1
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Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X. MYC phase separation selectively modulates the transcriptome. Nat Struct Mol Biol 2024; 31:1567-1579. [PMID: 38811792 DOI: 10.1038/s41594-024-01322-6] [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: 02/22/2023] [Accepted: 04/22/2024] [Indexed: 05/31/2024]
Abstract
Dysregulation and enhanced expression of MYC transcription factors (TFs) including MYC and MYCN contribute to the majority of human cancers. For example, MYCN is amplified up to several hundredfold in high-risk neuroblastoma. The resulting overexpression of N-myc aberrantly activates genes that are not activated at low N-myc levels and drives cell proliferation. Whether increasing N-myc levels simply mediates binding to lower-affinity binding sites in the genome or fundamentally changes the activation process remains unclear. One such activation mechanism that could become important above threshold levels of N-myc is the formation of aberrant transcriptional condensates through phase separation. Phase separation has recently been linked to transcriptional regulation, but the extent to which it contributes to gene activation remains an open question. Here we characterized the phase behavior of N-myc and showed that it can form dynamic condensates that have transcriptional hallmarks. We tested the role of phase separation in N-myc-regulated transcription by using a chemogenetic tool that allowed us to compare non-phase-separated and phase-separated conditions at equivalent N-myc levels, both of which showed a strong impact on gene expression compared to no N-myc expression. Interestingly, we discovered that only a small percentage (<3%) of N-myc-regulated genes is further modulated by phase separation but that these events include the activation of key oncogenes and the repression of tumor suppressors. Indeed, phase separation increases cell proliferation, corroborating the biological effects of the transcriptional changes. However, our results also show that >97% of N-myc-regulated genes are not affected by N-myc phase separation, demonstrating that soluble complexes of TFs with the transcriptional machinery are sufficient to activate transcription.
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Affiliation(s)
- Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Chan-I Chung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Koach
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hongjiang Liu
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ambuja Navalkar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao He
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Zhimin Ma
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Qian Zhao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Liang He
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yin Shen
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William A Weiss
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Center, University of California, San Francisco, San Francisco, CA, USA.
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2
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Osman EA, Rynes TP, Wang YL, Mruk K, McKeague M. Non-invasive single cell aptasensing in live cells and animals. Chem Sci 2024; 15:4770-4778. [PMID: 38550682 PMCID: PMC10967030 DOI: 10.1039/d3sc05735f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/18/2024] [Indexed: 04/04/2024] Open
Abstract
We report a genetically encoded aptamer biosensor platform for non-invasive measurement of drug distribution in cells and animals. We combined the high specificity of aptamer molecular recognition with the easy-to-detect properties of fluorescent proteins. We generated six encoded aptasensors, showcasing the platform versatility. The biosensors display high sensitivity and specificity for detecting their specific drug target over related analogs. We show dose dependent response of biosensor performance reaching saturating drug uptake levels in individual live cells. We designed our platform for integration into animal genomes; thus, we incorporated aptamer biosensors into zebrafish, an important model vertebrate. The biosensors enabled non-invasive drug biodistribution imaging in whole animals across different timepoints. To our knowledge, this is the first example of an aptamer biosensor-expressing transgenic vertebrate that is carried through generations. As such, our encoded platform addresses the need for non-invasive whole animal biosensing ideal for pharmacokinetic-pharmacodynamic analyses that can be expanded to other organisms and to detect diverse molecules of interest.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
| | - Thomas P Rynes
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Y Lucia Wang
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
| | - Karen Mruk
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Maureen McKeague
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
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3
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Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. Phase separation of YAP-MAML2 differentially regulates the transcriptome. Proc Natl Acad Sci U S A 2024; 121:e2310430121. [PMID: 38315854 PMCID: PMC10873646 DOI: 10.1073/pnas.2310430121] [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: 06/21/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024] Open
Abstract
Phase separation (PS) drives the formation of biomolecular condensates that are emerging biological structures involved in diverse cellular processes. Recent studies have unveiled PS-induced formation of several transcriptional factor (TF) condensates that are transcriptionally active, but how strongly PS promotes gene activation remains unclear. Here, we show that the oncogenic TF fusion Yes-associated protein 1-Mastermind like transcriptional coactivator 2 (YAP-MAML2) undergoes PS and forms liquid-like condensates that bear the hallmarks of transcriptional activity. Furthermore, we examined the contribution of PS to YAP-MAML2-mediated gene expression by developing a chemogenetic tool that dissolves TF condensates, allowing us to compare phase-separated and non-phase-separated conditions at identical YAP-MAML2 protein levels. We found that a small fraction of YAP-MAML2-regulated genes is further affected by PS, which include the canonical YAP target genes CTGF and CYR61, and other oncogenes. On the other hand, majority of YAP-MAML2-regulated genes are not affected by PS, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery. Our work opens new directions in understanding the role of PS in selective modulation of gene expression, suggesting differential roles of PS in biological processes.
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Affiliation(s)
- Chan-I. Chung
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Xiaoyu Yang
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Hongjiang Liu
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Zhimin Ma
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
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4
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Li X, Combs JD, Salaita K, Shu X. Polarized focal adhesion kinase activity within a focal adhesion during cell migration. Nat Chem Biol 2023; 19:1458-1468. [PMID: 37349581 PMCID: PMC10732478 DOI: 10.1038/s41589-023-01353-y] [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: 10/26/2022] [Accepted: 05/03/2023] [Indexed: 06/24/2023]
Abstract
Focal adhesion kinase (FAK) relays integrin signaling from outside to inside cells and contributes to cell adhesion and motility. However, the spatiotemporal dynamics of FAK activity in single FAs is unclear due to the lack of a robust FAK reporter, which limits our understanding of these essential biological processes. Here we have engineered a genetically encoded FAK activity sensor, dubbed FAK-separation of phases-based activity reporter of kinase (SPARK), which visualizes endogenous FAK activity in living cells and vertebrates. Our work reveals temporal dynamics of FAK activity during FA turnover. Most importantly, our study unveils polarized FAK activity at the distal tip of newly formed single FAs in the leading edge of a migrating cell. By combining FAK-SPARK with DNA tension probes, we show that tensions applied to FAs precede FAK activation and that FAK activity is proportional to the strength of tension. These results suggest tension-induced polarized FAK activity in single FAs, advancing the mechanistic understanding of cell migration.
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Affiliation(s)
- Xiaoquan Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
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5
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Spatiotemporal dynamics of focal adhesion kinase. Nat Chem Biol 2023; 19:1444-1445. [PMID: 37349580 DOI: 10.1038/s41589-023-01371-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
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6
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Li X, Chung CI, Yang J, Chaudhuri S, Munster PN, Shu X. ATM-SPARK: A GFP phase separation-based activity reporter of ATM. SCIENCE ADVANCES 2023; 9:eade3760. [PMID: 36857446 PMCID: PMC9977181 DOI: 10.1126/sciadv.ade3760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The kinase ataxia telangiectasia mutated (ATM) plays a key role in the DNA damage response (DDR). It is thus essential to visualize spatiotemporal dynamics of ATM activity during DDR. Here, we designed a robust ATM activity reporter based on phosphorylation-inducible green fluorescent protein phase separation, dubbed ATM-SPARK (separation of phases-based activity reporter of kinase). Upon ATM activation, it undergoes phase separation via multivalent interactions, forming intensely bright droplets. The reporter visualizes spatiotemporal dynamics of endogenous ATM activity in living cells, and its signal is proportional to the amount of DNA damage. ATM-SPARK also enables high-throughput screening of biological and small-molecule regulators. We identified the protein phosphatase 4 that blocks ATM activity. We also identified BGT226 as a potent ATM inhibitor with a median inhibitory concentration of ~3.8 nanomolars. Furthermore, BGT226 sensitizes cancer cells to the radiomimetic drug neocarzinostatin, suggesting that BGT226 might be combined with radiotherapeutic treatment. ATM-SPARK achieves large dynamic range, bright fluorescence, and simple signal pattern.
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Affiliation(s)
- Xiaoquan Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Chan-I Chung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - JunJiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sibapriya Chaudhuri
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Pamela N. Munster
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
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7
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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8
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Cell-type-specific, multicolor labeling of endogenous proteins with split fluorescent protein tags in Drosophila. Proc Natl Acad Sci U S A 2021; 118:2024690118. [PMID: 34074768 DOI: 10.1073/pnas.2024690118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The impact of the Drosophila experimental system on studies of modern biology cannot be understated. The ability to tag endogenously expressed proteins is essential to maximize the use of this model organism. Here, we describe a method for labeling endogenous proteins with self-complementing split fluorescent proteins (split FPs) in a cell-type-specific manner in Drosophila A short fragment of an FP coding sequence is inserted into a specific genomic locus while the remainder of the FP is expressed using an available GAL4 driver line. In consequence, complementation fluorescence allows examination of protein localization in particular cells. Besides, when inserting tandem repeats of the short FP fragment at the same genomic locus, we can substantially enhance the fluorescence signal. The enhanced signal is of great value in live-cell imaging at the subcellular level. We can also accomplish a multicolor labeling system with orthogonal split FPs. However, other orthogonal split FPs do not function for in vivo imaging besides split GFP. Through protein engineering and in vivo functional studies, we report a red split FP that we can use for duplexed visualization of endogenous proteins in intricate Drosophila tissues. Using the two orthogonal split FP systems, we have simultaneously imaged proteins that reside in distinct subsynaptic compartments. Our approach allows us to study the proximity between and localization of multiple proteins endogenously expressed in essentially any cell type in Drosophila.
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9
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Okuda KS, Keyser MS, Gurevich DB, Sturtzel C, Mason EA, Paterson S, Chen H, Scott M, Condon ND, Martin P, Distel M, Hogan BM. Live-imaging of endothelial Erk activity reveals dynamic and sequential signalling events during regenerative angiogenesis. eLife 2021; 10:62196. [PMID: 34003110 PMCID: PMC8175085 DOI: 10.7554/elife.62196] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
The formation of new blood vessel networks occurs via angiogenesis during development, tissue repair, and disease. Angiogenesis is regulated by intracellular endothelial signalling pathways, induced downstream of vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs). A major challenge in understanding angiogenesis is interpreting how signalling events occur dynamically within endothelial cell populations during sprouting, proliferation, and migration. Extracellular signal-regulated kinase (Erk) is a central downstream effector of Vegf-signalling and reports the signalling that drives angiogenesis. We generated a vascular Erk biosensor transgenic line in zebrafish using a kinase translocation reporter that allows live-imaging of Erk-signalling dynamics. We demonstrate the utility of this line to live-image Erk activity during physiologically relevant angiogenic events. Further, we reveal dynamic and sequential endothelial cell Erk-signalling events following blood vessel wounding. Initial signalling is dependent upon Ca2+ in the earliest responding endothelial cells, but is independent of Vegfr-signalling and local inflammation. The sustained regenerative response, however, involves a Vegfr-dependent mechanism that initiates concomitantly with the wound inflammatory response. This work reveals a highly dynamic sequence of signalling events in regenerative angiogenesis and validates a new resource for the study of vascular Erk-signalling in real-time.
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Affiliation(s)
- Kazuhide S Okuda
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Mikaela S Keyser
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - David B Gurevich
- School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, Bristol, United Kingdom.,Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Caterina Sturtzel
- Innovative Cancer Models, St Anna Kinderkrebsforschung, Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for preclinical drug screening (ZANDR), Vienna, Austria
| | - Elizabeth A Mason
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia
| | - Scott Paterson
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Huijun Chen
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Mark Scott
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Nicholas D Condon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Paul Martin
- School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, Bristol, United Kingdom
| | - Martin Distel
- Innovative Cancer Models, St Anna Kinderkrebsforschung, Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for preclinical drug screening (ZANDR), Vienna, Austria
| | - Benjamin M Hogan
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
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10
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Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nat Commun 2021; 12:856. [PMID: 33558528 PMCID: PMC7870846 DOI: 10.1038/s41467-020-18911-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 01/07/2023] Open
Abstract
Through the efforts of many groups, a wide range of fluorescent protein reporters and sensors based on green fluorescent protein and its relatives have been engineered in recent years. Here we explore the incorporation of sensing modalities into de novo designed fluorescence-activating proteins, called mini-fluorescence-activating proteins (mFAPs), that bind and stabilize the fluorescent cis-planar state of the fluorogenic compound DFHBI. We show through further design that the fluorescence intensity and specificity of mFAPs for different chromophores can be tuned, and the fluorescence made sensitive to pH and Ca2+ for real-time fluorescence reporting. Bipartite split mFAPs enable real-time monitoring of protein-protein association and (unlike widely used split GFP reporter systems) are fully reversible, allowing direct readout of association and dissociation events. The relative ease with which sensing modalities can be incorporated and advantages in smaller size and photostability make de novo designed fluorescence-activating proteins attractive candidates for optical sensor engineering.
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11
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Zhang Q, Wang L, Qian Q, Wang J, Cheng W, Han K. Target Area Extraction Algorithm for the In Vivo Fluorescence Imaging of Small Animals. ACS OMEGA 2020; 5:20100-20106. [PMID: 32832764 PMCID: PMC7439258 DOI: 10.1021/acsomega.0c01733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Bio-optical imaging can noninvasively describe specific biochemical reaction events in small animals using endogenous or exogenous imaging reagents to label cells, proteins, or DNA. The fluorescence optical bio-imaging system excites the fluorescent group to a high energy state by excitation light and then generates emission light. However, many substances in the organism will also emit fluorescence after being excited by the excitation light, and the nonspecific fluorescence generated will affect the detection sensitivity. This paper designs and develops a set of high-level biosafety in vivo fluorescence imaging system for small animals suitable for virology research and proposes a target area extraction algorithm for fluorescence images. The fluorescence image target extraction algorithm first maps the nonlinear separation data in the low-dimensional space to the high-dimensional space. Then, based on the analysis of the characteristics of the fluorescent region, a method for discriminating the target fluorescent region based on the two-step entropy function is proposed, and the real target fluorescent region is obtained according to the set connected region. Based on the experiment of collecting and analyzing the in vivo fluorescent images of mice, it is verified that the proposed algorithm can automatically extract the target fluorescent region better than the classical linear model. It shows that the proposed algorithm is less affected by background fluorescence, and the estimated separated spectrum based on this method is closer to the real target spectrum.
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Affiliation(s)
- Qiang Zhang
- Academy
for Engineering & Technology, Fudan
University, Shanghai 200433, P. R. China
- CAS
Key Laboratory of Bio-Medical
Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Lei Wang
- CAS
Key Laboratory of Bio-Medical
Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Qing Qian
- CAS
Key Laboratory of Bio-Medical
Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Jishuai Wang
- CAS
Key Laboratory of Bio-Medical
Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Wenbo Cheng
- CAS
Key Laboratory of Bio-Medical
Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Kun Han
- CAS
Key Laboratory of Bio-Medical
Diagnostics, Suzhou Institute of Biomedical
Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
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