1
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Zhu L, Man CW, Harrison RE, Wu Z, Limsakul P, Peng Q, Hashimoto M, Mamaril AP, Xu H, Liu L, Wang Y. Engineering a Programmed Death-Ligand 1-Targeting Monobody Via Directed Evolution for SynNotch-Gated Cell Therapy. ACS NANO 2024; 18:8531-8545. [PMID: 38456901 PMCID: PMC10958600 DOI: 10.1021/acsnano.4c01597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Programmed death-ligand 1 (PD-L1) is a promising target for cancer immunotherapy due to its ability to inhibit T cell activation; however, its expression on various noncancer cells may cause on-target off-tumor toxicity when designing PD-L1-targeting Chimeric Antigen Receptor (CAR) T cell therapies. Combining rational design and directed evolution of the human fibronectin-derived monobody scaffold, "PDbody" was engineered to bind to PD-L1 with a preference for a slightly lower pH, which is typical in the tumor microenvironment. PDbody was further utilized as a CAR to target the PD-L1-expressing triple negative MDA-MB-231 breast cancer cell line. To mitigate on-target off-tumor toxicity associated with targeting PD-L1, a Cluster of Differentiation 19 (CD19)-recognizing SynNotch IF THEN gate was integrated into the system. This CD19-SynNotch PDbody-CAR system was then expressed in primary human T cells to target CD19-expressing MDA-MB-231 cancer cells. These CD19-SynNotch PDbody-CAR T cells demonstrated both specificity and efficacy in vitro, accurately eradicating cancer targets in cytotoxicity assays. Moreover, in an in vivo bilateral murine tumor model, they exhibited the capability to effectively restrain tumor growth. Overall, CD19-SynNotch PDbody-CAR T cells represent a distinct development over previously published designs due to their increased efficacy, proliferative capability, and mitigation of off-tumor toxicity for solid tumor treatment.
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Affiliation(s)
- Linshan Zhu
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Alfred
E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
| | - Chi-Wei Man
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California, 92093 United States
| | - Reed E.S. Harrison
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Zhuohang Wu
- Alfred
E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
| | - Praopim Limsakul
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Division
of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
- Center of
Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Qin Peng
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518132, P.R. China
| | - Matthew Hashimoto
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony P. Mamaril
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Hongquan Xu
- Department
of Statistics, University of California, Los Angeles, California 90095, United States
| | - Longwei Liu
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Alfred
E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
| | - Yingxiao Wang
- Department
of Bioengineering & Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Alfred
E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
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2
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Knapinska AM, Onwuha-Ekpete L, Drotleff G, Twohill D, Chai C, Ernce A, Grande I, Rodríguez M, Tokmina-Roszyk D, Larson B, Fields GB. Analysis of Matrix Metalloproteinase Activity and Inhibition in Cancer Spheroids. Methods Mol Biol 2024; 2747:189-209. [PMID: 38038942 DOI: 10.1007/978-1-0716-3589-6_16] [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: 12/02/2023]
Abstract
The utilization of tumor spheroids and organoids has greatly facilitated mechanistic understanding of tumor growth and invasion and lead to more effective high-throughput analysis of potential chemotherapeutic agents. In spheroid and organoid systems, tumor invasion occurs in three dimensions and monitoring this behavior can be data intensive. Quantitative correlation of tumor invasion with protease activity can further exacerbate data storage issues. The present method utilizes the "Hit Pick" approach to provide quantitative analysis and correlation of tumor invasion and membrane type 1 matrix metalloproteinase (MT1-MMP) activity in a rapid fashion with greatly reduced data storage requirements compared with standard image analysis approaches. Inhibition of MT1-MMP activity in spheroids can also be monitored by the present approach.
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Affiliation(s)
- Anna M Knapinska
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
- Alphazyme, Jupiter, FL, USA
| | - Lillian Onwuha-Ekpete
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Gary Drotleff
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
- Alphazyme, Jupiter, FL, USA
| | - Destiny Twohill
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Cedric Chai
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Alexa Ernce
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Isabella Grande
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Michelle Rodríguez
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Dorota Tokmina-Roszyk
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | | | - Gregg B Fields
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA.
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3
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Knapinska AM, Drotleff G, Chai C, Twohill D, Ernce A, Tokmina-Roszyk D, Grande I, Rodriguez M, Larson B, Fields GB. Screening MT1-MMP Activity and Inhibition in Three-Dimensional Tumor Spheroids. Biomedicines 2023; 11:biomedicines11020562. [PMID: 36831098 PMCID: PMC9953393 DOI: 10.3390/biomedicines11020562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
Membrane type 1 matrix metalloproteinase (MT1-MMP) has been shown to be crucial for tumor angiogenesis, invasion, and metastasis, and thus MT1-MMP is a high priority target for potential cancer therapies. To properly evaluate MT1-MMP inhibitors, a screening protocol is desired by which enzyme activity can be quantified in a tumor microenvironment-like model system. In the present study, we applied a fluorogenic, collagen model triple-helical substrate to quantify MT1-MMP activity for tumor spheroids embedded in a collagen hydrogel. The substrate was designed to be MT1-MMP selective and to possess fluorescent properties compatible with cell-based assays. The proteolysis of the substrate correlated to glioma spheroid invasion. In turn, the application of either small molecule or protein-based MMP inhibitors reduced proteolytic activity and glioma spheroid invasion. The presence of MT1-MMP in glioma spheroids was confirmed by western blotting. Thus, spheroid invasion was dependent on MT1-MMP activity, and inhibitors of MT1-MMP and invasion could be conveniently screened in a high-throughput format. The combination of the fluorogenic, triple-helical substrate, the three-dimensional tumor spheroids embedded in collagen, and Hit-Pick software resulted in an easily adaptable in vivo-like tumor microenvironment for rapidly processing inhibitor potential for anti-cancer use.
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Affiliation(s)
- Anna M. Knapinska
- Alphazyme, Jupiter, FL 33458, USA
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Gary Drotleff
- Alphazyme, Jupiter, FL 33458, USA
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Cedric Chai
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Destiny Twohill
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Alexa Ernce
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Dorota Tokmina-Roszyk
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Isabella Grande
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Michelle Rodriguez
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
| | - Brad Larson
- Agilent Technologies, Raleigh, NC 27606, USA
| | - Gregg B. Fields
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, FL 33458, USA
- Correspondence:
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Charupanit K, Tipmanee V, Sutthibutpong T, Limsakul P. In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103353. [PMID: 35630830 PMCID: PMC9143596 DOI: 10.3390/molecules27103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
The accumulation of polyethylene terephthalate (PET) seriously harms the environment because of its high resistance to degradation. The recent discovery of the bacteria-secreted biodegradation enzyme, PETase, sheds light on PET recycling; however, the degradation efficiency is far from practical use. Here, in silico alanine scanning mutagenesis (ASM) and site-saturation mutagenesis (SSM) were employed to construct the protein sequence space from binding energy of the PETase–PET interaction to identify the number and position of mutation sites and their appropriate side-chain properties that could improve the PETase–PET interaction. The binding mechanisms of the potential PETase variant were investigated through atomistic molecular dynamics simulations. The results show that up to two mutation sites of PETase are preferable for use in protein engineering to enhance the PETase activity, and the proper side chain property depends on the mutation sites. The predicted variants agree well with prior experimental studies. Particularly, the PETase variants with S238C or Q119F could be a potential candidate for improving PETase. Our combination of in silico ASM and SSM could serve as an alternative protocol for protein engineering because of its simplicity and reliability. In addition, our findings could lead to PETase improvement, offering an important contribution towards a sustainable future.
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Affiliation(s)
- Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (K.C.); (V.T.)
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (K.C.); (V.T.)
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand;
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Praopim Limsakul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Center of Excellence for Trace Analysis and Biosensor (TAB-CoE), Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence:
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5
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Liu L, Limsakul P, Meng X, Huang Y, Harrison RES, Huang TS, Shi Y, Yu Y, Charupanit K, Zhong S, Lu S, Zhang J, Chien S, Sun J, Wang Y. Integration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries. Nat Commun 2021; 12:5031. [PMID: 34413312 PMCID: PMC8376904 DOI: 10.1038/s41467-021-25323-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
The limited sensitivity of Förster Resonance Energy Transfer (FRET) biosensors hinders their broader applications. Here, we develop an approach integrating high-throughput FRET sorting and next-generation sequencing (FRET-Seq) to identify sensitive biosensors with varying substrate sequences from large-scale libraries directly in mammalian cells, utilizing the design of self-activating FRET (saFRET) biosensor. The resulting biosensors of Fyn and ZAP70 kinases exhibit enhanced performance and enable the dynamic imaging of T-cell activation mediated by T cell receptor (TCR) or chimeric antigen receptor (CAR), revealing a highly organized ZAP70 subcellular activity pattern upon TCR but not CAR engagement. The ZAP70 biosensor elucidates the role of immunoreceptor tyrosine-based activation motif (ITAM) in affecting ZAP70 activation to regulate CAR functions. A saFRET biosensor-based high-throughput drug screening (saFRET-HTDS) assay further enables the identification of an FDA-approved cancer drug, Sunitinib, that can be repurposed to inhibit ZAP70 activity and autoimmune-disease-related T-cell activation.
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Affiliation(s)
- Longwei Liu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Praopim Limsakul
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- Center of Excellence for Trace Analysis and Biosensor, Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Xianhui Meng
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, P.R. China
| | - Yan Huang
- Department of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Reed E S Harrison
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Tse-Shun Huang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- BioLegend, San Diego, CA, USA
| | - Yiwen Shi
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Yiyan Yu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sheng Zhong
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Shu Chien
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
| | - Jie Sun
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, P.R. China.
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA.
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6
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Peng Q, Weng K, Li S, Xu R, Wang Y, Wu Y. A Perspective of Epigenetic Regulation in Radiotherapy. Front Cell Dev Biol 2021; 9:624312. [PMID: 33681204 PMCID: PMC7930394 DOI: 10.3389/fcell.2021.624312] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Radiation therapy (RT) has been employed as a tumoricidal modality for more than 100 years and on 470,000 patients each year in the United States. The ionizing radiation causes genetic changes and results in cell death. However, since the biological mechanism of radiation remains unclear, there is a pressing need to understand this mechanism to improve the killing effect on tumors and reduce the side effects on normal cells. DNA break and epigenetic remodeling can be induced by radiotherapy. Hence the modulation of histone modification enzymes may tune the radiosensitivity of cancer cells. For instance, histone deacetylase (HDAC) inhibitors sensitize irradiated cancer cells by amplifying the DNA damage signaling and inhibiting double-strand DNA break repair to influence the irradiated cells’ survival. However, the combination of epigenetic drugs and radiotherapy has only been evaluated in several ongoing clinical trials for limited cancer types, partly due to a lack of knowledge on the potential mechanisms on how radiation induces epigenetic regulation and chromatin remodeling. Here, we review recent advances of radiotherapy and radiotherapy-induced epigenetic remodeling and introduce related technologies for epigenetic monitoring. Particularly, we exploit the application of fluorescence resonance energy transfer (FRET) biosensors to visualize dynamic epigenetic regulations in single living cells and tissue upon radiotherapy and drug treatment. We aim to bridge FRET biosensor, epigenetics, and radiotherapy, providing a perspective of using FRET to assess epigenetics and provide guidance for radiotherapy to improve cancer treatment. In the end, we discuss the feasibility of a combination of epigenetic drugs and radiotherapy as new approaches for cancer therapeutics.
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Affiliation(s)
- Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Kegui Weng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States.,Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
| | - Shitian Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Richard Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yongzhong Wu
- Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
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7
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Limsakul P, Charupanit K, Moonla C, Jeerapan I. Advances in emergent biological recognition elements and bioelectronics for diagnosing COVID-19. EMERGENT MATERIALS 2021; 4:231-247. [PMID: 33718775 PMCID: PMC7937783 DOI: 10.1007/s42247-021-00175-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 05/04/2023]
Abstract
Coronaviruses pose a serious threat to public health. Tremendous efforts are dedicated to advance reliable and effective detection of coronaviruses. Currently, the coronavirus disease 2019 (COVID-19) diagnosis mainly relies on the detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic materials by using reverse transcription-polymerase chain reaction (RT-PCR) assay. However, simpler and more rapid and reliable alternatives are needed to meet high demand during the pandemic. Biosensor-based diagnosis approaches become alternatives for selectively and rapidly detecting virus particles because of their biorecognition elements consisting of biomaterials that are specific to virus biomarkers. Here, we summarize biorecognition materials, including antibodies and antibody-like molecules, that are designed to recognize SARS-CoV-2 biomarkers and the advances of recently developed biosensors for COVID-19 diagnosis. The design of biorecognition materials or layers is crucial to maximize biosensing performances, such as high selectivity and sensitivity of virus detection. Additionally, the recent representative achievements in developing bioelectronics for sensing coronavirus are included. This review includes scholarly articles, mainly published in 2020 and early 2021. In addition to capturing the fast development in the fields of applied materials and biodiagnosis, the outlook of this rapidly evolving technology is summarized. Early diagnosis of COVID-19 could help prevent the spread of this contagious disease and provide significant information to medical teams to treat patients.
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Affiliation(s)
- Praopim Limsakul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
| | - Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110 Thailand
| | - Chochanon Moonla
- School of Chemistry, Institute of Science, Suranaree University of Technology, 111, University Avenue, Nakhon Ratchasima, 30000 Thailand
| | - Itthipon Jeerapan
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112 Thailand
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8
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Kaur A, Kaur P, Ahuja S. Förster resonance energy transfer (FRET) and applications thereof. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5532-5550. [PMID: 33210685 DOI: 10.1039/d0ay01961e] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
FRET is a nonradiative process of energy transfer that is based on the dipole-dipole interactions between molecules that are fluorescent. Transfer of energy takes place rapidly from a donor molecule to an acceptor molecule in juxtaposition such as 0 to 10 nm without photonic radiation. FRET has occupied a center stage in biotechnology and biological studies. It is used to gain information on conformation changes in single molecules. The pharmaceutical industry has also developed large fluorescence detection systems with very small sample sizes, at the level of single molecules, using fluorescence correlation spectroscopy.
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Affiliation(s)
- Amrita Kaur
- Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, 147001, India
| | - Pardeep Kaur
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407, India.
| | - Sahil Ahuja
- Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, 147001, India
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9
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10
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Léger C, Yahia-Ammar A, Susumu K, Medintz IL, Urvoas A, Valerio-Lepiniec M, Minard P, Hildebrandt N. Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer. ACS NANO 2020; 14:5956-5967. [PMID: 32216328 DOI: 10.1021/acsnano.0c01410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprising small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET switches were used in a separation-free solution-phase assay to quantify different protein targets at sub-nanomolar concentrations and to measure the conformational changes with sub-nanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live-cell imaging of ligand-receptor interactions.
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Affiliation(s)
- Corentin Léger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Akram Yahia-Ammar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
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11
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Huang NF, Chaudhuri O, Cahan P, Wang A, Engler AJ, Wang Y, Kumar S, Khademhosseini A, Li S. Multi-scale cellular engineering: From molecules to organ-on-a-chip. APL Bioeng 2020; 4:010906. [PMID: 32161833 PMCID: PMC7054123 DOI: 10.1063/1.5129788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
Recent technological advances in cellular and molecular engineering have provided new
insights into biology and enabled the design, manufacturing, and manipulation of complex
living systems. Here, we summarize the state of advances at the molecular, cellular, and
multi-cellular levels using experimental and computational tools. The areas of focus
include intrinsically disordered proteins, synthetic proteins, spatiotemporally dynamic
extracellular matrices, organ-on-a-chip approaches, and computational modeling, which all
have tremendous potential for advancing fundamental and translational science.
Perspectives on the current limitations and future directions are also described, with the
goal of stimulating interest to overcome these hurdles using multi-disciplinary
approaches.
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Affiliation(s)
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Adam J Engler
- Department of Bioengineering, Jacob School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Yingxiao Wang
- Department of Bioengineering, Jacob School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | | | | | - Song Li
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
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12
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Gebauer M, Skerra A. Engineering of binding functions into proteins. Curr Opin Biotechnol 2019; 60:230-241. [DOI: 10.1016/j.copbio.2019.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
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13
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Qin Q, Laub S, Shi Y, Ouyang M, Peng Q, Zhang J, Wang Y, Lu S. Fluocell for Ratiometric and High-Throughput Live-Cell Image Visualization and Quantitation. FRONTIERS IN PHYSICS 2019; 7:154. [PMID: 33163483 PMCID: PMC7646842 DOI: 10.3389/fphy.2019.00154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Spatiotemporal regulation of molecular activities dictates cellular function and fate. Investigation of dynamic molecular activities in live cells often requires the visualization and quantitation of fluorescent ratio image sequences with subcellular resolution and in high throughput. Hence, there is a great need for convenient software tools specifically designed with these capabilities. Here we describe a well-characterized open-source software package, Fluocell, customized to visualize pixelwise ratiometric images and calculate ratio time courses with subcellular resolution and in high throughput. Fluocell also provides group statistics and kinetic analysis functions for the quantified time courses, as well as 3D structure and function visualization for ratio images. The application of Fluocell is demonstrated by the ratiometric analysis of intensity images for several single-chain Förster (or fluorescence) resonance energy transfer (FRET)-based biosensors, allowing efficient quantification of dynamic molecular activities in a heterogeneous population of single live cells. Our analysis revealed distinct activation kinetics of Fyn kinase in the cytosolic and membrane compartments, and visualized a 4D spatiotemporal distribution of epigenetic signals in mitotic cells. Therefore, Fluocell provides an integrated environment for ratiometric live-cell image visualization and analysis, which generates high-quality single-cell dynamic data and allows the quantitative machine-learning of biophysical and biochemical computational models for molecular regulations in cells and tissues.
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Affiliation(s)
- Qin Qin
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, San Diego, CA, United States
| | - Shannon Laub
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yiwen Shi
- Department of Mathematics, Center of Computational Mathematics, University of California, San Diego, San Diego, CA, United State
| | - Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Qin Peng
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, San Diego, CA, United States
| | - Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, San Diego, CA, United States
- Department of Mathematics, Center of Computational Mathematics, University of California, San Diego, San Diego, CA, United State
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14
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Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors. Curr Opin Struct Biol 2019; 57:31-38. [DOI: 10.1016/j.sbi.2019.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 11/21/2022]
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15
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FÖrster resonance energy transfer (FRET)-based biosensors for biological applications. Biosens Bioelectron 2019; 138:111314. [DOI: 10.1016/j.bios.2019.05.019] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022]
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16
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Pahwa S, Bhowmick M, Amar S, Cao J, Strongin AY, Fridman R, Weiss SJ, Fields GB. Characterization and regulation of MT1-MMP cell surface-associated activity. Chem Biol Drug Des 2018; 93:1251-1264. [PMID: 30480376 DOI: 10.1111/cbdd.13450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 12/19/2022]
Abstract
Quantitative assessment of MT1-MMP cell surface-associated proteolytic activity remains undefined. Presently, MT1-MMP was stably expressed and a cell-based FRET assay developed to quantify activity toward synthetic collagen-model triple-helices. To estimate the importance of cell surface localization and specific structural domains on MT1-MMP proteolysis, activity measurements were performed using a series of membrane-anchored MT1-MMP mutants and compared directly with those of soluble MT1-MMP. MT1-MMP activity (kcat /KM ) on the cell surface was 4.8-fold lower compared with soluble MT1-MMP, with the effect largely manifested in kcat . Deletion of the MT1-MMP cytoplasmic tail enhanced cell surface activity, with both kcat and KM values affected, while deletion of the hemopexin-like domain negatively impacted KM and increased kcat . Overall, cell surface localization of MT1-MMP restricts substrate binding and protein-coupled motions (based on changes in both kcat and KM ) for catalysis. Comparison of soluble and cell surface-bound MT2-MMP revealed 12.9-fold lower activity on the cell surface. The cell-based assay was utilized for small molecule and triple-helical transition state analog MMP inhibitors, which were found to function similarly in solution and at the cell surface. These studies provide the first quantitative assessments of MT1-MMP activity and inhibition in the native cellular environment of the enzyme.
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Affiliation(s)
- Sonia Pahwa
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida
| | - Manishabrata Bhowmick
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida
| | - Sabrina Amar
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida.,Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida
| | - Jian Cao
- Departments of Medicine/Cancer Prevention and Pathology, Stony Brook University, Stony Brook, New York
| | - Alex Y Strongin
- Cancer Research Center, Sanford Burnham Prebys Medical Research Institute, La Jolla, California
| | - Rafael Fridman
- Department of Pathology and the Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Stephen J Weiss
- Division of Molecular Medicine & Genetics, Department of Internal Medicine, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Gregg B Fields
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida.,Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida.,The Scripps Research Institute/Scripps Florida, Jupiter, Florida
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17
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Wu YT, Qiu X, Lindbo S, Susumu K, Medintz IL, Hober S, Hildebrandt N. Quantum Dot-Based FRET Immunoassay for HER2 Using Ultrasmall Affinity Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802266. [PMID: 30079524 DOI: 10.1002/smll.201802266] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/02/2018] [Indexed: 05/20/2023]
Abstract
Engineered scaffold affinity proteins are used in many biological applications with the aim of replacing natural antibodies. Although their very small sizes are beneficial for multivalent nanoparticle conjugation and efficient Förster resonance energy transfer (FRET), the application of engineered affinity proteins in such nanobiosensing formats has been largely neglected. Here, it is shown that very small (≈6.5 kDa) histidine-tagged albumin-binding domain-derived affinity proteins (ADAPTs) can efficiently self-assemble to zwitterionic ligand-coated quantum dots (QDs). These ADAPT-QD conjugates are significantly smaller than QD-conjugates based on IgG, Fab', or single-domain antibodies. Immediate applicability by the quantification of the human epidermal growth factor receptor 2 (HER2) in serum-containing samples using time-gated Tb-to-QD FRET detection on the clinical benchtop immunoassay analyzer KRYPTOR is demonstrated here. Limits of detection down to 40 × 10-12 m (≈8 ng mL-1 ) are in a relevant clinical concentration range and outperform previously tested assays with antibodies, antibody fragments, and nanobodies.
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Affiliation(s)
- Yu-Tang Wu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell, Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Orsay, France
| | - Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell, Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Orsay, France
| | - Sarah Lindbo
- Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC, USA
- KeyW Corporation, Hanover, MD, 21076, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Sophia Hober
- Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell, Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Orsay, France
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