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Iyer RR, Applegate CC, Arogundade OH, Bangru S, Berg IC, Emon B, Porras-Gomez M, Hsieh PH, Jeong Y, Kim Y, Knox HJ, Moghaddam AO, Renteria CA, Richard C, Santaliz-Casiano A, Sengupta S, Wang J, Zambuto SG, Zeballos MA, Pool M, Bhargava R, Gaskins HR. Inspiring a convergent engineering approach to measure and model the tissue microenvironment. Heliyon 2024; 10:e32546. [PMID: 38975228 PMCID: PMC11226808 DOI: 10.1016/j.heliyon.2024.e32546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/22/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024] Open
Abstract
Understanding the molecular and physical complexity of the tissue microenvironment (TiME) in the context of its spatiotemporal organization has remained an enduring challenge. Recent advances in engineering and data science are now promising the ability to study the structure, functions, and dynamics of the TiME in unprecedented detail; however, many advances still occur in silos that rarely integrate information to study the TiME in its full detail. This review provides an integrative overview of the engineering principles underlying chemical, optical, electrical, mechanical, and computational science to probe, sense, model, and fabricate the TiME. In individual sections, we first summarize the underlying principles, capabilities, and scope of emerging technologies, the breakthrough discoveries enabled by each technology and recent, promising innovations. We provide perspectives on the potential of these advances in answering critical questions about the TiME and its role in various disease and developmental processes. Finally, we present an integrative view that appreciates the major scientific and educational aspects in the study of the TiME.
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Affiliation(s)
- Rishyashring R. Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Catherine C. Applegate
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Opeyemi H. Arogundade
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian C. Berg
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Bashar Emon
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Marilyn Porras-Gomez
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pei-Hsuan Hsieh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoon Jeong
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yongdeok Kim
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hailey J. Knox
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Amir Ostadi Moghaddam
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Carlos A. Renteria
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Craig Richard
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ashlie Santaliz-Casiano
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sourya Sengupta
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha G. Zambuto
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Maria A. Zeballos
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Marcia Pool
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rohit Bhargava
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biochemical Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- NIH/NIBIB P41 Center for Label-free Imaging and Multiscale Biophotonics (CLIMB), University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - H. Rex Gaskins
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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3
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Komolov AS, Sannikova EP, Gorbunov AA, Gubaidullin II, Plokhikh KS, Konstantinova GE, Bulushova NV, Kuchin SV, Kozlov DG. Synthesis of biologically active proteins as L6KD-SUMO fusions forming inclusion bodies in Escherichia coli. Biotechnol Bioeng 2024; 121:535-550. [PMID: 37927002 DOI: 10.1002/bit.28587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 11/07/2023]
Abstract
A new platform has been developed to facilitate the production of biologically active proteins and peptides in Escherichia coli. The platform includes an N-terminal self-associating L6 KD peptide fused to the SUMO protein (small ubiquitin-like protein modifier) from the yeast Saccharomyces cerevisiae, which is known for its chaperone activity. The target proteins are fused at the C termini of the L6 KD-SUMO fusions, and the resulting three-component fusion proteins are synthesized and self-assembled in E. coli into so-called active inclusion bodies (AIBs). In vivo, the L6 KD-SUMO platform facilitates the correct folding of the target proteins and directs them into AIBs, greatly simplifying their purification. In vitro, the platform facilitates the effective separation of AIBs by centrifugation and subsequent target protein release using SUMO-specific protease. The properties of the AIBs were determined using five proteins with different sizes, folding efficiencies, quaternary structure, and disulfide modifications. Electron microscopy shows that AIBs are synthesized in the form of complex fibrillar structures resembling "loofah sponges" with unusually thick filaments. The obtained results indicate that the new platform has promising features and could be developed to facilitate the synthesis and purification of target proteins and protein complexes without the use of renaturation.
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Affiliation(s)
| | | | | | - Irek I Gubaidullin
- National Research Center "Kurchatov Institute", Moscow, Russia
- Kurchatov Genomic Center, National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Moscow, Russia
| | | | | | | | - Sergei V Kuchin
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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Jensen GC, Janis MK, Jara J, Abbasi N, Zastrow ML. Zinc-Induced Fluorescence Turn-On in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins. Biochemistry 2023; 62:2828-2840. [PMID: 37699411 PMCID: PMC11057272 DOI: 10.1021/acs.biochem.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to the near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 (All1280g2) from Nostoc sp. PCC7120 is a DXCF motif-containing protein that exhibits blue-light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. All1280g2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent All1280g2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here, we show that All1280g2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with a blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF from Synechocystis sp. PCC6803 (Slr1393g3). Zn2+ significantly enhances All1280g2-PEB fluorescence across a biologically relevant pH range from 6.0 to 9.0, with pH-dependent dissociation constants from 1 μM to ∼20-80 nM. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement. Mutation of the cysteine residue within the DXCF motif to alanine abolishes the zinc-induced fluorescence enhancement. Collectively, these results support the presence of a unique fluorescence-enhancing Zn2+ binding site in All1280g2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Jazzmin Jara
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Nasir Abbasi
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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Lin C, Liu L, Zou P. Functional imaging-guided cell selection for evolving genetically encoded fluorescent indicators. CELL REPORTS METHODS 2023; 3:100544. [PMID: 37671014 PMCID: PMC10475787 DOI: 10.1016/j.crmeth.2023.100544] [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: 01/23/2023] [Revised: 06/05/2023] [Accepted: 07/06/2023] [Indexed: 09/07/2023]
Abstract
Genetically encoded fluorescent indicators are powerful tools for tracking cellular dynamic processes. Engineering these indicators requires balancing screening dimensions with screening throughput. Herein, we present a functional imaging-guided photoactivatable cell selection platform, Faculae (functional imaging-activated molecular evolution), for linking microscopic phenotype with the underlying genotype in a pooled mutant library. Faculae is capable of assessing tens of thousands of variants in mammalian cells simultaneously while achieving photoactivation with single-cell resolution in seconds. To demonstrate the feasibility of this approach, we applied Faculae to perform multidimensional directed evolution for far-red genetically encoded calcium indicators (FR-GECIs) with improved brightness (Nier1b) and signal-to-baseline ratio (Nier1s). We anticipate that this image-based pooled screening method will facilitate the development of a wide variety of biomolecular tools.
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Affiliation(s)
- Chang Lin
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Lihao Liu
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
- Chinese Institute for Brain Research (CIBR), Beijing 102206, China
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6
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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7
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Hashizume R, Fujii H, Mehta S, Ota K, Qian Y, Zhu W, Drobizhev M, Nasu Y, Zhang J, Bito H, Campbell RE. A genetically encoded far-red fluorescent calcium ion biosensor derived from a biliverdin-binding protein. Protein Sci 2022; 31:e4440. [PMID: 36173169 PMCID: PMC9518226 DOI: 10.1002/pro.4440] [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: 07/04/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/09/2022]
Abstract
Far-red and near-infrared (NIR) genetically encoded calcium ion (Ca2+ ) indicators (GECIs) are powerful tools for in vivo and multiplexed imaging of neural activity and cell signaling. Inspired by a previous report to engineer a far-red fluorescent protein (FP) from a biliverdin (BV)-binding NIR FP, we have developed a far-red fluorescent GECI, designated iBB-GECO1, from a previously reported NIR GECI. iBB-GECO1 exhibits a relatively high molecular brightness, an inverse response to Ca2+ with ΔF/Fmin = -13, and a near-optimal dissociation constant (Kd ) for Ca2+ of 105 nM. We demonstrate the utility of iBB-GECO1 for four-color multiplexed imaging in MIN6 cells and five-color imaging in HEK293T cells. Like other BV-binding GECIs, iBB-GECO1 did not give robust signals during in vivo imaging of neural activity in mice, but did provide promising results that will guide future engineering efforts. SIGNIFICANCE: Genetically encoded calcium ion (Ca2+ ) indicators (GECIs) compatible with common far-red laser lines (~630-640 nm) on commercial microscopes are of critical importance for their widespread application to deep-tissue multiplexed imaging of neural activity. In this study, we engineered a far-red excitable fluorescent GECI, designated iBB-GECO1, that exhibits a range of preferable specifications such as high brightness, large fluorescence response to Ca2+ , and compatibility with multiplexed imaging in mammalian cells.
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Affiliation(s)
- Rina Hashizume
- Department of Chemistry, School of ScienceThe University of Tokyo, Bunkyo‐kuTokyoJapan
| | - Hajime Fujii
- Department of Neurochemistry, Graduate School of MedicineThe University of Tokyo, Bunkyo‐kuTokyoJapan
| | - Sohum Mehta
- Department of PharmacologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Keisuke Ota
- Department of Neurochemistry, Graduate School of MedicineThe University of Tokyo, Bunkyo‐kuTokyoJapan
| | - Yong Qian
- Department of ChemistryUniversity of AlbertaEdmontonAlbertaCanada
- McGovern Institute for Brain Research, MITCambridgeMassachusettsUSA
| | - Wenchao Zhu
- Department of Chemistry, School of ScienceThe University of Tokyo, Bunkyo‐kuTokyoJapan
| | - Mikhail Drobizhev
- Department of Microbiology and Cell BiologyMontana State UniversityBozemanMontanaUSA
| | - Yusuke Nasu
- Department of Chemistry, School of ScienceThe University of Tokyo, Bunkyo‐kuTokyoJapan
| | - Jin Zhang
- Department of PharmacologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Haruhiko Bito
- Department of Neurochemistry, Graduate School of MedicineThe University of Tokyo, Bunkyo‐kuTokyoJapan
| | - Robert E. Campbell
- Department of Chemistry, School of ScienceThe University of Tokyo, Bunkyo‐kuTokyoJapan
- Department of ChemistryUniversity of AlbertaEdmontonAlbertaCanada
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8
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Subach OM, Vlaskina AV, Agapova YK, Dorovatovskii PV, Nikolaeva AY, Ivashkina OI, Popov VO, Piatkevich KD, Khrenova MG, Smirnova TA, Boyko KM, Subach FV. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift. Int J Mol Sci 2021; 22:12887. [PMID: 34884694 PMCID: PMC8657457 DOI: 10.3390/ijms222312887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Genetically encoded red fluorescent proteins with a large Stokes shift (LSSRFPs) can be efficiently co-excited with common green FPs both under single- and two-photon microscopy, thus enabling dual-color imaging using a single laser. Recent progress in protein development resulted in a great variety of novel LSSRFPs; however, the selection of the right LSSRFP for a given application is hampered by the lack of a side-by-side comparison of the LSSRFPs' performance. In this study, we employed rational design and random mutagenesis to convert conventional bright RFP mScarlet into LSSRFP, called LSSmScarlet, characterized by excitation/emission maxima at 470/598 nm. In addition, we utilized the previously reported LSSRFPs mCyRFP1, CyOFP1, and mCRISPRed as templates for directed molecular evolution to develop their optimized versions, called dCyRFP2s, dCyOFP2s and CRISPRed2s. We performed a quantitative assessment of the developed LSSRFPs and their precursors in vitro on purified proteins and compared their brightness at 488 nm excitation in the mammalian cells. The monomeric LSSmScarlet protein was successfully utilized for the confocal imaging of the structural proteins in live mammalian cells and multicolor confocal imaging in conjugation with other FPs. LSSmScarlet was successfully applied for dual-color two-photon imaging in live mammalian cells. We also solved the X-ray structure of the LSSmScarlet protein at the resolution of 1.4 Å that revealed a hydrogen bond network supporting excited-state proton transfer (ESPT). Quantum mechanics/molecular mechanics molecular dynamic simulations confirmed the ESPT mechanism of a large Stokes shift. Structure-guided mutagenesis revealed the role of R198 residue in ESPT that allowed us to generate a variant with improved pH stability. Finally, we showed that LSSmScarlet protein is not appropriate for STED microscopy as a consequence of LSSRed-to-Red photoconversion with high-power 775 nm depletion light.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Yuliya K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Pavel V. Dorovatovskii
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Olga I. Ivashkina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir O. Popov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Tatiana A. Smirnova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
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The Cutting Edge of Disease Modeling: Synergy of Induced Pluripotent Stem Cell Technology and Genetically Encoded Biosensors. Biomedicines 2021; 9:biomedicines9080960. [PMID: 34440164 PMCID: PMC8392144 DOI: 10.3390/biomedicines9080960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/02/2021] [Indexed: 11/17/2022] Open
Abstract
The development of cell models of human diseases based on induced pluripotent stem cells (iPSCs) and a cell therapy approach based on differentiated iPSC derivatives has provided a powerful stimulus in modern biomedical research development. Moreover, it led to the creation of personalized regenerative medicine. Due to this, in the last decade, the pathological mechanisms of many monogenic diseases at the cell level have been revealed, and clinical trials of various cell products derived from iPSCs have begun. However, it is necessary to reach a qualitatively new level of research with cell models of diseases based on iPSCs for more efficient searching and testing of drugs. Biosensor technology has a great application prospect together with iPSCs. Biosensors enable researchers to monitor ions, molecules, enzyme activities, and channel conformation in live cells and use them in live imaging and drug screening. These probes facilitate the measurement of steady-state concentrations or activity levels and the observation and quantification of in vivo flux and kinetics. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of the false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the benefits of using biosensors in drug screening. Here, we discuss the possibilities of using biosensor technology in combination with cell models based on human iPSCs and gene editing systems. Furthermore, we focus on the current achievements and problems of using these methods.
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Camarca A, Varriale A, Capo A, Pennacchio A, Calabrese A, Giannattasio C, Murillo Almuzara C, D’Auria S, Staiano M. Emergent Biosensing Technologies Based on Fluorescence Spectroscopy and Surface Plasmon Resonance. SENSORS (BASEL, SWITZERLAND) 2021; 21:906. [PMID: 33572812 PMCID: PMC7866296 DOI: 10.3390/s21030906] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/23/2022]
Abstract
The purpose of this work is to provide an exhaustive overview of the emerging biosensor technologies for the detection of analytes of interest for food, environment, security, and health. Over the years, biosensors have acquired increasing importance in a wide range of applications due to synergistic studies of various scientific disciplines, determining their great commercial potential and revealing how nanotechnology and biotechnology can be strictly connected. In the present scenario, biosensors have increased their detection limit and sensitivity unthinkable until a few years ago. The most widely used biosensors are optical-based devices such as surface plasmon resonance (SPR)-based biosensors and fluorescence-based biosensors. Here, we will review them by highlighting how the progress in their design and development could impact our daily life.
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Affiliation(s)
- Alessandra Camarca
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Antonio Varriale
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
- URT-ISA at Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Alessandro Capo
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Angela Pennacchio
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Alessia Calabrese
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Cristina Giannattasio
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Carlos Murillo Almuzara
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Sabato D’Auria
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Maria Staiano
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
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