1
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Liu Y, Sundah NR, Ho NRY, Shen WX, Xu Y, Natalia A, Yu Z, Seet JE, Chan CW, Loh TP, Lim BY, Shao H. Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells. Nat Biomed Eng 2024; 8:909-923. [PMID: 38898172 DOI: 10.1038/s41551-024-01225-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/05/2024] [Indexed: 06/21/2024]
Abstract
Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.
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Affiliation(s)
- Yu Liu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Noah R Sundah
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Nicholas R Y Ho
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Wan Xiang Shen
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yun Xu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Zhonglang Yu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Ju Ee Seet
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Hospital, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tze Ping Loh
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Brian Y Lim
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Department of Computer Science, School of Computing, National University of Singapore, Singapore, Singapore.
| | - Huilin Shao
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
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2
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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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3
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Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R, Venturelli OS. Massively parallel single-cell sequencing of diverse microbial populations. Nat Methods 2024; 21:228-235. [PMID: 38233503 PMCID: PMC11089590 DOI: 10.1038/s41592-023-02157-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
Single-cell genetic heterogeneity is ubiquitous in microbial populations and an important aspect of microbial biology; however, we lack a broadly applicable and accessible method to study this heterogeneity in microbial populations. Here, we show a simple, robust and generalizable method for high-throughput single-cell sequencing of target genetic loci in diverse microbes using simple droplet microfluidics devices (droplet targeted amplicon sequencing; DoTA-seq). DoTA-seq serves as a platform to perform diverse assays for single-cell genetic analysis of microbial populations. Using DoTA-seq, we demonstrate the ability to simultaneously track the prevalence and taxonomic associations of >10 antibiotic-resistance genes and plasmids within human and mouse gut microbial communities. This workflow is a powerful and accessible platform for high-throughput single-cell sequencing of diverse microbial populations.
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Affiliation(s)
- Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jason Saba
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler D Ross
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Katie Krauska
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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4
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Prange CJ, Hu X, Tang L. Smart chemistry for traceless release of anticancer therapeutics. Biomaterials 2023; 303:122353. [PMID: 37925794 DOI: 10.1016/j.biomaterials.2023.122353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
In the design of delivery strategies for anticancer therapeutics, the controlled release of intact cargo at the destined tumor and metastasis locations is of particular importance. To this end, stimuli-responsive chemical linkers have been extensively investigated owing to their ability to respond to tumor-specific physiological stimuli, such as lowered pH, altered redox conditions, increased radical oxygen species and pathological enzymatic activities. To prevent premature action and off-target effects, anticancer therapeutics are chemically modified to be transiently inactivated, a strategy known as prodrug development. Prodrugs are reactivated upon stimuli-dependent release at the sites of interest. As most drugs and therapeutic proteins have the optimal activity when released from carriers in their native and original forms, traceless release mechanisms are increasingly investigated. In this review, we summarize the chemical toolkit for developing innovative traceless prodrug strategies for stimuli-responsive drug delivery and discuss the applications of these chemical modifications in anticancer treatment including cancer immunotherapy.
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Affiliation(s)
- Céline Jasmin Prange
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland; Institute of Chemical Sciences and Engineering, EPFL, Lausanne, CH-1015, Switzerland
| | - Xile Hu
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, CH-1015, Switzerland.
| | - Li Tang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland; Institute of Materials Science & Engineering, EPFL, Lausanne, CH-1015, Switzerland.
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5
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KIM S, KAMARULZAMAN L, TANIGUCHI Y. Recent methodological advances towards single-cell proteomics. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:306-327. [PMID: 37673661 PMCID: PMC10749393 DOI: 10.2183/pjab.99.021] [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: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 09/08/2023]
Abstract
Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and transcriptomic levels fail to address information on proteins that are central to many important biological processes. Single-cell proteomics enables understanding of the functional status of individual cells and is particularly crucial when the specimen is composed of heterogeneous entities of cells. With the growing importance of this field, significant methodological advancements have emerged recently. These include miniaturized and automated sample preparation, multi-omics analyses, and combined analyses of multiple techniques such as mass spectrometry and microscopy. Moreover, artificial intelligence and single-molecule detection technologies have advanced throughput and improved sensitivity limitations, respectively, over conventional methods. In this review, we summarize cutting-edge methodologies for single-cell proteomics and relevant emerging technologies that have been reported in the last 5 years, and provide an outlook on this research field.
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Affiliation(s)
- Sooyeon KIM
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Latiefa KAMARULZAMAN
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yuichi TANIGUCHI
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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6
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Zohra T, Saeed F, Ikram A, Khan T, Alam S, Adil M, Gul A, Almawash S, Ayaz M. Nanomedicine as a potential novel therapeutic approach against the dengue virus. Nanomedicine (Lond) 2023; 18:1567-1584. [PMID: 37753727 DOI: 10.2217/nnm-2022-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Dengue is an arbovirus infection which is transmitted by Aedes mosquitoes. Its prompt detection and effective treatment is a global health challenge. Various nanoparticle-based vaccines have been formulated to present immunogen (antigens) to instigate an immune response or prevent virus spread, but no specific treatment has been devised. This review explores the role of nanomedicine-based therapeutic agents against dengue virus, taking into consideration the applicable dengue virus assays that are sensitive, specific, have a short turnaround time and are inexpensive. Various kinds of metallic, polymeric and lipid nanoparticles with safe and effective profiles present an alternative strategy that could provide a better remedy for eradicating the dengue virus.
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Affiliation(s)
- Tanzeel Zohra
- Public Health Laboratories Division, National Institute of Health, Islamabad, 45500, Pakistan
| | - Faryal Saeed
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Ikram
- Public Health Laboratories Division, National Institute of Health, Islamabad, 45500, Pakistan
| | - Tariq Khan
- Department of Biotechnology, University of Malakand, University of Malakand, Chakdara, 18800 Dir (L), KP, Pakistan
| | - Siyab Alam
- Department of Biotechnology, University of Malakand, University of Malakand, Chakdara, 18800 Dir (L), KP, Pakistan
| | - Muhammad Adil
- Department of Biotechnology, University of Malakand, University of Malakand, Chakdara, 18800 Dir (L), KP, Pakistan
| | - Ayesha Gul
- Department of Chemical Engineering, Polytechnique Montreal, H3T IJ4, Canada
| | - Saud Almawash
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra, 11961, Saudi Arabia
| | - Muhammad Ayaz
- Department of Pharmacy, Faculty of Biological Sciences, University of Malakand, Chakdara, 18800 Dir (L), KP, Pakistan
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7
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Maingi V, Zhang Z, Thachuk C, Sarraf N, Chapman ER, Rothemund PWK. Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Nat Commun 2023; 14:1532. [PMID: 36941256 PMCID: PMC10027858 DOI: 10.1038/s41467-023-36996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Interactions between membrane proteins are essential for cell survival but are often poorly understood. Even the biologically functional ratio of components within a multi-subunit membrane complex-the native stoichiometry-is difficult to establish. Here we demonstrate digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors (modelling membrane proteins). Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence, which in principle is generalizable to any ratio. Similar single-molecule-in-bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.
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Affiliation(s)
- Vishal Maingi
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
| | - Zhao Zhang
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA
| | - Chris Thachuk
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
| | - Namita Sarraf
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
| | - Paul W K Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation & Neural Systems, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation + Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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8
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Cao W, Maza JC, Chernyak N, Flygare JA, Krska SW, Toste FD, Francis MB. Modification of Cysteine-Substituted Antibodies Using Enzymatic Oxidative Coupling Reactions. Bioconjug Chem 2023; 34:510-517. [PMID: 36787347 DOI: 10.1021/acs.bioconjchem.2c00576] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Cysteines are routinely used as site-specific handles to synthesize antibody-drug conjugates for targeted immunotherapy applications. Michael additions between thiols and maleimides are some of the most common methods for modifying cysteines, but these functional groups can be difficult to prepare on scale, and the resulting linkages have been shown to be reversible under some physiological conditions. Here, we show that the enzyme tyrosinase, which oxidizes conveniently accessed phenols to afford reactive ortho-quinone intermediates, can be used to attach phenolic cargo to cysteines engineered on antibody surfaces. The resulting linkages between the thiols and ortho-quinones are shown to be more resistant than maleimides to reversion under physiological conditions. Using this approach, we construct antibody conjugates bearing cytotoxic payloads, which exhibit targeted cell killing, and further demonstrate this method for the attachment of a variety of cargo to antibodies, including fluorophores and oligonucleotides.
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Affiliation(s)
- Wendy Cao
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Natalia Chernyak
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - John A Flygare
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Shane W Krska
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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9
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Biochemical analysis based on optical detection integrated microfluidic chip. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2022.116865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Ko J, Wilkovitsch M, Oh J, Kohler RH, Bolli E, Pittet MJ, Vinegoni C, Sykes DB, Mikula H, Weissleder R, Carlson JCT. Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes. Nat Biotechnol 2022; 40:1654-1662. [PMID: 35654978 PMCID: PMC9669087 DOI: 10.1038/s41587-022-01339-6] [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: 10/01/2021] [Accepted: 04/28/2022] [Indexed: 02/07/2023]
Abstract
Cells in complex organisms undergo frequent functional changes, but few methods allow comprehensive longitudinal profiling of living cells. Here we introduce scission-accelerated fluorophore exchange (SAFE), a method for multiplexed temporospatial imaging of living cells with immunofluorescence. SAFE uses a rapid bioorthogonal click chemistry to remove immunofluorescent signals from the surface of labeled cells, cycling the nanomolar-concentration reagents in seconds and enabling multiple rounds of staining of the same samples. It is non-toxic and functional in both dispersed cells and intact living tissues. We demonstrate multiparameter (n ≥ 14), non-disruptive imaging of murine peripheral blood mononuclear and bone marrow cells to profile cellular differentiation. We also show longitudinal multiplexed imaging of bone marrow progenitor cells as they develop into neutrophils over 6 days and real-time multiplexed cycling of living mouse hepatic tissues. We anticipate that SAFE will find broad utility for investigating physiologic dynamics in living systems.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Evangelia Bolli
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Mikael J Pittet
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Zurich, Switzerland
- AGORA Cancer Center, Lausanne, Switzerland
| | - Claudio Vinegoni
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannes Mikula
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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11
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Motohashi Y, Nishihara T, Tanabe K. Preparation of a multifunctional photoactivated prodrug on a streptavidin scaffold bearing a DNA aptamer. Bioorg Med Chem Lett 2022; 71:128819. [PMID: 35643261 DOI: 10.1016/j.bmcl.2022.128819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 11/19/2022]
Abstract
Prodrugs that present strong cytotoxicity toward specific cells have been utilized for cell-type selection and purification. In this study, we designed and prepared a multifunctional, photoactivated prodrug based on a streptavidin scaffold. Biotin-labeled DNA aptamer that recognizes the membrane antigen EpCAM, and biotin-labeled photoactivated prodrug bearing the antitumor camptothecin, were prepared. Both molecules were linked to the streptavidin scaffold by simple mixing. The resulting prodrug bound to the EpCAM-overexpressing SK-BR-3 target cells and showed cytotoxic effects upon photoirradiation, corresponding to cytotoxic drug release.
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Affiliation(s)
- Yuto Motohashi
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Tatsuya Nishihara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
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12
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Chen Y, Guo J. Multiplexed Single-Cell in Situ Protein Profiling. ACS MEASUREMENT SCIENCE AU 2022; 2:296-303. [PMID: 35996537 PMCID: PMC9389644 DOI: 10.1021/acsmeasuresciau.2c00011] [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] [Indexed: 06/15/2023]
Abstract
The ability to profile a large number of different proteins in individual cells in their native cellular locations is critical to accelerate our understanding of normal cell physiology and disease pathogenesis. Bulk cell protein quantification masks the cell heterogeneity in complex biological systems, while conventional immunofluorescence or immunohistochemistry are limited by their low multiplexing capacity. Recent technological advances in multiplexed protein imaging approaches allow many distinct proteins to be analyzed in single cells in situ. These methods will bring new insights into various biological and biomedical fields, such as cell type and subtype classification, signaling network regulation, tissue architecture, and disease diagnosis and prognosis, along with treatment monitoring. In this Review, we will describe the recent advances of multiplexed single-cell in situ protein profiling technologies, discuss their unique advantages and limitations, highlight their applications in biology and medicine, present the current challenges, and propose potential solutions.
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13
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Urbiola-Salvador V, Miroszewska D, Jabłońska A, Qureshi T, Chen Z. Proteomics approaches to characterize the immune responses in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119266. [PMID: 35390423 DOI: 10.1016/j.bbamcr.2022.119266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/01/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Despite the dynamic development of cancer research, annually millions of people die of cancer. The human immune system is the major 'guard' against tumor development. Unfortunately, cancer cells have the ability to evade the immune system and continue to grow. The proper understanding of the intricate immune response in tumorigenesis remains the holy grail of cancer immunology and designing effective immunotherapy. To decode the immune responses in cancer, in recent years, proteomics studies have received considerable attention. Proteomics studies focus on the detection and quantification of proteins, which are the effectors of biological functions, and as such, are proven to reflect the cell state more accurately, in comparison to genomic or transcriptomic studies. In this review, we discuss the proteomics studies applied to characterize the immune responses in cancer and tumor immune microenvironment heterogeneity. Further, we describe emerging single-cell proteomics approaches that have the potential to be applied in cancer immunity studies.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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14
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Oh J, Yoo TY, Saal TM, Tsay L, Faquin WC, Carlson JC, Deschler DG, Pai SI, Weissleder R. Multiplexed single-cell analysis of FNA allows accurate diagnosis of salivary gland tumors. Cancer Cytopathol 2022; 130:581-594. [PMID: 35666645 PMCID: PMC9542730 DOI: 10.1002/cncy.22594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/23/2022] [Indexed: 11/24/2022]
Abstract
Diagnosing salivary gland tumors (SGTs) through fine-needle aspiration (FNA) biopsies is challenging due to the overlapping cytomorphologic features between benign and malignant tumors. The authors developed an innovative, multiplexed cycling technology for the rapid analyses of single cells obtained from FNA that can facilitate the molecular analyses and diagnosis of SGTs. Antibodies against 29 protein markers associated with 7 SGT subtypes were validated and chemically modified via custom linker-bio-orthogonal probes (FAST). Single-cell homogenates and FNA samples were profiled by FAST cyclic imaging and computational analysis. A prediction model was generated using a training set of 151,926 cells from primary SGTs (N = 26) and validated on a separate cohort (N = 30). Companion biomarker testing, such as neurotrophic tyrosine receptor kinase (NTRK), was also assessed with the FAST technology. The FAST molecular diagnostic assay was able to distinguish between benign and malignant SGTs with an accuracy of 0.86 for single-cell homogenate samples and 0.88 for FNA samples. Profiling of multiple markers as compared to a single marker increased the diagnostic accuracy (0.82 as compared to 0.65-0.74, respectively), independent of the cell number sampled. NTRK expression was also assessed by the FAST assay, highlighting the potential therapeutic application of this technology. Application of the novel multiplexed single-cell technology facilitates rapid biomarker testing from FNA samples at low cost. The customizable and modular FAST-FNA approach has relevance to multiple pathologies and organ systems where cytologic samples are often scarce and/or indeterminate resulting in improved diagnostic workflows and timely therapeutic clinical decision-making.
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Affiliation(s)
- Juhyun Oh
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusetts
- Department of RadiologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Tae Yeon Yoo
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusetts
| | - Talia M. Saal
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusetts
| | - Lisa Tsay
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusetts
| | - William C. Faquin
- Department of PathologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Jonathan C.T. Carlson
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusetts
- Mass General Cancer CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Daniel G. Deschler
- Department of OtolaryngologyMassachusetts Eye and Ear InfirmaryBostonMassachusetts
- Department of Otology and LaryngologyHarvard Medical SchoolBostonMassachusetts
| | - Sara I. Pai
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusetts
- Mass General Cancer CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
- Department of SurgeryMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Ralph Weissleder
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusetts
- Department of RadiologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusetts
- Mass General Cancer CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
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15
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Yang L, Ball A, Liu J, Jain T, Li YM, Akhter F, Zhu D, Wang J. Cyclic microchip assay for measurement of hundreds of functional proteins in single neurons. Nat Commun 2022; 13:3548. [PMID: 35729174 PMCID: PMC9213506 DOI: 10.1038/s41467-022-31336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Despite the fact that proteins carry out nearly all cellular functions and mark the differences of cells, the existing single-cell tools can only analyze dozens of proteins, a scale far from full characterization of cells and tissue yet. Herein, we present a single-cell cyclic multiplex in situ tagging (CycMIST) technology that affords the comprehensive functional proteome profiling of single cells. We demonstrate the technology by detecting 182 proteins that include surface markers, neuron function proteins, neurodegeneration markers, signaling pathway proteins, and transcription factors. Further studies on cells derived from the 5XFAD mice, an Alzheimer's Disease (AD) model, validate the utility of our technology and reveal the deep heterogeneity of brain cells. Through comparison with control mouse cells, we have identified differentially expressed proteins in AD pathology. Our technology could offer new insights into cell machinery and thus may advance many fields including drug discovery, molecular diagnostics, and clinical studies.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Avery Ball
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jesse Liu
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
- Programs of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Firoz Akhter
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Donghui Zhu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
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16
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Seo J, Sim Y, Kim J, Kim H, Cho I, Nam H, Yoon YG, Chang JB. PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements. Nat Commun 2022; 13:2475. [PMID: 35513404 PMCID: PMC9072354 DOI: 10.1038/s41467-022-30168-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/20/2022] [Indexed: 12/19/2022] Open
Abstract
Ultra-multiplexed fluorescence imaging requires the use of spectrally overlapping fluorophores to label proteins and then to unmix the images of the fluorophores. However, doing this remains a challenge, especially in highly heterogeneous specimens, such as the brain, owing to the high degree of variation in the emission spectra of fluorophores in such specimens. Here, we propose PICASSO, which enables more than 15-color imaging of spatially overlapping proteins in a single imaging round without using any reference emission spectra. PICASSO requires an equal number of images and fluorophores, which enables such advanced multiplexed imaging, even with bandpass filter-based microscopy. We show that PICASSO can be used to achieve strong multiplexing capability in diverse applications. By combining PICASSO with cyclic immunofluorescence staining, we achieve 45-color imaging of the mouse brain in three cycles. PICASSO provides a tool for multiplexed imaging with high accessibility and accuracy for a broad range of researchers.
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Affiliation(s)
- Junyoung Seo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Yeonbo Sim
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Korea
| | - Jeewon Kim
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hyunwoo Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - In Cho
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hoyeon Nam
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Young-Gyu Yoon
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
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17
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Wu Z, Xiao M, Lai W, Sun Y, Li L, Hu Z, Pei H. Nucleic Acid-Based Cell Surface Engineering Strategies and Their Applications. ACS APPLIED BIO MATERIALS 2022; 5:1901-1915. [DOI: 10.1021/acsabm.1c01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhongdong Wu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yueyang Sun
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zongqian Hu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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18
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He Q, Liu Y, Li K, Wu Y, Wang T, Tan Y, Jiang T, Liu X, Liu Z. Deoxyribonucleic acid anchored on cell membranes for biomedical application. Biomater Sci 2021; 9:6691-6717. [PMID: 34494042 DOI: 10.1039/d1bm01057c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
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Affiliation(s)
- Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China. .,Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, P. R. China
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19
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Lau RP, Kim TH, Rao J. Advances in Imaging Modalities, Artificial Intelligence, and Single Cell Biomarker Analysis, and Their Applications in Cytopathology. Front Med (Lausanne) 2021; 8:689954. [PMID: 34277664 PMCID: PMC8282905 DOI: 10.3389/fmed.2021.689954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Several advances in recent decades in digital imaging, artificial intelligence, and multiplex modalities have improved our ability to automatically analyze and interpret imaging data. Imaging technologies such as optical coherence tomography, optical projection tomography, and quantitative phase microscopy allow analysis of tissues and cells in 3-dimensions and with subcellular granularity. Improvements in computer vision and machine learning have made algorithms more successful in automatically identifying important features to diagnose disease. Many new automated multiplex modalities such as antibody barcoding with cleavable DNA (ABCD), single cell analysis for tumor phenotyping (SCANT), fast analytical screening technique fine needle aspiration (FAST-FNA), and portable fluorescence-based image cytometry analyzer (CytoPAN) are under investigation. These have shown great promise in their ability to automatically analyze several biomarkers concurrently with high sensitivity, even in paucicellular samples, lending themselves well as tools in FNA. Not yet widely adopted for clinical use, many have successfully been applied to human samples. Once clinically validated, some of these technologies are poised to change the routine practice of cytopathology.
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Affiliation(s)
- Ryan P. Lau
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
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20
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Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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21
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Single-cell technologies and analyses in hematopoiesis and hematological malignancies. Exp Hematol 2021; 98:1-13. [PMID: 33979683 DOI: 10.1016/j.exphem.2021.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 01/03/2023]
Abstract
In recent years, single-cell technologies have emerged as breakthrough techniques that enable the characterization of hematopoietic cell populations of normal and malignant tissue samples and will be combined in the near future with bulk technologies, currently used in clinical practice, to improve diagnosis, prognosis, and the search for novel molecular targets. These single-cell methods have the advantage of not masking cell-to-cell variation features and involve the study of genetic, epigenetic, transcriptional, and proteomic landscapes from a single-cell perspective. Latest advances in this field have enabled the development of novel strategies that significantly increase both sensitivity and high throughput. In this review, we emphasize emerging techniques aimed at assessing individual or multiomic parameters at single-cell resolution and analyze how these technologies have helped us understand hematopoietic variability and identify unknown and/or rare subpopulations. We also summarize the impact of these single-cell profiling strategies on the characterization of cell diversity within the tumor and the clonal evolution of multiple hematological malignancies in samples from untreated and treated patients, which provide valuable information for diagnosis, prognosis, and future treatments and explain why current therapies may fail. However, despite these improvements, new challenges lie ahead.
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22
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Chandrasekaran AR, MacIsaac M, Vilcapoma J, Hansen CH, Yang D, Wong WP, Halvorsen K. DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling. NANO LETTERS 2021; 21:469-475. [PMID: 33395311 PMCID: PMC8059342 DOI: 10.1021/acs.nanolett.0c03929] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Molecular biomarkers play a key role in the clinic, aiding in diagnostics and prognostics, and in the research laboratory, contributing to our basic understanding of diseases. Detecting multiple and diverse molecular biomarkers within a single accessible assay would have great utility, providing a more comprehensive picture for clinical evaluation and research, but is a challenge with standard methods. Here, we report programmable DNA nanoswitches for multiplexed detection of up to 6 biomarkers at once with each combination of biomarkers producing a unique barcode signature among 64 possibilities. As a defining feature of our method, we show "mixed multiplexing" for simultaneous barcoded detection of different types of biomolecules, for example, DNA, RNA, antibody, and protein in a single assay. To demonstrate clinical potential, we show multiplexed detection of a prostate cancer biomarker panel in serum that includes two microRNA sequences and prostate specific antigen.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, New York, New York 12222, United States
| | - Molly MacIsaac
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, New York, New York 12222, United States
| | - Clinton H Hansen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, New York, New York 12222, United States
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23
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Zhang P, Wang W, Fu H, Rich J, Su X, Bachman H, Xia J, Zhang J, Zhao S, Zhou J, Huang TJ. Deterministic droplet coding via acoustofluidics. LAB ON A CHIP 2020; 20:4466-4473. [PMID: 33103674 PMCID: PMC7688411 DOI: 10.1039/d0lc00538j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Droplet microfluidics has become an indispensable tool for biomedical research and lab-on-a-chip applications owing to its unprecedented throughput, precision, and cost-effectiveness. Although droplets can be generated and screened in a high-throughput manner, the inability to label the inordinate amounts of droplets hinders identifying the individual droplets after generation. Herein, we demonstrate an acoustofluidic platform that enables on-demand, real-time dispensing, and deterministic coding of droplets based on their volumes. By dynamically splitting the aqueous flow using an oil jet triggered by focused traveling surface acoustic waves, a sequence of droplets with deterministic volumes can be continuously dispensed at a throughput of 100 Hz. These sequences encode barcoding information through the combination of various droplet lengths. As a proof-of-concept, we encoded droplet sequences into end-to-end packages (e.g., a series of 50 droplets), which consisted of an address barcode with binary volumetric combinations and a sample package with consistent volumes for hosting analytes. This acoustofluidics-based, deterministic droplet coding technique enables the tagging of droplets with high capacity and high error-tolerance, and can potentially benefit various applications involving single cell phenotyping and multiplexed screening.
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Affiliation(s)
- Peiran Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Wei Wang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
- ASIC and System State Key Laboratory, School of Microelectronics, Fudan University, Shanghai 200433, P. R. China
| | - Hai Fu
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
- Department of Fluid Control and Automation, School of Mechanics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150000, P. R. China
| | - Joseph Rich
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Xingyu Su
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Hunter Bachman
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Jianping Xia
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Jinxin Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Shuaiguo Zhao
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Jia Zhou
- ASIC and System State Key Laboratory, School of Microelectronics, Fudan University, Shanghai 200433, P. R. China
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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24
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Wilkovitsch M, Haider M, Sohr B, Herrmann B, Klubnick J, Weissleder R, Carlson JCT, Mikula H. A Cleavable C 2-Symmetric trans-Cyclooctene Enables Fast and Complete Bioorthogonal Disassembly of Molecular Probes. J Am Chem Soc 2020; 142:19132-19141. [PMID: 33119297 PMCID: PMC7662912 DOI: 10.1021/jacs.0c07922] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistry is bridging the divide between static chemical connectivity and the dynamic physiologic regulation of molecular state, enabling in situ transformations that drive multiple technologies. In spite of maturing mechanistic understanding and new bioorthogonal bond-cleavage reactions, the broader goal of molecular ON/OFF control has been limited by the inability of existing systems to achieve both fast (i.e., seconds to minutes, not hours) and complete (i.e., >99%) cleavage. To attain the stringent performance characteristics needed for high fidelity molecular inactivation, we have designed and synthesized a new C2-symmetric trans-cyclooctene linker (C2TCO) that exhibits excellent biological stability and can be rapidly and completely cleaved with functionalized alkyl-, aryl-, and H-tetrazines, irrespective of click orientation. By incorporation of C2TCO into fluorescent molecular probes, we demonstrate highly efficient extracellular and intracellular bioorthogonal disassembly via omnidirectional tetrazine-triggered cleavage.
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Affiliation(s)
- Martin Wilkovitsch
- Institute
of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Maximilian Haider
- Institute
of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Barbara Sohr
- Institute
of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Barbara Herrmann
- Institute
of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Jenna Klubnick
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
| | - Ralph Weissleder
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jonathan C. T. Carlson
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
- Cancer
Center, Massachusetts General Hospital and
Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Hannes Mikula
- Institute
of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
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25
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Pai SI, Faquin WC, Sadow PM, Pittet MJ, Weissleder R. New technology on the horizon: Fast analytical screening technique FNA (FAST-FNA) enables rapid, multiplex biomarker analysis in head and neck cancers. Cancer Cytopathol 2020; 128:782-791. [PMID: 32841527 PMCID: PMC8276888 DOI: 10.1002/cncy.22305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 01/26/2023]
Abstract
PD-L1 profiling was recently approved by the US Food and Drug Administration as a companion diagnostic for anti-PD1 treatment in patients with head and neck cancer, ushering in a new era for precision medicine. However, the routine development and implementation of such testing is still limited by current clinical workflows and the lack of better and more comprehensive alternatives. In this review, the authors discuss the real-world challenges of clinically based biomarker testing and highlight the advantages of developing fine-needle aspiration (FNA)-based biomarker testing that would enable frequent and serial tumor sampling. A conceptual and technological innovation is introduced, fast analytical screening technique (FAST)-FNA (FAST chemistry-enabled FNA), which is being developed to inform immunotherapy treatment options in patients with head and neck cancer and to assist with the development of the next generation of predictive biomarkers.
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Affiliation(s)
- Sara I. Pai
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - William C. Faquin
- Division of Head and Neck Pathology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter M. Sadow
- Division of Head and Neck Pathology, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mikael J. Pittet
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts
- Division of Interventional Radiology, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
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26
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Shen W, Zheng J, Zhou Z, Zhang D. Approaches for the synthesis of o-nitrobenzyl and coumarin linkers for use in photocleavable biomaterials and bioconjugates and their biomedical applications. Acta Biomater 2020; 115:75-91. [PMID: 32853806 DOI: 10.1016/j.actbio.2020.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022]
Abstract
Photocleavable biomaterials and bioconjugates are particularly interesting because light sources are easy to obtain and the responsiveness of materials is convenient to control. In recent years, various photocleavable biomaterials and bioconjugates have been synthesized for the control of payload release, regulation of biomolecule activity, 3D cell culture, and investigation of molecular mechanisms. Photocleavable linkers are crucial components of photocleavable biomaterials, which significantly influence the photoresponsive capabilities of materials. Photosensitive molecules, such as o-nitrobenzyls and coumarins, have been extensively developed as photocleavable linkers. In the present review, we provide comprehensive knowledge regarding the synthetic strategies of o-nitrobenzyl and coumarin derived linkers with various functional groups and their applications for the construction of photocleavable biomaterials and bioconjugates. Finally, the biomedical applications of o-nitrobenzyl and coumarin-based photocleavable biomaterials and bioconjugates will be summarized and discussed.
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27
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Pham T, Tyagi A, Wang YS, Guo J. Single-cell proteomic analysis. WIREs Mech Dis 2020; 13:e1503. [PMID: 32748522 DOI: 10.1002/wsbm.1503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
Abstract
The ability to comprehensively profile proteins in every individual cell of complex biological systems is crucial to advance our understanding of normal physiology and disease pathogenesis. Conventional bulk cell experiments mask the cell heterogeneity in the population, while the single-cell imaging methods suffer from the limited multiplexing capacities. Recent advances in microchip-, mass spectrometry-, and reiterative staining-based technologies have enabled comprehensive protein profiling in single cells. These approaches will bring new insights into a variety of biological and biomedical fields, such as signaling network regulation, cell heterogeneity, tissue architecture, disease diagnosis, and treatment monitoring. In this article, we will review the recent advances in the development of single-cell proteomic technologies, describe their advantages, discuss the current limitations and challenges, and propose potential solutions. We will also highlight the wide applications of these technologies in biology and medicine. This article is categorized under: Cancer > Molecular and Cellular Physiology.
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Affiliation(s)
- Thai Pham
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Ankush Tyagi
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Yu-Sheng Wang
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Jia Guo
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
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Yang L, George J, Wang J. Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies. Proteomics 2020; 20:e1900226. [PMID: 31729152 PMCID: PMC7225074 DOI: 10.1002/pmic.201900226] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/14/2019] [Indexed: 12/20/2022]
Abstract
The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single-cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well-established methods for single-cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining-based techniques for single-cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single-cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single-cell proteomic technologies in cell biology and medical research are discussed.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
| | - Justin George
- Department of Chemistry, State University of New York, University at Albany, Albany, NY 12222
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
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29
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Marquard AN, Carlson JCT, Weissleder R. Expanding the Scope of Antibody Rebridging with New Pyridazinedione-TCO Constructs. Bioconjug Chem 2020; 31:1616-1623. [PMID: 32286045 PMCID: PMC7788567 DOI: 10.1021/acs.bioconjchem.0c00155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Disulfide rebridging methods have recently emerged as a route to hinge region-specific antibody modification, and there exist numerous examples of successful rebridging chemistry applied to clinically relevant human IgG1 antibodies. Here, dibromopyridazinedione disulfide rebridging is adapted to fast trans-cyclooctene/tetrazine (TCO/Tz) bioorthogonal ligations and extended beyond therapeutic human IgG1 antibodies for the first time to include mouse and rat monoclonal antibodies integral to multiplexed analytical diagnostics. In spite of a common architecture, only a subset of antibody host species and IgG isotype subclasses can be rebridged, highlighting the intricate relationship between hinge region sequence, structure, biological activity, and the conjugation chemistry of IgG antibodies.
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Affiliation(s)
- Angela N. Marquard
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA
| | - Jonathan C. T. Carlson
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
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30
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Ko J, Oh J, Ahmed MS, Carlson JCT, Weissleder R. Ultra-fast cycling for multiplexed cellular fluorescence imaging. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 132:6906-6913. [PMID: 34366494 PMCID: PMC8340598 DOI: 10.1002/ange.201915153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 11/11/2022]
Abstract
Rapid analysis of single and scant cell populations is essential in modern diagnostics, yet existing methods are often limited and slow. Here we describe an ultra-fast, highly efficient cycling method for the analysis of single cells based on unique linkers for tetrazine (Tz) / trans-cyclooctene (TCO) mediated quenching. Surprisingly, the quenching reaction rates were more than 3 orders of magnitude faster (t1/2 < 1 sec) than predicted. This allowed multi-cycle staining and immune cell profiling within an hour, leveraging the accelerated kinetics to open new diagnostic possibilities for rapid cellular analyses.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
| | - Maaz S. Ahmed
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
| | - Jonathan C. T. Carlson
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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31
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Ko J, Oh J, Ahmed MS, Carlson JCT, Weissleder R. Ultra-fast Cycling for Multiplexed Cellular Fluorescence Imaging. Angew Chem Int Ed Engl 2020; 59:6839-6846. [PMID: 32004403 DOI: 10.1002/anie.201915153] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/08/2020] [Indexed: 12/26/2022]
Abstract
Rapid analysis of single and scant cell populations is essential in modern diagnostics, yet existing methods are often limited and slow. Herein, we describe an ultra-fast, highly efficient cycling method for the analysis of single cells based on unique linkers for tetrazine (Tz)/trans-cyclooctene (TCO)-mediated quenching. Surprisingly, the quenching reaction rates were more than 3 orders of magnitude faster (t1/2 <1 s) than predicted. This allowed multi-cycle staining and immune cell profiling within an hour, leveraging the accelerated kinetics to open new diagnostic possibilities for rapid cellular analyses.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Maaz S Ahmed
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.,Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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32
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Xiong M, Liu Q, Tang D, Liu L, Kong G, Fu X, Yang C, Lyu Y, Meng HM, Ke G, Zhang XB. “Apollo Program” in Nanoscale: Landing and Exploring Cell-Surface with DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2020; 3:2723-2742. [DOI: 10.1021/acsabm.9b01193] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Qin Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiaoyi Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Chan Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
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33
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Smith LD, Willard MC, Smith JP, Cunningham BT. Development of a Linker-Mediated Immunoassay Using Chemically Transitioned Nanosensors. Anal Chem 2020; 92:3627-3635. [DOI: 10.1021/acs.analchem.9b04518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Lucas D. Smith
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Michael C. Willard
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Jordan P. Smith
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Brian T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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34
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O’Donnell ST, Ross RP, Stanton C. The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. Front Microbiol 2020; 10:3084. [PMID: 32047482 PMCID: PMC6997344 DOI: 10.3389/fmicb.2019.03084] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.
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Affiliation(s)
- Shane Thomas O’Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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35
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36
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Stiller C, Aghelpasand H, Frick T, Westerlund K, Ahmadian A, Karlström AE. Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates. Bioconjug Chem 2019; 30:2790-2798. [PMID: 31609586 DOI: 10.1021/acs.bioconjchem.9b00548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Antibody-DNA conjugates are powerful tools for DNA-assisted protein analysis. Growing usage of these methods demands efficient production of high-quality conjugates. We developed an easy and fast synthesis route yielding covalent antibody-DNA conjugates with a defined conjugation site and low batch-to-batch variability. We utilize the Z domain from protein A, containing the unnatural amino acid 4-benzoylphenylalanine (BPA) for photoaffinity labeling of the antibodies' Fc region. Z(xBPA) domains are C-terminally modified with triple-glycine (G3)-modified DNA-oligonucleotides via enzymatic Sortase A coupling. We show reliable modification of the most commonly used IgG's. To prove our conjugates' functionality, we detected antibody-antigen binding events in an assay called Droplet Barcode Sequencing for Protein analysis (DBS-Pro). It confirms not only retained functionality for both conjugate parts but also the potential of using DBS-Pro for quantifying protein abundances. As intermediates are easily storable and our approach is modular, it offers a convenient strategy for screening various antibody-DNA conjugates using the same starting material.
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Affiliation(s)
- Christiane Stiller
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
| | - Hooman Aghelpasand
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Tobias Frick
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Kristina Westerlund
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
| | - Afshin Ahmadian
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
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37
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Liu X, Yu S, Feng C, Mao D, Li J, Zhu X. In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices. Crit Rev Anal Chem 2019; 51:8-19. [PMID: 31613139 DOI: 10.1080/10408347.2019.1674631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.
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Affiliation(s)
- Xiaohao Liu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Sinuo Yu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Jinlong Li
- Department of Laboratory Medicine, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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38
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Chen P, Chen D, Li S, Ou X, Liu BF. Microfluidics towards single cell resolution protein analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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39
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Li N, Zhang W, Li Y, Lin JM. Analysis of cellular biomolecules and behaviors using microfluidic chip and fluorescence method. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Dovgan I, Koniev O, Kolodych S, Wagner A. Antibody-Oligonucleotide Conjugates as Therapeutic, Imaging, and Detection Agents. Bioconjug Chem 2019; 30:2483-2501. [PMID: 31339691 DOI: 10.1021/acs.bioconjchem.9b00306] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibody-oligonucleotide conjugates (AOCs) are a novel class of synthetic chimeric biomolecules that has been continually gaining traction in different fields of modern biotechnology. This is mainly due to the unique combination of the properties of their two constituents, exceptional targeting abilities and antibody biodistribution profiles, in addition to an extensive scope of oligonucleotide functional and structural roles. Combining these two classes of biomolecules in one chimeric construct has therefore become an important milestone in the development of numerous biotechnological applications, including imaging (DNA-PAINT), detection (PLA, PEA), and therapeutics (targeted siRNA/antisense delivery). Numerous synthetic approaches have been developed to access AOCs ranging from stochastic chemical bioconjugation to site-specific conjugation with reactive handles, introduced into antibody sequences through protein engineering. This Review gives a general overview of the current status of AOC applications with a specific emphasis on the synthetic methods used for their preparation. The reported synthetic techniques are discussed in terms of their practical aspects and limitations. The importance of the development of novel methods for the facile generation of AOCs possessing a defined constitution is highlighted as a priority in AOC research to ensure the advance of their new applications.
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Affiliation(s)
- Igor Dovgan
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
| | - Oleksandr Koniev
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Sergii Kolodych
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
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41
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Sundah NR, Ho NRY, Lim GS, Natalia A, Ding X, Liu Y, Seet JE, Chan CW, Loh TP, Shao H. Barcoded DNA nanostructures for the multiplexed profiling of subcellular protein distribution. Nat Biomed Eng 2019; 3:684-694. [PMID: 31285580 DOI: 10.1038/s41551-019-0417-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 05/14/2019] [Indexed: 11/09/2022]
Abstract
Massively parallel DNA sequencing is established, yet high-throughput protein profiling remains challenging. Here, we report a barcoding approach that leverages the combinatorial sequence content and the configurational programmability of DNA nanostructures for high-throughput multiplexed profiling of the subcellular expression and distribution of proteins in whole cells. The barcodes are formed by in situ hybridization of tetrahedral DNA nanostructures and short DNA sequences conjugated with protein-targeting antibodies, and by nanostructure-assisted ligation (either enzymatic or chemical) of the nanostructures and exogenous DNA sequences bound to nanoparticles of different sizes (which cause these localization sequences to differentially distribute across subcellular compartments). Compared with linear DNA barcoding, the nanostructured barcodes enhance the signal by more than 100-fold. By implementing the barcoding approach on a microfluidic device for the analysis of rare patient samples, we show that molecular subtypes of breast cancer can be accurately classified and that subcellular spatial markers of disease aggressiveness can be identified.
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Affiliation(s)
- Noah R Sundah
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Nicholas R Y Ho
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Geok Soon Lim
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Xianguang Ding
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Yu Liu
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Ju Ee Seet
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Hospital, Singapore, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tze Ping Loh
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Huilin Shao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore. .,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore. .,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore. .,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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42
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Abstract
Characterization of spatial protein expression for multiple targets from a single tissue is difficult to perform, especially due to the limitations of multiplex immunohistochemistry and tissue heterogeneity. Therefore, a new technology is required that permits detailed and simultaneous expression profiling of proteins within a defined region of interest (ROI). To address this unmet need, NanoString Technologies developed a new technology, GeoMxTM digital spatial profiling (DSP), which currently enables simultaneous and guided detection of up to 40 antibodies (probes) from a single formalin-fixed paraffin-embedded (FFPE) tissue. DSP probes are tagged with unique photocleavable DNA oligos that are released after guided ultraviolet exposure in specific ROIs. Digital quantification of the released oligos by NanoString's nCounter® system provides a detailed expression profile of proteins within these discrete ROIs. In this article, we will describe our experience with the GeoMx DSP platform using cancer FFPE tissues. These expression profiles will provide better characterization and understanding of tumor heterogeneity and the tumor micro-environment, enabling the improvement of patient therapy and the identification of potential biomarker signatures. The purpose of this article is to offer potential future users an independent insight into the DSP platform and a comprehensive idea of usability, including advantages and current limitations of the technology based on our current experience with the beta version of NanoString's DSP platform as part of the DSP beta-testing program. The GeoMxTM Digital Spatial Profiling (DSP) platform is a non-destructive technique for regional in-depth protein expression profiling. Using oligonucleotide detection technologies, the GeoMxTM DSP enables simultaneous high-level multiplexing on a single FFPE tissue. Here, we focus on our current experience derived from our biomarker research using the beta version of the DSP instrument. GeoMxTM digital spatial profiling is a high-level multiplexing technique. Regional and quantitative protein signature analysis of a single formalin-fixed paraffin-embedded tissue. Independent view on the advantages and limitations of the platform. Helpful tool towards personalized immunotherapies.
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Zhang K, Huang W, Li H, Xie M, Wang J. Ultrasensitive detection of hERG potassium channel in single-cell with photocleavable and entropy-driven reactions by using an electrochemical biosensor. Biosens Bioelectron 2019; 132:310-318. [DOI: 10.1016/j.bios.2019.02.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 12/23/2022]
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Wang C, Yang L, Wang Z, He J, Shi Q. Highly multiplexed profiling of cell surface proteins on single circulating tumor cells based on antibody and cellular barcoding. Anal Bioanal Chem 2019; 411:5373-5382. [PMID: 30820628 DOI: 10.1007/s00216-019-01666-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 01/26/2019] [Accepted: 02/04/2019] [Indexed: 11/27/2022]
Abstract
Circulating tumor cells (CTCs) are extraordinarily rare in blood samples and represent a real-time "liquid biopsy" of tumors. Although genetic and transcriptional sequencing of single CTCs has been reported, these methods fail to provide phenotypic and functional information of CTCs such as protein levels of surface proteins. Studies of single-cell proteomic assays of CTCs have been rare because of a lack of single-cell proteomic methods to handle and analyze rare cells in a high background of non-target cells with high sensitivity, throughput, and multiplexing capacity. Here, we develop a microchip-assisted single-cell proteomic method for profiling surface proteins of CTCs based on antibody and cellular DNA barcoding strategy. We combine DNA-encoded antibody tags and cell indexes to profile 15 proteins in ~ 100 single rare cells simultaneously, and use high-throughput sequencing as the readout to generate surface protein profiles of CTCs according to their cell indexes and antibody-derived protein barcodes. A 6400-well microchip and the automated puncher are used to rapidly retrieve single CTCs from enriched CTC population with minimal cell loss (~ 10%). This technological platform integrates reliable isolation and proteomic analysis of single CTCs and can be extendable to ~ 100 proteins in hundreds of rare cells with single-cell precision.
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Affiliation(s)
- Chunying Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Minhang District, Shanghai, 200240, China
| | - Liu Yang
- Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 201620, China
| | - Zhuo Wang
- Minhang Branch, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201100, China
| | - Jianjun He
- Abmart (Shanghai) Inc., Shanghai, 200233, China
| | - Qihui Shi
- Minhang Branch, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201100, China.
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45
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Decalf J, Albert ML, Ziai J. New tools for pathology: a user's review of a highly multiplexed method for in situ analysis of protein and RNA expression in tissue. J Pathol 2019; 247:650-661. [PMID: 30570141 DOI: 10.1002/path.5223] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 12/18/2022]
Abstract
Tumor cell heterogeneity and tumor cell-stromal interactions are being explored as determinants of disease progression and treatment resistance in solid tumor and hematological malignancies. As such, tools simultaneously capable of highly multiplexed profiling of tissues' protein and RNA content, as well as interrogation of rare or single cells, are required to precisely characterize constituent tumor cell populations, infiltrating lymphocytes and stromal elements. Access to spatial relationships will enable more precise characterization of tumors, support patient stratification and may help to identify novel drug targets. Multiple platforms are being developed to address these critical unmet needs. The NanoString digital spatial profiling (DSP) platform enables highly multiplexed, spatial assessment of protein and/or RNA targets in tissues by detecting oligonucleotide barcodes conjugated via a photocleavable linker to primary antibodies or nucleic acid probes. Although this platform enables high-dimensional spatial interrogation of tissue protein and RNA expression, a detailed understanding of its composition, function and chemistry is advisable to guide experimental design and data interpretation. The purpose of this review is to provide an independent, comprehensive description of the DSP technology, including an overview of NanoString's capture and antibody barcode conjugation chemistries, experimental workflow, data output and analysis methods. The DSP technology will be discussed in the context of other highly multiplexed immunohistochemistry methods, including imaging mass cytometry and multiplexed ion beam imaging, to inform potential users of the advantages and limitations of each. Additional issues such as preanalytical variability, sampling and specimen adequacy will be considered with respect to the platforms to inform potential experimental design. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jérémie Decalf
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Matthew L Albert
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - James Ziai
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
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46
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Chang YF, Huang YQ, Wu KM, Jou AFJ, Shih NY, Ho JAA. Diagnosing the RGS11 Lung Cancer Biomarker: The Integration of Competitive Immunoassay and Isothermal Nucleic Acid Exponential Amplification Reaction. Anal Chem 2019; 91:3327-3335. [DOI: 10.1021/acs.analchem.8b04374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ying-Feng Chang
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Qi Huang
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Kun-Ming Wu
- Chest Division, Department of Internal Medicine, Mackay Memorial Hospital, New Taipei 25160, Taiwan
- Department of Nursing, Mackay Junior College of Medicine, Nursing, and Management, Taipei 25245, Taiwan
- Department of Medicine, Mackay Medical College, New Taipei 25245, Taiwan
| | - Amily Fang-Ju Jou
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Neng-Yao Shih
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaoshiung Medical University, Kaoshiung, Taiwan
| | - Ja-an Annie Ho
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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47
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Abstract
Barcoded bioassays are ready to promote bioanalysis and biomedicine toward the point of care.
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Affiliation(s)
- Mingzhu Yang
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
| | - Yong Liu
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
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48
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Jorge AF, Eritja R. Overview of DNA Self-Assembling: Progresses in Biomedical Applications. Pharmaceutics 2018; 10:E268. [PMID: 30544945 PMCID: PMC6320858 DOI: 10.3390/pharmaceutics10040268] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature's assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.
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Affiliation(s)
- Andreia F Jorge
- Coimbra Chemistry Centre (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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49
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Li M, Anand RK. Integration of marker-free selection of single cells at a wireless electrode array with parallel fluidic isolation and electrical lysis. Chem Sci 2018; 10:1506-1513. [PMID: 30809368 PMCID: PMC6354902 DOI: 10.1039/c8sc04804e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 11/25/2018] [Indexed: 01/01/2023] Open
Abstract
We present integration of selective single-cell capture at an array of wireless electrodes (bipolar electrodes, BPEs) with transfer into chambers, reagent exchange, fluidic isolation and rapid electrical lysis in a single platform, thus minimizing sample loss and manual intervention steps. The whole process is achieved simply by exchanging the solution in a single inlet reservoir and by adjusting the applied voltage at a pair of driving electrodes, thus making this approach particularly well-suited for a broad range of research and clinical applications. Further, the use of BPEs allows the array to be scalable to increase throughput. Specific innovations reported here include the incorporation of a leak channel to balance competing flow paths, the use of 'split BPEs' to create a distinct recapture and electrical lysis point within the reaction chamber, and the dual purposing of an ionic liquid as an immiscible phase to seal the chambers and as a conductive medium to permit electrical lysis at the split BPEs.
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Affiliation(s)
- Min Li
- Department of Chemistry , Iowa State University , Ames , IA 50011 , USA .
| | - Robbyn K Anand
- Department of Chemistry , Iowa State University , Ames , IA 50011 , USA .
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50
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Giedt RJ, Pathania D, Carlson JCT, McFarland PJ, Del Castillo AF, Juric D, Weissleder R. Single-cell barcode analysis provides a rapid readout of cellular signaling pathways in clinical specimens. Nat Commun 2018; 9:4550. [PMID: 30382095 PMCID: PMC6208406 DOI: 10.1038/s41467-018-07002-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/06/2018] [Indexed: 12/23/2022] Open
Abstract
Serial tissue sampling has become essential in guiding modern targeted and personalized cancer treatments. An alternative to image guided core biopsies are fine needle aspirates (FNA) that yield cells rather than tissues but are much better tolerated and have lower complication rates. The efficient pathway analysis of such cells in the clinic has been difficult, time consuming and costly. Here we develop an antibody-DNA barcoding approach where harvested cells can be rapidly re-stained through the use of custom designed oligonucleotide-fluorophore conjugates. We show that this approach can be used to interrogate drug-relevant pathways in scant clinical samples. Using the PI3K/PTEN/CDK4/6 pathways in breast cancer as an example, we demonstrate how analysis can be performed in tandem with trial enrollment and can evaluate downstream signaling following therapeutic inhibition. This approach should allow more widespread use of scant single cell material in clinical samples.
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Affiliation(s)
- Randy J Giedt
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Divya Pathania
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
- MGH Cancer Center, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Philip J McFarland
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | | | - Dejan Juric
- MGH Cancer Center, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA.
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.
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