the present review will highlight the importance of spatial transcriptomic and spatial proteomics analysis along with the joint use of other sequencing technologies and their implications in cancers and immune-oncology. In the near future, advances in spatial profiling technologies will undoubtedly expand our understanding of tumor biology and highlight possible precision therapeutic targets for cancer patients.
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Affiliation(s)
- Bian Hu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Muhammad Sajid
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rong Lv
- Blood Transfusion Laboratory, Anhui Blood Center, Hefei, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
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31
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Zhu H, Shen W, Luo C, Liu F. An integrated microfluidic device for multiplexed imaging of spatial gene expression patterns of Drosophila embryos. LAB ON A CHIP 2022; 22:4081-4092. [PMID: 36165088 DOI: 10.1039/d2lc00514j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To reveal the underlying mechanism of the biological function of multicellular systems, it is important to obtain comprehensive spatial gene expression profiles. Among the emerging single-cell spatial-omics techniques, immunofluorescence (IF)-based iterative multiplexed imaging is a promising approach. However, the conventional method is usually costly, time-consuming, labor-intensive, and has low throughput. Moreover, it has yet to be demonstrated in intact multicellular organisms. Here, we developed an integrated microfluidic system to overcome these challenges for quantitatively measuring multiple protein profiles sequentially in situ in the same Drosophila embryo. We designed an array of hydrodynamic trapping sites to automatically capture over ten Drosophila embryos with orientation selectivity at more than 90% trapping rates. We also optimized the geometry of confinement and the on-chip IF protocol to achieve the same high signal-to-noise ratio as the off-chip traditional IF experiments. Moreover, we developed an efficient de-staining protocol by combining on-chip antibody stripping and fluorophore bleaching. Using the same secondary antibody to sequentially stain different genes, we confirmed that the de-stained genes have no detectable interference with the subsequently stained genes, and the gene expression profiles are preserved after multiple cycles of staining and de-staining processes. This preliminary test shows that our newly developed integrated microfluidic system can be a powerful tool for multiplexed imaging of Drosophila embryos. Our work opens a new avenue to design microfluidic chips for multicellular organisms and single-cell spatial-omics techniques.
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Affiliation(s)
- Hongcun Zhu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
| | - Wenting Shen
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China
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32
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Zhang Q, Miyamoto A, Watanabe S, Arimori T, Sakai M, Tomisaki M, Kiuchi T, Takagi J, Watanabe N. Engineered fast-dissociating antibody fragments for multiplexed super-resolution microscopy. CELL REPORTS METHODS 2022; 2:100301. [PMID: 36313806 PMCID: PMC9606137 DOI: 10.1016/j.crmeth.2022.100301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 08/31/2022] [Indexed: 05/22/2023]
Abstract
Image reconstruction by integrating exchangeable single-molecule localization (IRIS) achieves multiplexed super-resolution imaging by high-density labeling with fast exchangeable fluorescent probes. However, previous methods to develop probes for individual targets required a great amount of time and effort. Here, we introduce a method for generating recombinant IRIS probes with a new mutagenesis strategy that can be widely applied to existing antibody sequences. Several conserved tyrosine residues at the base of complementarity-determining regions were identified as candidate sites for site-directed mutagenesis. With a high probability, mutations at candidate sites accelerated the off rate of recombinant antibody-based probes without compromising specific binding. We were able to develop IRIS probes from five monoclonal antibodies and three single-domain antibodies. We demonstrate multiplexed localization of endogenous proteins in primary neurons that visualizes small synaptic connections with high binding density. It is now practically feasible to generate fast-dissociating fluorescent probes for multitarget super-resolution imaging.
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Affiliation(s)
- Qianli Zhang
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Akitoshi Miyamoto
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Shin Watanabe
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Takao Arimori
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masanori Sakai
- Kyoto University Faculty of Engineering, Kyoto 606-8317, Japan
| | - Madoka Tomisaki
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Tai Kiuchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Naoki Watanabe
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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33
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Zhang Y, Wang G, Huang P, Sun E, Kweon J, Li Q, Zhe J, Ying LL, Zhang HF. Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. Anal Chem 2022; 94:13834-13841. [PMID: 36165784 PMCID: PMC9859736 DOI: 10.1021/acs.analchem.2c02417] [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: 02/02/2023]
Abstract
Super-resolution microscopy can capture spatiotemporal organizations of protein interactions with resolution down to 10 nm; however, the analyses of more than two proteins involving low-abundance protein are challenging because spectral crosstalk and heterogeneities of individual fluorescent labels result in molecular misidentification. Here we developed a deep learning-based imaging analysis method for spectroscopic single-molecule localization microscopy to minimize molecular misidentification in three-color super-resolution imaging. We characterized the 3-fold reduction of molecular misidentification in the new imaging method using pure samples of different photoswitchable fluorophores and visualized three distinct subcellular proteins in U2-OS cell lines. We further validated the protein counts and interactions of TOMM20, DRP1, and SUMO1 in a well-studied biological process, Staurosporine-induced apoptosis, by comparing the imaging results with Western-blot analyses of different subcellular portions.
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Affiliation(s)
- Yang Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Gaoxiang Wang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Hematology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei, 430030, China
| | - Peizhou Huang
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Edison Sun
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Qianru Li
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Ji Zhe
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Leslie L. Ying
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
- Department of Electrical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
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34
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Efficient DNA fluorescence labeling via base excision trapping. Nat Commun 2022; 13:5043. [PMID: 36028479 PMCID: PMC9418136 DOI: 10.1038/s41467-022-32494-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.
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35
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Sirinakis G, Allgeyer ES, Cheng J, St Johnston D. Quantitative comparison of spinning disk geometries for PAINT based super-resolution microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3773-3785. [PMID: 35991926 PMCID: PMC9352288 DOI: 10.1364/boe.459490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
PAINT methods that use DNA- or protein- based exchangeable probes have become popular for super-resolution imaging and have been combined with spinning disk confocal microscopy for imaging thicker samples. However, the widely available spinning disks used for routine biological imaging are not optimized for PAINT-based applications and may compromise resolution and imaging speed. Here, we use Drosophila egg chambers in the presence of the actin-binding peptide Lifeact to study the performance of four different spinning disk geometries. We find that disk geometries with higher light collection efficiency perform better for PAINT-based super-resolution imaging due to increased photon numbers and, subsequently, detection of more blinking events.
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Affiliation(s)
- George Sirinakis
- The Gurdon Institute & the Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Edward S Allgeyer
- The Gurdon Institute & the Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Jinmei Cheng
- The Gurdon Institute & the Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China
| | - Daniel St Johnston
- The Gurdon Institute & the Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
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36
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Shi L, Klimas A, Gallagher B, Cheng Z, Fu F, Wijesekara P, Miao Y, Ren X, Zhao Y, Min W. Super-Resolution Vibrational Imaging Using Expansion Stimulated Raman Scattering Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200315. [PMID: 35521971 PMCID: PMC9284179 DOI: 10.1002/advs.202200315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is an emerging technology that provides high chemical specificity for endogenous biomolecules and can circumvent common constraints of fluorescence microscopy including limited capabilities to probe small biomolecules and difficulty resolving many colors simultaneously. However, the resolution of SRS microscopy remains governed by the diffraction limit. To overcome this, a new technique called molecule anchorable gel-enabled nanoscale Imaging of Fluorescence and stimulated Raman scattering microscopy (MAGNIFIERS) that integrates SRS microscopy with expansion microscopy (ExM) is described. MAGNIFIERS offers chemical-specific nanoscale imaging with sub-50 nm resolution and has scalable multiplexity when combined with multiplex Raman probes and fluorescent labels. MAGNIFIERS is used to visualize nanoscale features in a label-free manner with CH vibration of proteins, lipids, and DNA in a broad range of biological specimens, from mouse brain, liver, and kidney to human lung organoid. In addition, MAGNIFIERS is applied to track nanoscale features of protein synthesis in protein aggregates using metabolic labeling of small metabolites. Finally, MAGNIFIERS is used to demonstrate 8-color nanoscale imaging in an expanded mouse brain section. Overall, MAGNIFIERS is a valuable platform for super-resolution label-free chemical imaging, high-resolution metabolic imaging, and highly multiplexed nanoscale imaging, thus bringing SRS to nanoscopy.
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Affiliation(s)
- Lixue Shi
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
| | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Brendan Gallagher
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Feifei Fu
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Piyumi Wijesekara
- Department of Biomedical EngineeringCarnegie Mellon UniversityPittsburghPA15143USA
| | - Yupeng Miao
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
| | - Xi Ren
- Department of Biomedical EngineeringCarnegie Mellon UniversityPittsburghPA15143USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Wei Min
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
- Kavli Institute for Brain ScienceColumbia UniversityNew YorkNY10027USA
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37
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Ma J, Peng Z, Ma L, Diao L, Shao X, Zhao Z, Liu L, Zhang L, Huang C, Liu M. A Multiple-Target Simultaneous Detection Method for Immunosorbent Assay and Immunospot Assay. Anal Chem 2022; 94:8704-8714. [PMID: 35649130 DOI: 10.1021/acs.analchem.2c01087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzyme-linked immunosorbent assay (ELISA) is one of the most common methods in biological studies, and enzyme-linked immunospot (ELISpot) is a method to measure specific cell numbers by detecting protein secretion at a single-cell level. However, these two current methods can only detect one signal at one time and the sensitivity is not high enough to test low-concentration samples, which are major shortcomings in systematically analyzing the samples of interest. Herein, we demonstrated fluorescence-based oligo-linked immunosorbent assay (FOLISA) and fluorescence-based oligo-linked immunospot (FOLISPOT), which utilized DNA-barcoded antibodies to provide a highly multiplexed method with signal amplification. Signal amplification and simultaneous multiple-target detection were achieved by DNA complementary pairing and modular orthogonal DNA concatemers. By comparing FOLISA with traditional ELISA and comparing FOLISPOT with traditional ELISPOT, we found that the detection sensitivities of FOLISA and FOLISPOT are much higher than those of traditional ELISA and ELISPOT. The detection limit of ELISA is around 3 pg/mL, and the detection limit of FOLISA is below 0.06 pg/mL. FOLISPOT can detect more spots than ELISPOT and can detect targets that are undetectable for ELISPOT. Furthermore, FOLISA and FOLISPOT allowed sequential detection of multiple targets by using a single dye or multiple dyes in one round and sequential detection in multiple rounds. Thus, FOLISA and FOLISPOT enabled simultaneous detection of a large number of targets, significantly improved the detection sensitivity, and overcame the shortcomings of ELISA and ELISPOT. Overall, FOLISA and FOLISPOT presented effective and general platforms for rapid and multiplexed detection of antigens or antibodies with high sensitivity, either in laboratory tests or potentially in clinic tests.
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Affiliation(s)
- Jianting Ma
- Kunshan Hospital of Traditional Chinese Medicine, Suzhou, Kunshan 215300, People's Republic of China.,Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Zuofu Peng
- AlphaX (Beijing) Biotech Co., Ltd., Beijing 100083, People's Republic of China
| | - Lin Ma
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Lu Diao
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Xinyu Shao
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Soochow University, Suzhou 215006, People's Republic of China
| | - Zhiming Zhao
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Lele Liu
- Kunshan Hospital of Traditional Chinese Medicine, Suzhou, Kunshan 215300, People's Republic of China
| | - Liang Zhang
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Chenrong Huang
- Department of Clinical Pharmacology, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215123, People's Republic of China
| | - Mi Liu
- Kunshan Hospital of Traditional Chinese Medicine, Suzhou, Kunshan 215300, People's Republic of China.,Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, People's Republic of China
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38
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Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J. Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Nat Methods 2022; 19:554-559. [PMID: 35501386 PMCID: PMC9133131 DOI: 10.1038/s41592-022-01464-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/23/2022] [Indexed: 11/21/2022]
Abstract
DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution microscopy method that can acquire high-fidelity images at nanometer resolution. It suffers, however, from high background and slow imaging speed, both of which can be attributed to the presence of unbound fluorophores in solution. Here we present two-color fluorogenic DNA-PAINT, which uses improved imager probe and docking strand designs to solve these problems. These self-quenching single-stranded DNA probes are conjugated with a fluorophore and quencher at the terminals, which permits an increase in fluorescence by up to 57-fold upon binding and unquenching. In addition, the engineering of base pair mismatches between the fluorogenic imager probes and docking strands allowed us to achieve both high fluorogenicity and the fast binding kinetics required for fast imaging. We demonstrate a 26-fold increase in imaging speed over regular DNA-PAINT and show that our new implementation enables three-dimensional super-resolution DNA-PAINT imaging without optical sectioning.
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Affiliation(s)
- Kenny K H Chung
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Zhao Zhang
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Nathan D Williams
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Bennett Rollins
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Yang Yang
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - David Baddeley
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University, New Haven, CT, USA.
- Nanobiology Institute, Yale University, West Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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39
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Malle MG, Löffler PMG, Bohr SSR, Sletfjerding MB, Risgaard NA, Jensen SB, Zhang M, Hedegård P, Vogel S, Hatzakis NS. Single-particle combinatorial multiplexed liposome fusion mediated by DNA. Nat Chem 2022; 14:558-565. [PMID: 35379901 DOI: 10.1038/s41557-022-00912-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/17/2022] [Indexed: 12/22/2022]
Abstract
Combinatorial high-throughput methodologies are central for both screening and discovery in synthetic biochemistry and biomedical sciences. They are, however, often reliant on large-scale analyses and thus limited by a long running time and excessive materials cost. We here present a single-particle combinatorial multiplexed liposome fusion mediated by DNA for parallelized multistep and non-deterministic fusion of individual subattolitre nanocontainers. We observed directly the efficient (>93%) and leakage free stochastic fusion sequences for arrays of surface-tethered target liposomes with six freely diffusing populations of cargo liposomes, each functionalized with individual lipidated single-stranded DNA and fluorescently barcoded by a distinct ratio of chromophores. The stochastic fusion resulted in a distinct permutation of fusion sequences for each autonomous nanocontainer. Real-time total internal reflection imaging allowed the direct observation of >16,000 fusions and 566 distinct fusion sequences accurately classified using machine learning. The high-density arrays of surface-tethered target nanocontainers (~42,000 containers per mm2) offers entire combinatorial multiplex screens using only picograms of material.
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Affiliation(s)
- Mette Galsgaard Malle
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Berg Sletfjerding
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Simon Bo Jensen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Hedegård
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark. .,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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40
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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41
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Dhiman S, Andrian T, Gonzalez BS, Tholen MME, Wang Y, Albertazzi L. Can super-resolution microscopy become a standard characterization technique for materials chemistry? Chem Sci 2022; 13:2152-2166. [PMID: 35310478 PMCID: PMC8864713 DOI: 10.1039/d1sc05506b] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
The characterization of newly synthesized materials is a cornerstone of all chemistry and nanotechnology laboratories. For this purpose, a wide array of analytical techniques have been standardized and are used routinely by laboratories across the globe. With these methods we can understand the structure, dynamics and function of novel molecular architectures and their relations with the desired performance, guiding the development of the next generation of materials. Moreover, one of the challenges in materials chemistry is the lack of reproducibility due to improper publishing of the sample preparation protocol. In this context, the recent adoption of the reporting standard MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature) for material characterization and details of experimental protocols aims to provide complete, reproducible and reliable sample preparation for the scientific community. Thus, MIRIBEL should be immediately adopted in publications by scientific journals to overcome this challenge. Besides current standard spectroscopy and microscopy techniques, there is a constant development of novel technologies that aim to help chemists unveil the structure of complex materials. Among them super-resolution microscopy (SRM), an optical technique that bypasses the diffraction limit of light, has facilitated the study of synthetic materials with multicolor ability and minimal invasiveness at nanometric resolution. Although still in its infancy, the potential of SRM to unveil the structure, dynamics and function of complex synthetic architectures has been highlighted in pioneering reports during the last few years. Currently, SRM is a sophisticated technique with many challenges in sample preparation, data analysis, environmental control and automation, and moreover the instrumentation is still expensive. Therefore, SRM is currently limited to expert users and is not implemented in characterization routines. This perspective discusses the potential of SRM to transition from a niche technique to a standard routine method for material characterization. We propose a roadmap for the necessary developments required for this purpose based on a collaborative effort from scientists and engineers across disciplines.
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Affiliation(s)
- Shikha Dhiman
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Teodora Andrian
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
| | - Beatriz Santiago Gonzalez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Applied Physics, Eindhoven University of Technology Postbus 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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42
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Unterauer EM, Jungmann R. Quantitative Imaging With DNA-PAINT for Applications in Synaptic Neuroscience. Front Synaptic Neurosci 2022; 13:798267. [PMID: 35197837 PMCID: PMC8860300 DOI: 10.3389/fnsyn.2021.798267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/21/2021] [Indexed: 12/02/2022] Open
Abstract
Super-resolution (SR) microscopy techniques have been advancing the understanding of neuronal protein networks and interactions. Unraveling the arrangement of proteins with molecular resolution provided novel insights into neuron cytoskeleton structure and actin polymerization dynamics in synaptic spines. Recent improvements in quantitative SR imaging have been applied to synaptic protein clusters and with improved multiplexing technology, the interplay of multiple protein partners in synaptic active zones has been elucidated. While all SR techniques come with benefits and drawbacks, true molecular quantification is a major challenge with the most complex requirements for labeling reagents and careful experimental design. In this perspective, we provide an overview of quantitative SR multiplexing and discuss in greater detail the quantification and multiplexing capabilities of the SR technique DNA-PAINT. Using predictable binding kinetics of short oligonucleotides, DNA-PAINT provides two unique approaches to address multiplexed molecular quantification: qPAINT and Exchange-PAINT. With precise and accurate quantification and spectrally unlimited multiplexing, DNA-PAINT offers an attractive route to unravel complex protein interaction networks in neurons. Finally, while the SR community has been pushing technological advances from an imaging technique perspective, the development of universally available, small, efficient, and quantitative labels remains a major challenge in the field.
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Affiliation(s)
- Eduard M. Unterauer
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
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43
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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44
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Makino K, Susaki EA, Endo M, Asanuma H, Kashida H. Color-Changing Fluorescent Barcode Based on Strand Displacement Reaction Enables Simple Multiplexed Labeling. J Am Chem Soc 2022; 144:1572-1579. [DOI: 10.1021/jacs.1c09844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Koki Makino
- Department of Bimolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Motomu Endo
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Hiroyuki Asanuma
- Department of Bimolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiromu Kashida
- Department of Bimolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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45
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Arista-Romero M, Delcanale P, Pujals S, Albertazzi L. Nanoscale Mapping of Recombinant Viral Proteins: From Cells to Virus-Like Particles. ACS PHOTONICS 2022; 9:101-109. [PMID: 35083366 PMCID: PMC8778639 DOI: 10.1021/acsphotonics.1c01154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 05/17/2023]
Abstract
Influenza recombinant proteins and virus-like particles (VLPs) play an important role in vaccine development (e.g., CadiFlu-S). However, their production from mammalian cells suffers from low yields and lack of control of the final VLPs. To improve these issues, characterization techniques able to visualize and quantify the different steps of the process are needed. Fluorescence microscopy represents a powerful tool able to image multiple protein targets; however, its limited resolution hinders the study of viral constructs. Here, we propose the use of super-resolution microscopy and in particular of DNA-point accumulation for imaging in nanoscale topography (DNA-PAINT) microscopy as a characterization method for recombinant viral proteins on both cells and VLPs. We were able to quantify the amount of the three main influenza proteins (hemagglutinin (HA), neuraminidase (NA), and ion channel matrix protein 2 (M2)) per cell and per VLP with nanometer resolution and single-molecule sensitivity, proving that DNA-PAINT is a powerful technique to characterize recombinant viral constructs.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
| | - Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco area delle Scienze 7/A, 43124 Parma, Italy
| | - Silvia Pujals
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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46
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Lee MY, Bedia JS, Bhate SS, Barlow GL, Phillips D, Fantl WJ, Nolan GP, Schürch CM. CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images. BMC Bioinformatics 2022; 23:46. [PMID: 35042474 PMCID: PMC8767664 DOI: 10.1186/s12859-022-04570-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Algorithmic cellular segmentation is an essential step for the quantitative analysis of highly multiplexed tissue images. Current segmentation pipelines often require manual dataset annotation and additional training, significant parameter tuning, or a sophisticated understanding of programming to adapt the software to the researcher's need. Here, we present CellSeg, an open-source, pre-trained nucleus segmentation and signal quantification software based on the Mask region-convolutional neural network (R-CNN) architecture. CellSeg is accessible to users with a wide range of programming skills. RESULTS CellSeg performs at the level of top segmentation algorithms in the 2018 Kaggle Data Challenge both qualitatively and quantitatively and generalizes well to a diverse set of multiplexed imaged cancer tissues compared to established state-of-the-art segmentation algorithms. Automated segmentation post-processing steps in the CellSeg pipeline improve the resolution of immune cell populations for downstream single-cell analysis. Finally, an application of CellSeg to a highly multiplexed colorectal cancer dataset acquired on the CO-Detection by indEXing (CODEX) platform demonstrates that CellSeg can be integrated into a multiplexed tissue imaging pipeline and lead to accurate identification of validated cell populations. CONCLUSION CellSeg is a robust cell segmentation software for analyzing highly multiplexed tissue images, accessible to biology researchers of any programming skill level.
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Affiliation(s)
- Michael Y Lee
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Computer Science, Stanford, CA, 94305, USA
| | - Jacob S Bedia
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Salil S Bhate
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Graham L Barlow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Darci Phillips
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christian M Schürch
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
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47
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Oleksiievets N, Sargsyan Y, Thiele JC, Mougios N, Sograte-Idrissi S, Nevskyi O, Gregor I, Opazo F, Thoms S, Enderlein J, Tsukanov R. Fluorescence lifetime DNA-PAINT for multiplexed super-resolution imaging of cells. Commun Biol 2022; 5:38. [PMID: 35017652 PMCID: PMC8752799 DOI: 10.1038/s42003-021-02976-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/08/2021] [Indexed: 11/08/2022] Open
Abstract
DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution technique highly suitable for multi-target (multiplexing) bio-imaging. However, multiplexed imaging of cells is still challenging due to the dense and sticky environment inside a cell. Here, we combine fluorescence lifetime imaging microscopy (FLIM) with DNA-PAINT and use the lifetime information as a multiplexing parameter for targets identification. In contrast to Exchange-PAINT, fluorescence lifetime PAINT (FL-PAINT) can image multiple targets simultaneously and does not require any fluid exchange, thus leaving the sample undisturbed and making the use of flow chambers/microfluidic systems unnecessary. We demonstrate the potential of FL-PAINT by simultaneous imaging of up to three targets in a cell using both wide-field FLIM and 3D time-resolved confocal laser scanning microscopy (CLSM). FL-PAINT can be readily combined with other existing techniques of multiplexed imaging and is therefore a perfect candidate for high-throughput multi-target bio-imaging.
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Affiliation(s)
- Nazar Oleksiievets
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Yelena Sargsyan
- Department of Child and Adolescent Health, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Jan Christoph Thiele
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Nikolaos Mougios
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Oleksii Nevskyi
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Ingo Gregor
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
- NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center Göttingen, 37073, Göttingen, Germany
- Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen, Germany.
| | - Roman Tsukanov
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany.
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48
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Andrian T, Pujals S, Albertazzi L. Quantifying the effect of PEG architecture on nanoparticle ligand availability using DNA-PAINT. NANOSCALE ADVANCES 2021; 3:6876-6881. [PMID: 34977461 PMCID: PMC8650147 DOI: 10.1039/d1na00696g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
The importance of PEG architecture on nanoparticle (NP) functionality is known but still difficult to investigate, especially at a single particle level. Here, we apply DNA Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT), a super-resolution microscopy (SRM) technique, to study the surface functionality in poly(lactide-co-glycolide)-poly(ethylene glycol) (PLGA-PEG) NPs with different PEG structures. We demonstrated how the length of the PEG spacer can influence the accessibility of surface chemical functionality, highlighting the importance of SRM techniques to support the rational design of functionalized NPs.
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Affiliation(s)
- Teodora Andrian
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology Baldiri Reixac 15-21 08028 Barcelona Spain
| | - Silvia Pujals
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology Baldiri Reixac 15-21 08028 Barcelona Spain
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology Baldiri Reixac 15-21 08028 Barcelona Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology 5612AZ Eindhoven The Netherlands
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49
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site‐Specific DNA‐Antibody Bioconjugation by Using Benzoylacrylic‐Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Daniel R. Whiten
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE) Milstein Building, Granta Park Cambridge CB21 6GH UK
- Current address: Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- UK Dementia Research Institute University of Cambridge Cambridge CB2 0XY UK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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50
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021; 60:25905-25913. [PMID: 34555238 PMCID: PMC9297960 DOI: 10.1002/anie.202109713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 12/27/2022]
Abstract
Many bioconjugation strategies for DNA oligonucleotides and antibodies suffer limitations, such as site-specificity, stoichiometry and hydrolytic instability of the conjugates, which makes them unsuitable for biological applications. Here, we report a new platform for the preparation of DNA-antibody bioconjugates with a simple benzoylacrylic acid pentafluorophenyl ester reagent. Benzoylacrylic-labelled oligonucleotides prepared with this reagent can be site-specifically conjugated to a range of proteins and antibodies through accessible cysteine residues. The homogeneity of the prepared DNA-antibody bioconjugates was confirmed by a new LC-MS protocol and the bioconjugate probes were used in fluorescence or super-resolution microscopy cell imaging experiments. This work demonstrates the versatility and robustness of our bioconjugation protocol that gives site-specific, well-defined and plasma-stable DNA-antibody bioconjugates for biological applications.
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Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Libby Brown
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Daniel R. Whiten
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Yukun Zuo
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Peter Ravn
- AstraZenecaR&D BioPharmaceuticals Unit|Antibody Discovery & Protein Engineering (ADPE)Milstein Building, Granta ParkCambridgeCB21 6GHUK
- Current address: Department of Biotherapeutic DiscoveryH. Lundbeck A/SOttiliavej 9, 2500ValbyDenmark
| | - David Klenerman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- UK Dementia Research InstituteUniversity of CambridgeCambridgeCB2 0XYUK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
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