1551
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Pitsalidis C, Pappa AM, Boys AJ, Fu Y, Moysidou CM, van Niekerk D, Saez J, Savva A, Iandolo D, Owens RM. Organic Bioelectronics for In Vitro Systems. Chem Rev 2021; 122:4700-4790. [PMID: 34910876 DOI: 10.1021/acs.chemrev.1c00539] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bioelectronics have made strides in improving clinical diagnostics and precision medicine. The potential of bioelectronics for bidirectional interfacing with biology through continuous, label-free monitoring on one side and precise control of biological activity on the other has extended their application scope to in vitro systems. The advent of microfluidics and the considerable advances in reliability and complexity of in vitro models promise to eventually significantly reduce or replace animal studies, currently the gold standard in drug discovery and toxicology testing. Bioelectronics are anticipated to play a major role in this transition offering a much needed technology to push forward the drug discovery paradigm. Organic electronic materials, notably conjugated polymers, having demonstrated technological maturity in fields such as solar cells and light emitting diodes given their outstanding characteristics and versatility in processing, are the obvious route forward for bioelectronics due to their biomimetic nature, among other merits. This review highlights the advances in conjugated polymers for interfacing with biological tissue in vitro, aiming ultimately to develop next generation in vitro systems. We showcase in vitro interfacing across multiple length scales, involving biological models of varying complexity, from cell components to complex 3D cell cultures. The state of the art, the possibilities, and the challenges of conjugated polymers toward clinical translation of in vitro systems are also discussed throughout.
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Affiliation(s)
- Charalampos Pitsalidis
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi 127788, UAE.,Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Anna-Maria Pappa
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi 127788, UAE
| | - Alexander J Boys
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Ying Fu
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, U.K
| | - Chrysanthi-Maria Moysidou
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Douglas van Niekerk
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Janire Saez
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,Microfluidics Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain.,Ikerbasque, Basque Foundation for Science, E-48011 Bilbao, Spain
| | - Achilleas Savva
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Donata Iandolo
- INSERM, U1059 Sainbiose, Université Jean Monnet, Mines Saint-Étienne, Université de Lyon, 42023 Saint-Étienne, France
| | - Róisín M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
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1552
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Harberts J, Bours K, Siegmund M, Hedrich C, Glatza M, Schöler HR, Haferkamp U, Pless O, Zierold R, Blick RH. Culturing human iPSC-derived neural progenitor cells on nanowire arrays: mapping the impact of nanowire length and array pitch on proliferation, viability, and membrane deformation. NANOSCALE 2021; 13:20052-20066. [PMID: 34842880 DOI: 10.1039/d1nr04352h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanowire arrays used as cell culture substrates build a potent tool for advanced biological applications such as cargo delivery and biosensing. The unique topography of nanowire arrays, however, renders them a challenging growth environment for cells and explains why only basic cell lines have been employed in existing studies. Here, we present the culturing of human induced pluripotent stem cell-derived neural progenitor cells on rectangularly arranged nanowire arrays: In detail, we mapped the impact on proliferation, viability, and topography-induced membrane deformation across a multitude of array pitches (1, 3, 5, 10 μm) and nanowire lengths (1.5, 3, 5 μm). Against the intuitive expectation, a reduced proliferation was found on the arrays with the smallest array pitch of 1 μm and long NWs. Typically, cells settle in a fakir-like state on such densely-spaced nanowires and thus experience no substantial stress caused by nanowires indenting the cell membrane. However, imaging of F-actin showed a distinct reorganization of the cytoskeleton along the nanowire tips in the case of small array pitches interfering with regular proliferation. For larger pitches, the cell numbers depend on the NW lengths but proliferation generally continued although heavy deformations of the cell membrane were observed caused by the encapsulation of the nanowires. Moreover, we noticed a strong interaction of the nanowires with the nucleus in terms of squeezing and indenting. Remarkably, the cell viability is maintained at about 85% despite the massive deformation of the cells. Considering the enormous potential of human induced stem cells to study neurodegenerative diseases and the high cellular viability combined with a strong interaction with nanowire arrays, we believe that our results pave the way to apply nanowire arrays to human stem cells for future applications in stem cell research and regenerative medicine.
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Affiliation(s)
- Jann Harberts
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Katja Bours
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Malte Siegmund
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Carina Hedrich
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Michael Glatza
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Undine Haferkamp
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Ole Pless
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Robert Zierold
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Robert H Blick
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Material Science and Engineering, College of Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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1553
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Larasati Y, Boudou C, Koval A, Katanaev VL. Unlocking the Wnt pathway: Therapeutic potential of selective targeting FZD 7 in cancer. Drug Discov Today 2021; 27:777-792. [PMID: 34915171 DOI: 10.1016/j.drudis.2021.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/09/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023]
Abstract
The Wnt signaling is of paramount pathophysiological importance. Despite showing promising anticancer activities in pre-clinical studies, current Wnt pathway inhibitors face complications in clinical trials resulting from on-target toxicity. Hence, the targeting of pathway component(s) that are essential for cancer but dispensable for normal physiology is key to the development of a safe Wnt signaling inhibitor. Frizzled7 (FZD7) is a Wnt pathway receptor that is redundant in healthy tissues but crucial in various cancers. FZD7 modulates diverse aspects of carcinogenesis, including cancer growth, metastasis, maintenance of cancer stem cells, and chemoresistance. In this review, we describe state-of-the-art knowledge of the functions of FZD7 in carcinogenesis and adult tissue homeostasis. Next, we overview the development of small molecules and biomolecules that target FZD7. Finally, we discuss challenges and possibilities in developing FZD7-selective antagonists.
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Affiliation(s)
- Yonika Larasati
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Cédric Boudou
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Alexey Koval
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia.
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1554
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Recent Developments in Surface Topography-Modulated Neurogenesis. BIOCHIP JOURNAL 2021. [DOI: 10.1007/s13206-021-00040-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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1555
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Dabbagh SR, Alseed MM, Saadat M, Sitti M, Tasoglu S. Biomedical Applications of Magnetic Levitation. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Sajjad Rahmani Dabbagh
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
- Koç University Arçelik Research Center for Creative Industries (KUAR) Koç University Sariyer Istanbul Turkey 34450
| | - M. Munzer Alseed
- Institute of Biomedical Engineering Boğaziçi University Çengelköy Istanbul Turkey 34684
| | - Milad Saadat
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
| | - Metin Sitti
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
- School of Medicine Koç University Istanbul 34450 Turkey
- Physical Intelligence Department Max Planck Institute for Intelligent Systems 70569 Stuttgart Germany
| | - Savas Tasoglu
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
- Koç University Arçelik Research Center for Creative Industries (KUAR) Koç University Sariyer Istanbul Turkey 34450
- Institute of Biomedical Engineering Boğaziçi University Çengelköy Istanbul Turkey 34684
- Physical Intelligence Department Max Planck Institute for Intelligent Systems 70569 Stuttgart Germany
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1556
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Caballero D, Abreu CM, Lima AC, Neves NN, Reis RL, Kundu SC. Precision biomaterials in cancer theranostics and modelling. Biomaterials 2021; 280:121299. [PMID: 34871880 DOI: 10.1016/j.biomaterials.2021.121299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023]
Abstract
Despite significant achievements in the understanding and treatment of cancer, it remains a major burden. Traditional therapeutic approaches based on the 'one-size-fits-all' paradigm are becoming obsolete, as demonstrated by the increasing number of patients failing to respond to treatments. In contrast, more precise approaches based on individualized genetic profiling of tumors have already demonstrated their potential. However, even more personalized treatments display shortcomings mainly associated with systemic delivery, such as low local drug efficacy or specificity. A large amount of effort is currently being invested in developing precision medicine-based strategies for improving the efficiency of cancer theranostics and modelling, which are envisioned to be more accurate, standardized, localized, and less expensive. To this end, interdisciplinary research fields, such as biomedicine, material sciences, pharmacology, chemistry, tissue engineering, and nanotechnology, must converge for boosting the precision cancer ecosystem. In this regard, precision biomaterials have emerged as a promising strategy to detect, model, and treat cancer more efficiently. These are defined as those biomaterials precisely engineered with specific theranostic functions and bioactive components, with the possibility to be tailored to the cancer patient needs, thus having a vast potential in the increasing demand for more efficient treatments. In this review, we discuss the latest advances in the field of precision biomaterials in cancer research, which are expected to revolutionize disease management, focusing on their uses for cancer modelling, detection, and therapeutic applications. We finally comment on the needed requirements to accelerate their application in the clinic to improve cancer patient prognosis.
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Affiliation(s)
- David Caballero
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco, 4805-017, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
| | - Catarina M Abreu
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco, 4805-017, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Ana C Lima
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco, 4805-017, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno N Neves
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco, 4805-017, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L Reis
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco, 4805-017, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Subhas C Kundu
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco, 4805-017, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
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1557
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Pathmasiri KC, Nguyen TTA, Khamidova N, Cologna SM. Mass spectrometry-based lipid analysis and imaging. CURRENT TOPICS IN MEMBRANES 2021; 88:315-357. [PMID: 34862030 DOI: 10.1016/bs.ctm.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for in situ mapping of analytes across a sample. With growing interest in lipid biochemistry, the ability to perform such mapping without antibodies has opened many opportunities for MSI and lipid analysis. Herein, we discuss the basics of MSI with particular emphasis on MALDI mass spectrometry and lipid analysis. A discussion of critical advancements as well as protocol details are provided to the reader. In addition, strategies for improving the detection of lipids, as well as applications in biomedical research, are presented.
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Affiliation(s)
- Koralege C Pathmasiri
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Thu T A Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Nigina Khamidova
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States; Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, United States.
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1558
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Tupone MG, Panella G, d’Angelo M, Castelli V, Caioni G, Catanesi M, Benedetti E, Cimini A. An Update on Graphene-Based Nanomaterials for Neural Growth and Central Nervous System Regeneration. Int J Mol Sci 2021; 22:13047. [PMID: 34884851 PMCID: PMC8657785 DOI: 10.3390/ijms222313047] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Thanks to their reduced size, great surface area, and capacity to interact with cells and tissues, nanomaterials present some attractive biological and chemical characteristics with potential uses in the field of biomedical applications. In this context, graphene and its chemical derivatives have been extensively used in many biomedical research areas from drug delivery to bioelectronics and tissue engineering. Graphene-based nanomaterials show excellent optical, mechanical, and biological properties. They can be used as a substrate in the field of tissue engineering due to their conductivity, allowing to study, and educate neural connections, and guide neural growth and differentiation; thus, graphene-based nanomaterials represent an emerging aspect in regenerative medicine. Moreover, there is now an urgent need to develop multifunctional and functionalized nanomaterials able to arrive at neuronal cells through the blood-brain barrier, to manage a specific drug delivery system. In this review, we will focus on the recent applications of graphene-based nanomaterials in vitro and in vivo, also combining graphene with other smart materials to achieve the best benefits in the fields of nervous tissue engineering and neural regenerative medicine. We will then highlight the potential use of these graphene-based materials to construct graphene 3D scaffolds able to stimulate neural growth and regeneration in vivo for clinical applications.
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Affiliation(s)
- Maria Grazia Tupone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
- Center for Microscopy, University of L’Aquila, 67100 L’Aquila, Italy
| | - Gloria Panella
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
| | - Michele d’Angelo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
| | - Vanessa Castelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
| | - Giulia Caioni
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
| | - Mariano Catanesi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
| | - Elisabetta Benedetti
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
| | - Annamaria Cimini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.G.T.); (G.P.); (M.d.); (V.C.); (G.C.); (M.C.); (A.C.)
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
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1559
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Wu Y, Zhou Y, Qin X, Liu Y. From cell spheroids to vascularized cancer organoids: Microfluidic tumor-on-a-chip models for preclinical drug evaluations. BIOMICROFLUIDICS 2021; 15:061503. [PMID: 34804315 PMCID: PMC8589468 DOI: 10.1063/5.0062697] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/16/2021] [Indexed: 05/14/2023]
Abstract
Chemotherapy is one of the most effective cancer treatments. Starting from the discovery of new molecular entities, it usually takes about 10 years and 2 billion U.S. dollars to bring an effective anti-cancer drug from the benchtop to patients. Due to the physiological differences between animal models and humans, more than 90% of drug candidates failed in phase I clinical trials. Thus, a more efficient drug screening system to identify feasible compounds and pre-exclude less promising drug candidates is strongly desired. For their capability to accurately construct in vitro tumor models derived from human cells to reproduce pathological and physiological processes, microfluidic tumor chips are reliable platforms for preclinical drug screening, personalized medicine, and fundamental oncology research. This review summarizes the recent progress of the microfluidic tumor chip and highlights tumor vascularization strategies. In addition, promising imaging modalities for enhancing data acquisition and machine learning-based image analysis methods to accurately quantify the dynamics of tumor spheroids are introduced. It is believed that the microfluidic tumor chip will serve as a high-throughput, biomimetic, and multi-sensor integrated system for efficient preclinical drug evaluation in the future.
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Affiliation(s)
- Yue Wu
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Yuyuan Zhou
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Xiaochen Qin
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Yaling Liu
- Author to whom correspondence should be addressed:
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1560
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Unger MS, Blank M, Enzlein T, Hopf C. Label-free cell assays to determine compound uptake or drug action using MALDI-TOF mass spectrometry. Nat Protoc 2021; 16:5533-5558. [PMID: 34759382 DOI: 10.1038/s41596-021-00624-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022]
Abstract
Cell-based assays for compound screening and profiling are fundamentally important in life sciences, chemical biology and pharmaceutical research. Most cell assays measure the amount of a single reporter molecule or cellular endpoint, and require the use of fluorescence or other labeled materials. Consequently, there is high demand for label-free technologies that enable multiple biomolecules or endpoints to be measured simultaneously. Here, we describe how to develop, optimize and validate MALDI-TOF mass spectrometry (MS) cell assays that can be used to measure cellular uptake of transporter substrates, to monitor cellular drug target engagement or to discover cellular drug-response markers. In uptake assays, intracellular accumulation of a transporter substrate and its inhibition by test compounds is measured. In drug response assays, changes to multiple cellular metabolites or to abundant posttranslational protein modifications are monitored as reporters of drug activity. We detail a ten-part optimization protocol with every part taking 1-2 d that leads to a final 2 d optimized procedure, which includes cell treatment, transfer, MALDI MS-specific sample preparation, quantification using stable-isotope-labeled standards, MALDI-TOF MS data acquisition, data processing and analysis. Key considerations for validation and automation of MALDI-TOF MS cell assays are outlined. Overall, label-free MS cell-based assays offer speed, sensitivity, accuracy and versatility in drug research.
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Affiliation(s)
- Melissa S Unger
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Martina Blank
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany.,Structural Molecular Biology Laboratory (LABIME), Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Thomas Enzlein
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany.
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1561
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Controllable genome editing with split-engineered base editors. Nat Chem Biol 2021; 17:1262-1270. [PMID: 34663942 PMCID: PMC8981362 DOI: 10.1038/s41589-021-00880-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022]
Abstract
DNA deaminase enzymes play key roles in immunity and have recently been harnessed for their biotechnological applications. In base editors (BEs), the combination of DNA deaminase mutator activity with CRISPR-Cas localization confers the powerful ability to directly convert one target DNA base into another. While efforts have been made to improve targeting efficiency and precision, all BEs so far use a constitutively active DNA deaminase. The absence of regulatory control over promiscuous deaminase activity remains a major limitation to accessing the widespread potential of BEs. Here, we reveal sites that permit splitting of DNA cytosine deaminases into two inactive fragments, whose reapproximation reconstitutes activity. These findings allow for the development of split-engineered BEs (seBEs), which newly enable small-molecule control over targeted mutator activity. We show that the seBE strategy facilitates robust regulated editing with BE scaffolds containing diverse deaminases, offering a generalizable solution for temporally controlling precision genome editing.
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1562
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Gökçe F, Ravaynia PS, Modena MM, Hierlemann A. What is the future of electrical impedance spectroscopy in flow cytometry? BIOMICROFLUIDICS 2021; 15:061302. [PMID: 34917226 PMCID: PMC8651262 DOI: 10.1063/5.0073457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/02/2023]
Abstract
More than 20 years ago, electrical impedance spectroscopy (EIS) was proposed as a potential characterization method for flow cytometry. As the setup is comparably simple and the method is label-free, EIS has attracted considerable interest from the research community as a potential alternative to standard optical methods, such as fluorescence-activated cell sorting (FACS). However, until today, FACS remains by and large the laboratory standard with highly developed capabilities and broad use in research and clinical settings. Nevertheless, can EIS still provide a complement or alternative to FACS in specific applications? In this Perspective, we will give an overview of the current state of the art of EIS in terms of technologies and capabilities. We will then describe recent advances in EIS-based flow cytometry, compare the performance to that of FACS methods, and discuss potential prospects of EIS in flow cytometry.
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Affiliation(s)
- Furkan Gökçe
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Paolo S. Ravaynia
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mario M. Modena
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andreas Hierlemann
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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1563
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Azoxystrobin Impairs Neuronal Migration and Induces ROS Dependent Apoptosis in Cortical Neurons. Int J Mol Sci 2021; 22:ijms222212495. [PMID: 34830376 PMCID: PMC8622671 DOI: 10.3390/ijms222212495] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Fungicides often cause genotoxic stress and neurodevelopmental disorders such as autism (ASD). Fungicide-azoxystrobin (AZOX) showed acute and chronic toxicity to various organisms, and remained a concern for ill effects in developing neurons. We evaluated the neurotoxicity of AZOX in developing mouse brains, and observed prenatal exposure to AZOX reduced neuronal viability, neurite outgrowth, and cortical migration process in developing brains. The 50% inhibitory concentration (IC50) of AZOX for acute (24 h) and chronic (7 days) exposures were 30 and 10 μM, respectively. Loss in viability was due to the accumulation of reactive oxygen species (ROS), and inhibited neurite outgrowth was due to the deactivation of mTORC1 kinase activity. Pretreatment with ROS scavenger- N-acetylcysteine (NAC) reserved the viability loss and forced activation of mTORC1 kinase revived the neurite outgrowth in AZOX treated neurons. Intra-amniotic injection of AZOX coupled with in utero electroporation of GFP-labelled plasmid in E15.5 mouse was performed and 20 mg/kg AZOX inhibited radial neuronal migration. Moreover, the accumulation of mitochondria was significantly reduced in AZOX treated primary neurons, indicative of mitochondrial deactivation and induction of apoptosis, which was quantified by Bcl2/Bax ratio and caspase 3 cleavage assay. This study elucidated the neurotoxicity of AZOX and explained the possible cure from it.
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1564
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The molecular mechanisms of ferroptosis and its role in cardiovascular disease. Biomed Pharmacother 2021; 145:112423. [PMID: 34800783 DOI: 10.1016/j.biopha.2021.112423] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023] Open
Abstract
Ferroptosis is a programmed iron-dependent cell death characterized by accumulation of lipid peroxides (LOOH) and redox disequilibrium. Ferroptosis shows unique characteristics in biology, chemistry, and gene levels, compared to other cell death forms. The metabolic disorder of intracellular LOOH catalyzed by iron causes the inactivity of GPX4, disrupts the redox balance, and triggers cell death. Metabolism of amino acid, iron, and lipid, including associated pathways, is considered as a specific hallmark of ferroptosis. Epidemiological studies and animal experiments have shown that ferroptosis plays an important character in the pathophysiology of cardiovascular disease such as atherosclerosis, myocardial infarction (MI), ischemia/reperfusion (I/R), heart failure (HF), cardiac hypertrophy, cardiomyopathy, and abdominal aortic aneurysm (AAA). This review systematically summarized the latest research progress on the mechanisms of ferroptosis. Then we report the contribution of ferroptosis in cardiovascular diseases. Finally, we discuss and analyze the therapeutic approaches targeting for ferroptosis associated with cardiovascular diseases.
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1565
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Thevis M, Kuuranne T, Geyer H. Annual banned-substance review: Analytical approaches in human sports drug testing 2020/2021. Drug Test Anal 2021; 14:7-30. [PMID: 34788500 DOI: 10.1002/dta.3199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Most core areas of anti-doping research exploit and rely on analytical chemistry, applied to studies aiming at further improving the test methods' analytical sensitivity, the assays' comprehensiveness, the interpretation of metabolic profiles and patterns, but also at facilitating the differentiation of natural/endogenous substances from structurally identical but synthetically derived compounds and comprehending the athlete's exposome. Further, a continuously growing number of advantages of complementary matrices such as dried blood spots have been identified and transferred from research to sports drug testing routine applications, with an overall gain of valuable additions to the anti-doping field. In this edition of the annual banned-substance review, literature on recent developments in anti-doping published between October 2020 and September 2021 is summarized and discussed, particularly focusing on human doping controls and potential applications of new testing strategies to substances and methods of doping specified in the World Anti-Doping Agency's 2021 Prohibited List.
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Affiliation(s)
- Mario Thevis
- Center for Preventive Doping Research, Institute of Biochemistry, German Sport University Cologne, Cologne, Germany.,European Monitoring Center for Emerging Doping Agents, Cologne, Germany
| | - Tiia Kuuranne
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine, Genève and Lausanne, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Epalinges, Switzerland
| | - Hans Geyer
- Center for Preventive Doping Research, Institute of Biochemistry, German Sport University Cologne, Cologne, Germany.,European Monitoring Center for Emerging Doping Agents, Cologne, Germany
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1566
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Doyle SE, Snow F, Duchi S, O’Connell CD, Onofrillo C, Di Bella C, Pirogova E. 3D Printed Multiphasic Scaffolds for Osteochondral Repair: Challenges and Opportunities. Int J Mol Sci 2021; 22:12420. [PMID: 34830302 PMCID: PMC8622524 DOI: 10.3390/ijms222212420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/19/2022] Open
Abstract
Osteochondral (OC) defects are debilitating joint injuries characterized by the loss of full thickness articular cartilage along with the underlying calcified cartilage through to the subchondral bone. While current surgical treatments can provide some relief from pain, none can fully repair all the components of the OC unit and restore its native function. Engineering OC tissue is challenging due to the presence of the three distinct tissue regions. Recent advances in additive manufacturing provide unprecedented control over the internal microstructure of bioscaffolds, the patterning of growth factors and the encapsulation of potentially regenerative cells. These developments are ushering in a new paradigm of 'multiphasic' scaffold designs in which the optimal micro-environment for each tissue region is individually crafted. Although the adoption of these techniques provides new opportunities in OC research, it also introduces challenges, such as creating tissue interfaces, integrating multiple fabrication techniques and co-culturing different cells within the same construct. This review captures the considerations and capabilities in developing 3D printed OC scaffolds, including materials, fabrication techniques, mechanical function, biological components and design.
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Affiliation(s)
- Stephanie E. Doyle
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000, Australia; (F.S.)
- ACMD, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia; (S.D.); (C.O.); (C.D.B.)
| | - Finn Snow
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000, Australia; (F.S.)
| | - Serena Duchi
- ACMD, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia; (S.D.); (C.O.); (C.D.B.)
- Department of Surgery, The University of Melbourne, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Cathal D. O’Connell
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000, Australia; (F.S.)
- ACMD, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia; (S.D.); (C.O.); (C.D.B.)
| | - Carmine Onofrillo
- ACMD, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia; (S.D.); (C.O.); (C.D.B.)
- Department of Surgery, The University of Melbourne, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Claudia Di Bella
- ACMD, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia; (S.D.); (C.O.); (C.D.B.)
- Department of Surgery, The University of Melbourne, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia
- Department of Orthopaedics, St Vincent’s Hospital Melbourne, Fitzroy, VIC 3065, Australia
| | - Elena Pirogova
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC 3000, Australia; (F.S.)
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1567
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Intracellular nanoscale architecture as a master regulator of calcium carbonate crystallization in marine microalgae. Proc Natl Acad Sci U S A 2021; 118:2025670118. [PMID: 34772804 DOI: 10.1073/pnas.2025670118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2021] [Indexed: 11/18/2022] Open
Abstract
Unicellular marine microalgae are responsible for one of the largest carbon sinks on Earth. This is in part due to intracellular formation of calcium carbonate scales termed coccoliths. Traditionally, the influence of changing environmental conditions on this process has been estimated using poorly constrained analogies to crystallization mechanisms in bulk solution, yielding ambiguous predictions. Here, we elucidated the intracellular nanoscale environment of coccolith formation in the model species Pleurochrysis carterae using cryoelectron tomography. By visualizing cells at various stages of the crystallization process, we reconstructed a timeline of coccolith development. The three-dimensional data portray the native-state structural details of coccolith formation, uncovering the crystallization mechanism, and how it is spatially and temporally controlled. Most strikingly, the developing crystals are only tens of nanometers away from delimiting membranes, resulting in a highly confined volume for crystal growth. We calculate that the number of soluble ions that can be found in such a minute volume at any given time point is less than the number needed to allow the growth of a single atomic layer of the crystal and that the uptake of single protons can markedly affect nominal pH values. In such extreme confinement, the crystallization process is expected to depend primarily on the regulation of ion fluxes by the living cell, and nominal ion concentrations, such as pH, become the result, rather than a driver, of the crystallization process. These findings call for a new perspective on coccolith formation that does not rely exclusively on solution chemistry.
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1568
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Coentro JQ, May U, Prince S, Zwaagstra J, Ritvos O, Järvinen TAH, Zeugolis DI. Adapting the Scar-in-a-Jar to Skin Fibrosis and Screening Traditional and Contemporary Anti-Fibrotic Therapies. Front Bioeng Biotechnol 2021; 9:756399. [PMID: 34765594 PMCID: PMC8576412 DOI: 10.3389/fbioe.2021.756399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/11/2021] [Indexed: 12/14/2022] Open
Abstract
Skin fibrosis still constitutes an unmet clinical need. Although pharmacological strategies are at the forefront of scientific and technological research and innovation, their clinical translation is hindered by the poor predictive capacity of the currently available in vitro fibrosis models. Indeed, customarily utilised in vitro scarring models are conducted in a low extracellular matrix milieu, which constitutes an oxymoron for the in-hand pathophysiology. Herein, we coupled macromolecular crowding (enhances and accelerates extracellular matrix deposition) with transforming growth factor β1 (TGFβ1; induces trans-differentiation of fibroblasts to myofibroblasts) in human dermal fibroblast cultures to develop a skin fibrosis in vitro model and to screen a range of anti-fibrotic families (corticosteroids, inhibitors of histone deacetylases, inhibitors of collagen crosslinking, inhibitors of TGFβ1 and pleiotropic inhibitors of fibrotic activation). Data obtained demonstrated that macromolecular crowding combined with TGFβ1 significantly enhanced collagen deposition and myofibroblast transformation. Among the anti-fibrotic compounds assessed, trichostatin A (inhibitors of histone deacetylases); serelaxin and pirfenidone (pleiotropic inhibitors of fibrotic activation); and soluble TGFβ receptor trap (inhibitor of TGFβ signalling) resulted in the highest decrease of collagen type I deposition (even higher than triamcinolone acetonide, the gold standard in clinical practice). This study further advocates the potential of macromolecular crowding in the development of in vitro pathophysiology models.
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Affiliation(s)
- João Q Coentro
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL) and Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), National University of Ireland Galway (NUI Galway), Galway, Ireland
| | - Ulrike May
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Stuart Prince
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - John Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | | | - Tero A H Järvinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Tampere University Hospital, Tampere, Finland
| | - Dimitrios I Zeugolis
- Regenerative, Modular and Developmental Engineering Laboratory (REMODEL) and Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), National University of Ireland Galway (NUI Galway), Galway, Ireland.,Regenerative, Modular and Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular and Biomedical Research and School of Mechanical and Materials Engineering, University College Dublin (UCD), Dublin, Ireland
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1569
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Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
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Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
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1570
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Park Y, Chung TS, Lee G, Rogers JA. Materials Chemistry of Neural Interface Technologies and Recent Advances in Three-Dimensional Systems. Chem Rev 2021; 122:5277-5316. [PMID: 34739219 DOI: 10.1021/acs.chemrev.1c00639] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Advances in materials chemistry and engineering serve as the basis for multifunctional neural interfaces that span length scales from individual neurons to neural networks, neural tissues, and complete neural systems. Such technologies exploit electrical, electrochemical, optical, and/or pharmacological modalities in sensing and neuromodulation for fundamental studies in neuroscience research, with additional potential to serve as routes for monitoring and treating neurodegenerative diseases and for rehabilitating patients. This review summarizes the essential role of chemistry in this field of research, with an emphasis on recently published results and developing trends. The focus is on enabling materials in diverse device constructs, including their latest utilization in 3D bioelectronic frameworks formed by 3D printing, self-folding, and mechanically guided assembly. A concluding section highlights key challenges and future directions.
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Affiliation(s)
- Yoonseok Park
- Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, Illinois 60208, United States
| | - Ted S Chung
- Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, Illinois 60208, United States.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Geumbee Lee
- Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, Illinois 60208, United States
| | - John A Rogers
- Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, Illinois 60208, United States.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.,Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Neurological Surgery, Northwestern University, Evanston, Illinois 60208, United States
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1571
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Frischmon C, Sorenson C, Winikoff M, Adamala KP. Build-a-Cell: Engineering a Synthetic Cell Community. Life (Basel) 2021; 11:life11111176. [PMID: 34833052 PMCID: PMC8618533 DOI: 10.3390/life11111176] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
Build-a-Cell is a global network of researchers that aims to develop synthetic living cells within the next decade. These cells will revolutionize the biotechnology industry by providing scientists and engineers with a more complete understanding of biology. Researchers can already replicate many cellular functions individually, but combining them into a single cell remains a significant challenge. This integration step will require the type of large-scale collaboration made possible by Build-a-Cell's open, collective structure. Beyond the lab, Build-a-Cell addresses policy issues and biosecurity concerns associated with synthetic cells. The following review discusses Build-a-Cell's history, function, and goals.
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Affiliation(s)
- Caroline Frischmon
- Science Communication Lab., BioTechnology Institute, University of Minnesota, Minneapolis, MN 55108, USA; (C.F.); (M.W.)
| | - Carlise Sorenson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Michael Winikoff
- Science Communication Lab., BioTechnology Institute, University of Minnesota, Minneapolis, MN 55108, USA; (C.F.); (M.W.)
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence:
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1572
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Collins JT, Knapper J, McDermott SJ, Ayazi F, Bumke KE, Stirling J, Bowman RW. Simplifying the OpenFlexure microscope software with the web of things. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211158. [PMID: 34804575 PMCID: PMC8595986 DOI: 10.1098/rsos.211158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
We present the OpenFlexure Microscope software stack which provides computer control of our open source motorised microscope. Our diverse community of users needs both graphical and script-based interfaces. We split the control code into client and server applications interfaced via a web API conforming to the W3C Web of Things standard. A graphical interface is viewed either in a web browser or in our cross-platform Electron application, and gives basic interactive control including common operations such as Z stack acquisition and tiled scanning. Automated control is possible from Python and Matlab, or any language that supports HTTP requests. Network control makes the software stack more robust, allows multiple microscopes to be controlled by one computer, and facilitates sharing of equipment. Graphical and script-based clients can run simultaneously, making it easier to monitor ongoing experiments. We have included an extension mechanism to add functionality, for example controlling additional hardware components or adding automation routines. Using a Web of Things approach has resulted in a user-friendly and extremely versatile software control solution for the OpenFlexure Microscope, and we believe this approach could be generalized in the future to make automated experiments involving several instruments much easier to implement.
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Affiliation(s)
- Joel T. Collins
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, UK
| | - Joe Knapper
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, UK
| | | | - Filip Ayazi
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Kaspar E. Bumke
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, UK
| | - Julian Stirling
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, UK
| | - Richard W. Bowman
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, UK
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1573
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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1574
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Zhuang P, Chiang YH, Fernanda MS, He M. Using Spheroids as Building Blocks Towards 3D Bioprinting of Tumor Microenvironment. Int J Bioprint 2021; 7:444. [PMID: 34805601 PMCID: PMC8600307 DOI: 10.18063/ijb.v7i4.444] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer still ranks as a leading cause of mortality worldwide. Although considerable efforts have been dedicated to anticancer therapeutics, progress is still slow, partially due to the absence of robust prediction models. Multicellular tumor spheroids, as a major three-dimensional (3D) culture model exhibiting features of avascular tumors, gained great popularity in pathophysiological studies and high throughput drug screening. However, limited control over cellular and structural organization is still the key challenge in achieving in vivo like tissue microenvironment. 3D bioprinting has made great strides toward tissue/organ mimicry, due to its outstanding spatial control through combining both cells and materials, scalability, and reproducibility. Prospectively, harnessing the power from both 3D bioprinting and multicellular spheroids would likely generate more faithful tumor models and advance our understanding on the mechanism of tumor progression. In this review, the emerging concept on using spheroids as a building block in 3D bioprinting for tumor modeling is illustrated. We begin by describing the context of the tumor microenvironment, followed by an introduction of various methodologies for tumor spheroid formation, with their specific merits and drawbacks. Thereafter, we present an overview of existing 3D printed tumor models using spheroids as a focus. We provide a compilation of the contemporary literature sources and summarize the overall advancements in technology and possibilities of using spheroids as building blocks in 3D printed tissue modeling, with a particular emphasis on tumor models. Future outlooks about the wonderous advancements of integrated 3D spheroidal printing conclude this review.
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Affiliation(s)
- Pei Zhuang
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, 32610, USA
| | - Yi-Hua Chiang
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, 32610, USA
| | | | - Mei He
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, 32610, USA
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1575
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Short-Time Impedance Spectroscopy Using a Mode-Switching Nonsinusoidal Oscillator: Applicability to Biological Tissues and Continuous Measurement. SENSORS 2021; 21:s21216951. [PMID: 34770258 PMCID: PMC8587290 DOI: 10.3390/s21216951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 01/04/2023]
Abstract
Herein, we propose an impedance spectroscopy method using a mode-switching nonsinusoidal oscillator and apply this method for measuring the impedance of biological tissues and continuous impedance measurement. To obtain impedance spectra over a wide frequency range, we fabricated a novel nonsinusoidal oscillator incorporating binary counters and analog switches. This oscillator could periodically switch oscillation frequency through the mode switching of the feedback resistor. From the oscillation waveform at each oscillation frequency of this circuit (oscillator), we determined the impedance spectrum of a measured object using the discrete-time Fourier transform. Subsequently, we obtained the broad impedance spectrum of the measured object by merging odd-order harmonic spectral components up to the 19th order for each oscillation frequency. From the measured spectrum, the resistive and capacitive components of the circuit simulating bioimpedance were estimated with high accuracy. Moreover, the proposed method was used to measure the impedance of porcine myocardium; changes in the impedance spectrum of the myocardial tissue due to coagulation could be measured. Furthermore, rapid variations in the resistance value of a CdS photocell could be continuously measured using the proposed method.
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1576
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Rens EG, Edelstein-Keshet L. Cellular Tango: how extracellular matrix adhesion choreographs Rac-Rho signaling and cell movement. Phys Biol 2021; 18. [PMID: 34544056 DOI: 10.1088/1478-3975/ac2888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022]
Abstract
The small GTPases Rac and Rho are known to regulate eukaryotic cell shape, promoting front protrusion (Rac) or rear retraction (Rho) of the cell edge. Such cell deformation changes the contact and adhesion of cell to the extracellular matrix (ECM), while ECM signaling through integrin receptors also affects GTPase activity. We develop and investigate a model for this three-way feedback loop in 1D and 2D spatial domains, as well as in a fully deforming 2D cell shapes with detailed adhesion-bond biophysics. The model consists of reaction-diffusion equations solved numerically with open-source software, Morpheus, and with custom-built cellular Potts model simulations. We find a variety of patterns and cell behaviors, including persistent polarity, flipped front-back cell polarity oscillations, spiral waves, and random protrusion-retraction. We show that the observed spatial patterns depend on the cell shape, and vice versa.
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Affiliation(s)
- Elisabeth G Rens
- Delft Institute of Applied Mathematics, Delft University of Technology, Delft, The Netherlands.,Department of Mathematics, University of British Columbia, Vancouver, Canada
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1577
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Song J, Choi H, Koh SK, Park D, Yu J, Kang H, Kim Y, Cho D, Jeon NL. High-Throughput 3D In Vitro Tumor Vasculature Model for Real-Time Monitoring of Immune Cell Infiltration and Cytotoxicity. Front Immunol 2021; 12:733317. [PMID: 34630415 PMCID: PMC8500473 DOI: 10.3389/fimmu.2021.733317] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/03/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in anticancer therapy have shown dramatic improvements in clinical outcomes, and adoptive cell therapy has emerged as a type of immunotherapy that can modulate immune responses by transferring engineered immune cells. However, a small percentage of responders and their toxicity remain as challenges. Three-dimensional (3D) in vitro models of the tumor microenvironment (TME) have the potential to provide a platform for assessing and predicting responses to therapy. This paper describes an in vitro 3D tumor model that incorporates clusters of colorectal cancer (CRC) cells around perfusable vascular networks to validate immune-cell-mediated cytotoxicity against cancer cells. The platform is based on an injection-molded 3D co-culture model and composed of 28 microwells where separate identical vascularized cancer models can be formed. It allows robust hydrogel patterning for 3D culture that enables high-throughput experimentation. The uniformity of the devices resulted in reproducible experiments that allowed 10× more experiments to be performed when compared to conventional polydimethylsiloxane (PDMS)-based microfluidic devices. To demonstrate its capability, primary natural killer (NK) cells were introduced into the vascularized tumor network, and their activities were monitored using live-cell imaging. Extravasation, migration, and cytotoxic activity against six types of CRC cell lines were tested and compared. The consensus molecular subtypes (CMS) of CRC with distinct immune responses resulted in the highest NK cell cytotoxicity against CMS1 cancer cells. These results show the potential of our vascularized tumor model for understanding various steps involved in the immune response for the assessment of adoptive cell therapy.
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Affiliation(s)
- Jiyoung Song
- Department of Mechanical Engineering, Seoul National University, Seoul, South Korea
| | - Hyeri Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Seung Kwon Koh
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
| | - Dohyun Park
- Department of Mechanical Engineering, Seoul National University, Seoul, South Korea
| | - James Yu
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Habin Kang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Youngtaek Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, South Korea
| | - Duck Cho
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea.,Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Noo Li Jeon
- Department of Mechanical Engineering, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea.,Institute of Advanced Machines and Design (SNU-IAMD), Seoul National University, Seoul, South Korea
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1578
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Moschetta M, Chiacchiaretta M, Cesca F, Roy I, Athanassiou A, Benfenati F, Papadopoulou EL, Bramini M. Graphene Nanoplatelets Render Poly(3-Hydroxybutyrate) a Suitable Scaffold to Promote Neuronal Network Development. Front Neurosci 2021; 15:731198. [PMID: 34616276 PMCID: PMC8488094 DOI: 10.3389/fnins.2021.731198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/13/2021] [Indexed: 12/22/2022] Open
Abstract
The use of composite biomaterials as innovative bio-friendly neuronal interfaces has been poorly developed so far. Smart strategies to target neuro-pathologies are currently exploiting the mixed and complementary characteristics of composite materials to better design future neural interfaces. Here we present a polymer-based scaffold that has been rendered suitable for primary neurons by embedding graphene nanoplatelets (GnP). In particular, the growth, network formation, and functionality of primary neurons on poly(3-hydroxybutyrate) [P(3HB)] polymer supports functionalized with various concentrations of GnP were explored. After growing primary cortical neurons onto the supports for 14 days, all specimens were found to be biocompatible, revealing physiological growth and maturation of the neuronal network. When network functionality was investigated by whole patch-clamp measurements, pure P(3HB) led to changes in the action potential waveform and reduction in firing frequency, resulting in decreased neuronal excitability. However, the addition of GnP to the polymer matrix restored the electrophysiological parameters to physiological values. Interestingly, a low concentration of graphene was able to promote firing activity at a low level of injected current. The results indicate that the P(3HB)/GnP composites show great potential for electrical interfacing with primary neurons to eventually target central nervous system disorders.
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Affiliation(s)
- Matteo Moschetta
- Center for Synaptic Neuroscience and Technologies, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Martina Chiacchiaretta
- Center for Synaptic Neuroscience and Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Ipsita Roy
- Department of Materials Science and Engineering, Faculty of Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technologies, Istituto Italiano di Tecnologia, Genova, Italy.,IRCSS, Ospedale Policlinico San Martino, Genova, Italy
| | | | - Mattia Bramini
- Center for Synaptic Neuroscience and Technologies, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Cell Biology, Faculty of Science, University of Granada, Granada, Spain
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1579
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Flavonoids against non-physiologic inflammation attributed to cancer initiation, development, and progression—3PM pathways. EPMA J 2021; 12:559-587. [PMID: 34950252 PMCID: PMC8648878 DOI: 10.1007/s13167-021-00257-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022]
Abstract
AbstractInflammation is an essential pillar of the immune defense. On the other hand, chronic inflammation is considered a hallmark of cancer initiation and progression. Chronic inflammation demonstrates a potential to induce complex changes at molecular, cellular, and organ levels including but not restricted to the stagnation and impairment of healing processes, uncontrolled production of aggressive ROS/RNS, triggered DNA mutations and damage, compromised efficacy of the DNA repair machinery, significantly upregulated cytokine/chemokine release and associated patho-physiologic protein synthesis, activated signaling pathways involved in carcinogenesis and tumor progression, abnormal tissue remodeling, and created pre-metastatic niches, among others. The anti-inflammatory activities of flavonoids demonstrate clinically relevant potential as preventive and therapeutic agents to improve individual outcomes in diseases linked to the low-grade systemic and chronic inflammation, including cancers. To this end, flavonoids are potent modulators of pro-inflammatory gene expression being, therefore, of great interest as agents selectively suppressing molecular targets within pro-inflammatory pathways. This paper provides in-depth analysis of anti-inflammatory properties of flavonoids, highlights corresponding mechanisms and targeted molecular pathways, and proposes potential treatment models for multi-level cancer prevention in the framework of predictive, preventive, and personalized medicine (PPPM / 3PM). To this end, individualized profiling and patient stratification are essential for implementing targeted anti-inflammatory approaches. Most prominent examples are presented for the proposed application of flavonoid-conducted anti-inflammatory treatments in overall cancer management.
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1580
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Nokhbatolfoghahaei H, Rad MR, Paknejad Z, Ardeshirylajimi A, Khojasteh A. Identification osteogenic signaling pathways following mechanical stimulation: A systematic review. Curr Stem Cell Res Ther 2021; 17:772-792. [PMID: 34615453 DOI: 10.2174/1574888x16666211006105915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022]
Abstract
INTRODUCTION It has been shown that mechanical forces can induce or promote osteogenic differentiation as well as remodeling of the new created bone tissues. To apply this characteristic in bone tissue engineering, it is important to know which mechanical stimuli through which signaling pathway has a more significant impact on osteogenesis. METHODS In this systematic study, an electronic search was conducted using PubMed and Google Scholar databases. This study has been prepared and organized according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Included studies were first categorized according to the in vivo and in vitro studies. RESULTS Six types of mechanical stresses were used in these articles and the most commonly used mechanical force and cell source were tension and bone marrow-derived mesenchymal stem cells (BMMSCs), respectively. These forces were able to trigger twelve signaling pathways in which Wnt pathway was so prominent. CONCLUSION 1) Although specific signaling pathways are induced through specific mechanical forces, Wnt signaling pathways are predominantly activated by almost all types of force/stimulation, 2) All signaling pathways regulate expression of RUNX2, which is known as a master regulator of osteogenesis, 3) In Tension force, the mode of force administration, i.e, continuous or non-continuous tension is more important than the percentage of elongation.
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Affiliation(s)
- Hanieh Nokhbatolfoghahaei
- Dental Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Maryam Rezai Rad
- Dental Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Zahrasadat Paknejad
- Medical nanotechnology and tissue engineering research Center, Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Abdolreza Ardeshirylajimi
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran. Iran
| | - Arash Khojasteh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran. Iran
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1581
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Woloschuk RM, Reed PMM, Jaikaran ASI, Demmans KZ, Youn J, Kanelis V, Uppalapati M, Woolley GA. Structure-based design of a photoswitchable affibody scaffold. Protein Sci 2021; 30:2359-2372. [PMID: 34590762 DOI: 10.1002/pro.4196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Photo-control of affinity reagents offers a general approach for high-resolution spatiotemporal control of diverse molecular processes. In an effort to develop general design principles for a photo-controlled affinity reagent, we took a structure-based approach to the design of a photoswitchable Z-domain, among the simplest of affinity reagent scaffolds. A chimera, designated Z-PYP, of photoactive yellow protein (PYP) and the Z-domain, was designed based on the concept of mutually exclusive folding. NMR analysis indicated that, in the dark, the PYP domain of the chimera was folded, and the Z-domain was unfolded. Blue light caused loss of structure in PYP and a two- to sixfold change in the apparent affinity of Z-PYP for its target as determined using size exclusion chromatography, UV-Vis based assays, and enyzme-linked immunosorbent assay (ELISA). A thermodynamic model indicated that mutations to decrease Z-domain folding energy would alter target affinity without loss of switching. This prediction was confirmed experimentally with a double alanine mutant in helix 3 of the Z-domain of the chimera (Z-PYP-AA) showing >30-fold lower dark-state binding and no loss in switching. The effect of decreased dark-state binding affinity was tested in a two-hybrid transcriptional control format and enabled pronounced light/dark differences in yeast growth in vivo. Finally, the design was transferable to the αZ-Taq affibody enabling tunable light-dependent binding both in vitro and in vivo to the Z-Taq target. This system thus provides a framework for the focused development of light switchable affibodies for a range of targets.
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Affiliation(s)
- Ryan M Woloschuk
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna S I Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karl Z Demmans
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey Youn
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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1582
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Chen X, Kang R, Kroemer G, Tang D. Organelle-specific regulation of ferroptosis. Cell Death Differ 2021; 28:2843-2856. [PMID: 34465893 PMCID: PMC8481335 DOI: 10.1038/s41418-021-00859-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Ferroptosis, a cell death modality characterized by iron-dependent lipid peroxidation, is involved in the development of multiple pathological conditions, including ischemic tissue damage, infection, neurodegeneration, and cancer. The cellular machinery responsible for the execution of ferroptosis integrates multiple pro-survival or pro-death signals from subcellular organelles and then 'decides' whether to engage the lethal process or not. Here, we outline the evidence implicating different organelles (including mitochondria, lysosomes, endoplasmic reticulum, lipid droplets, peroxisomes, Golgi apparatus, and nucleus) in the ignition or avoidance of ferroptosis, while emphasizing their potential relevance for human disease and their targetability for pharmacological interventions.
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Affiliation(s)
- Xin Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, The Third Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| | - Daolin Tang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, The Third Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA.
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1583
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Mariano A, Lubrano C, Bruno U, Ausilio C, Dinger NB, Santoro F. Advances in Cell-Conductive Polymer Biointerfaces and Role of the Plasma Membrane. Chem Rev 2021; 122:4552-4580. [PMID: 34582168 PMCID: PMC8874911 DOI: 10.1021/acs.chemrev.1c00363] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The plasma membrane
(PM) is often described as a wall, a physical
barrier separating the cell cytoplasm from the extracellular matrix
(ECM). Yet, this wall is a highly dynamic structure that can stretch,
bend, and bud, allowing cells to respond and adapt to their surrounding
environment. Inspired by shapes and geometries found in the biological
world and exploiting the intrinsic properties of conductive polymers
(CPs), several biomimetic strategies based on substrate dimensionality
have been tailored in order to optimize the cell–chip coupling.
Furthermore, device biofunctionalization through the use of ECM proteins
or lipid bilayers have proven successful approaches to further maximize
interfacial interactions. As the bio-electronic field aims at narrowing
the gap between the electronic and the biological world, the possibility
of effectively disguising conductive materials to “trick”
cells to recognize artificial devices as part of their biological
environment is a promising approach on the road to the seamless platform
integration with cells.
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Affiliation(s)
- Anna Mariano
- Tissue Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy
| | - Claudia Lubrano
- Tissue Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy.,Dipartimento di Chimica, Materiali e Produzione Industriale, Università di Napoli Federico II, 80125 Naples, Italy
| | - Ugo Bruno
- Tissue Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy.,Dipartimento di Chimica, Materiali e Produzione Industriale, Università di Napoli Federico II, 80125 Naples, Italy
| | - Chiara Ausilio
- Tissue Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy
| | - Nikita Bhupesh Dinger
- Tissue Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy.,Dipartimento di Chimica, Materiali e Produzione Industriale, Università di Napoli Federico II, 80125 Naples, Italy
| | - Francesca Santoro
- Tissue Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy
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1584
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Kumar S, Rullan M, Khammash M. Rapid prototyping and design of cybergenetic single-cell controllers. Nat Commun 2021; 12:5651. [PMID: 34561433 PMCID: PMC8463601 DOI: 10.1038/s41467-021-25754-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
The design and implementation of synthetic circuits that operate robustly in the cellular context is fundamental for the advancement of synthetic biology. However, their practical implementation presents challenges due to low predictability of synthetic circuit design and time-intensive troubleshooting. Here, we present the Cyberloop, a testing framework to accelerate the design process and implementation of biomolecular controllers. Cellular fluorescence measurements are sent in real-time to a computer simulating candidate stochastic controllers, which in turn compute the control inputs and feed them back to the controlled cells via light stimulation. Applying this framework to yeast cells engineered with optogenetic tools, we examine and characterize different biomolecular controllers, test the impact of non-ideal circuit behaviors such as dilution on their operation, and qualitatively demonstrate improvements in controller function with certain network modifications. From this analysis, we derive conditions for desirable biomolecular controller performance, thereby avoiding pitfalls during its biological implementation.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Marc Rullan
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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1585
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Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1694. [PMID: 34553495 DOI: 10.1002/wrna.1694] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cell-free environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Martyna Kordyś
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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1586
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Harberts J, Siegmund M, Schnelle M, Zhang T, Lei Y, Yu L, Zierold R, Blick RH. Robust neuronal differentiation of human iPSC-derived neural progenitor cells cultured on densely-spaced spiky silicon nanowire arrays. Sci Rep 2021; 11:18819. [PMID: 34552130 PMCID: PMC8458299 DOI: 10.1038/s41598-021-97820-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/29/2021] [Indexed: 11/12/2022] Open
Abstract
Nanostructured cell culture substrates featuring nanowire (NW) arrays have been applied to a variety of basic cell lines and rodent neurons to investigate cellular behavior or to stimulate cell responses. However, patient-derived human neurons-a prerequisite for studying e.g. neurodegenerative diseases efficiently-are rarely employed due to sensitive cell culture protocols and usually long culturing periods. Here, we present human patient induced pluripotent stem cell-derived neurons cultured on densely-spaced spiky silicon NW arrays (600 NWs/ 100 µm[Formula: see text] with NW lengths of 1 µm) which show mature electrophysiological characteristics after only 20 days of culturing. Exemplary neuronal growth and network formation on the NW arrays are demonstrated using scanning electron microscopy and immunofluorescence microscopy. The cells and neurites rest in a fakir-like settling state on the NWs only in contact with the very NW tips shown by cross-sectional imaging of the cell/NW interface using focused ion beam milling and confocal laser scanning microscopy. Furthermore, the NW arrays promote the cell culture by slightly increasing the share of differentiated neurons determined by the quantification of immunofluorescence microscopy images. The electrophysiological functionality of the neurons is confirmed with patch-clamp recordings showing the excellent capability to fire action potentials. We believe that the short culturing time to obtain functional human neurons generated from patient-derived neural progenitor cells and the robustness of this differentiation protocol to produce these neurons on densely-spaced spiky nanowire arrays open up new pathways for stem cell characterization and neurodegenerative disease studies.
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Affiliation(s)
- Jann Harberts
- Center for Hybrid Nanostructures, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Malte Siegmund
- Center for Hybrid Nanostructures, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Matteo Schnelle
- Center for Hybrid Nanostructures, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Ting Zhang
- School of Electronics Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Yakui Lei
- School of Electronics Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Linwei Yu
- School of Electronics Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Robert Zierold
- Center for Hybrid Nanostructures, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Robert H Blick
- Center for Hybrid Nanostructures, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Material Science and Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
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1587
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Wilson LT, Tipping WJ, Wetherill C, Henley Z, Faulds K, Graham D, Mackay SP, Tomkinson NCO. Mitokyne: A Ratiometric Raman Probe for Mitochondrial pH. Anal Chem 2021; 93:12786-12792. [PMID: 34505518 DOI: 10.1021/acs.analchem.1c03075] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondrial pH (pHmito) is intimately related to mitochondrial function, and aberrant values for pHmito are linked to several disease states. We report the design, synthesis, and application of mitokyne 1-the first small molecule pHmito sensor for stimulated Raman scattering (SRS) microscopy. This ratiometric probe can determine subtle changes in pHmito in response to external stimuli and the inhibition of both the electron transport chain and ATP synthase with small molecule inhibitors. In addition, 1 was also used to monitor mitochondrial dynamics in a time-resolved manner with subcellular spatial resolution during mitophagy providing a powerful tool for dissecting the molecular and cell biology of this critical organelle.
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Affiliation(s)
- Liam T Wilson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - William J Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Zoë Henley
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Simon P Mackay
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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1588
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Kim J, Jang J, Cho DW. Recapitulating the Cancer Microenvironment Using Bioprinting Technology for Precision Medicine. MICROMACHINES 2021; 12:1122. [PMID: 34577765 PMCID: PMC8472267 DOI: 10.3390/mi12091122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 12/20/2022]
Abstract
The complex and heterogenous nature of cancer contributes to the development of cancer cell drug resistance. The construction of the cancer microenvironment, including the cell-cell interactions and extracellular matrix (ECM), plays a significant role in the development of drug resistance. Traditional animal models used in drug discovery studies have been associated with feasibility issues that limit the recapitulation of human functions; thus, in vitro models have been developed to reconstruct the human cancer system. However, conventional two-dimensional and three-dimensional (3D) in vitro cancer models are limited in their ability to emulate complex cancer microenvironments. Advances in technologies, including bioprinting and cancer microenvironment reconstruction, have demonstrated the potential to overcome some of the limitations of conventional models. This study reviews some representative bioprinted in vitro models used in cancer research, particularly fabrication strategies for modeling and consideration of essential factors needed for the reconstruction of the cancer microenvironment. In addition, we highlight recent studies that applied such models, including application in precision medicine using advanced bioprinting technologies to fabricate biomimetic cancer models. Furthermore, we discuss current challenges in 3D bioprinting and suggest possible strategies to construct in vitro models that better mimic the pathophysiology of the cancer microenvironment for application in clinical settings.
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Affiliation(s)
- Jisoo Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea;
| | - Jinah Jang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea;
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Department of Creative IT Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul 03722, Korea
| | - Dong-Woo Cho
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea;
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul 03722, Korea
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1589
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Luo Z, Zhou X, Mandal K, He N, Wennerberg W, Qu M, Jiang X, Sun W, Khademhosseini A. Reconstructing the tumor architecture into organoids. Adv Drug Deliv Rev 2021; 176:113839. [PMID: 34153370 PMCID: PMC8560135 DOI: 10.1016/j.addr.2021.113839] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023]
Abstract
Cancer remains a leading health burden worldwide. One of the challenges hindering cancer therapy development is the substantial discrepancies between the existing cancer models and the tumor microenvironment (TME) of human patients. Constructing tumor organoids represents an emerging approach to recapitulate the pathophysiological features of the TME in vitro. Over the past decade, various approaches have been demonstrated to engineer tumor organoids as in vitro cancer models, such as incorporating multiple cellular populations, reconstructing biophysical and chemical traits, and even recapitulating structural features. In this review, we focus on engineering approaches for building tumor organoids, including biomaterial-based, microfabrication-assisted, and synthetic biology-facilitated strategies. Furthermore, we summarize the applications of engineered tumor organoids in basic cancer research, cancer drug discovery, and personalized medicine. We also discuss the challenges and future opportunities in using tumor organoids for broader applications.
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Affiliation(s)
- Zhimin Luo
- Department of Bioengineering, California NanoSystems Institute and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, CA 90095, USA; School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xingwu Zhou
- Department of Bioengineering, California NanoSystems Institute and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kalpana Mandal
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90064, USA
| | - Na He
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Wally Wennerberg
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90064, USA
| | - Moyuan Qu
- Department of Bioengineering, California NanoSystems Institute and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, and Cancer Center of Zhejiang University, Hangzhou 310006, China
| | - Xing Jiang
- Department of Bioengineering, California NanoSystems Institute and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, CA 90095, USA; School of Nursing, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wujin Sun
- Department of Bioengineering, California NanoSystems Institute and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90064, USA.
| | - Ali Khademhosseini
- Department of Bioengineering, California NanoSystems Institute and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90064, USA; Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, Department of Radiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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1590
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Lin W, Gandhi S, Oviedo Lara AR, Thomas AK, Helbig R, Zhang Y. Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102349. [PMID: 34309086 DOI: 10.1002/adma.202102349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Indexed: 06/13/2023]
Abstract
The in situ synthesis of biomolecules on glass surfaces for direct bioscreening can be a powerful tool in the fields of pharmaceutical sciences, biomaterials, and chemical biology. However, it is still challenging to 1) achieve this conventional multistep combinatorial synthesis on glass surfaces with small feature sizes and high yields and 2) develop a surface which is compatible with solid-phase syntheses, as well as the subsequent bioscreening. This work reports an amphiphilic coating of a glass surface on which small droplets of polar aprotic organic solvents can be deposited with an enhanced contact angle and inhibited motion to permit fully automated multiple rounds of the combinatorial synthesis of small-molecule compounds and peptides. This amphiphilic coating can be switched into a hydrophilic network for protein- and cell-based screening. Employing this in situ synthesis method, chemical space can be probed via array technology with unprecedented speed for various applications, such as lead discovery/optimization in medicinal chemistry and biomaterial development.
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Affiliation(s)
- Weilin Lin
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Shanil Gandhi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alan Rodrigo Oviedo Lara
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alvin K Thomas
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Hohe Strasse 6, 01069, Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence "Physics of Life", Technische Universität Dresden, 01062, Dresden, Germany
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1591
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Manoilov KY, Verkhusha VV, Shcherbakova DM. A guide to the optogenetic regulation of endogenous molecules. Nat Methods 2021; 18:1027-1037. [PMID: 34446923 DOI: 10.1038/s41592-021-01240-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/09/2021] [Indexed: 12/26/2022]
Abstract
Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs.
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Affiliation(s)
- Kyrylo Yu Manoilov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Science Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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1592
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Shin HJ, Ku KB, Kim HS, Moon HW, Jeong GU, Hwang I, Yoon GY, Lee S, Lee S, Ahn DG, Kim KD, Kwon YC, Kim BT, Kim SJ, Kim C. Receptor-binding domain of SARS-CoV-2 spike protein efficiently inhibits SARS-CoV-2 infection and attachment to mouse lung. Int J Biol Sci 2021; 17:3786-3794. [PMID: 34671199 PMCID: PMC8495392 DOI: 10.7150/ijbs.61320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/13/2021] [Indexed: 01/05/2023] Open
Abstract
COVID-19, caused by a novel coronavirus, SARS-CoV-2, poses a serious global threat. It was first reported in 2019 in China and has now dramatically spread across the world. It is crucial to develop therapeutics to mitigate severe disease and viral spread. The receptor-binding domains (RBDs) in the spike protein of SARS-CoV and MERS-CoV have shown anti-viral activity in previous reports suggesting that this domain has high potential for development as therapeutics. To evaluate the potential antiviral activity of recombinant SARS-CoV-2 RBD proteins, we determined the RBD residues of SARS-CoV-2 using a homology search with RBD of SARS-CoV. For efficient expression and purification, the signal peptide of spike protein was identified and used to generate constructs expressing recombinant RBD proteins. Highly purified RBD protein fused with the Fc domain of human IgG showed potent anti-viral efficacy, which was better than that of a protein fused with a histidine tag. Intranasally pre-administrated RBD protein also inhibited the attachment of SARS-COV-2 to mouse lungs. These findings indicate that RBD protein could be used for the prevention and treatment of SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, South Korea
| | - Chonsaeng Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, South Korea
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1593
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Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1. Toxins (Basel) 2021; 13:toxins13080585. [PMID: 34437455 PMCID: PMC8402508 DOI: 10.3390/toxins13080585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 01/31/2023] Open
Abstract
The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing.
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1594
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Nagahama K, Aoyama S, Ueda N, Kimura Y, Katayama T, Ono K. Biological Tissue-Inspired Living Self-Healing Hydrogels Based on Cadherin-Mediated Specific Cell-Cell Adhesion. ACS Macro Lett 2021; 10:1073-1079. [PMID: 35549121 DOI: 10.1021/acsmacrolett.1c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Regarding synthetic self-healing materials, as healing reactions occur at the molecular level, bond formation occurs when healing chemicals are nanometer distances apart. However, motility of healing chemicals in materials is quite limited, permitting only passive diffusion, which reduces the chance of bond formation. By contrast, biological-tissues exhibit significant high-performance self-healing, and cadherin-mediated cell-cell adhesion is a key mechanism in the healing process. This is because cells are capable of a certain level of motility and actively migrate to damage sites, thereby achieving cell-cell adhesion with high efficacy. Here, we report biological-tissue-inspired, self-healing hydrogels in which azide-modified living cells are covalently cross-linked with alkyne-modified alginate polymers via bioorthogonal reactions. As a proof-of-concept, we demonstrate their unique self-healing capabilities originating from cadherin-mediated adhesion between cells incorporated into the gels as mobile healing mechanism. This study provides an example of self-healing material incorporating living components into a synthetic material to promote self-healing.
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Affiliation(s)
- Koji Nagahama
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Seika Aoyama
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Natsumi Ueda
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Yuka Kimura
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Tokitaka Katayama
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Kimika Ono
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
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1595
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Schmitt T, Waschke J. Autoantibody-Specific Signalling in Pemphigus. Front Med (Lausanne) 2021; 8:701809. [PMID: 34434944 PMCID: PMC8381052 DOI: 10.3389/fmed.2021.701809] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/08/2021] [Indexed: 12/11/2022] Open
Abstract
Pemphigus is a severe autoimmune disease impairing barrier functions of epidermis and mucosa. Autoantibodies primarily target the desmosomal adhesion molecules desmoglein (Dsg) 1 and Dsg 3 and induce loss of desmosomal adhesion. Strikingly, autoantibody profiles in pemphigus correlate with clinical phenotypes. Mucosal-dominant pemphigus vulgaris (PV) is characterised by autoantibodies (PV-IgG) against Dsg3 whereas epidermal blistering in PV and pemphigus foliaceus (PF) is associated with autoantibodies against Dsg1. Therapy in pemphigus is evolving towards specific suppression of autoantibody formation and autoantibody depletion. Nevertheless, during the acute phase and relapses of the disease additional treatment options to stabilise desmosomes and thereby rescue keratinocyte adhesion would be beneficial. Therefore, the mechanisms by which autoantibodies interfere with adhesion of desmosomes need to be characterised in detail. Besides direct inhibition of Dsg adhesion, autoantibodies engage signalling pathways interfering with different steps of desmosome turn-over. With this respect, recent data indicate that autoantibodies induce separate signalling responses in keratinocytes via specific signalling complexes organised by Dsg1 and Dsg3 which transfer the signal of autoantibody binding into the cell. This hypothesis may also explain the different clinical pemphigus phenotypes.
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Affiliation(s)
- Thomas Schmitt
- Ludwig-Maximilian-Universität München, Anatomische Anstalt, Lehrstuhl Anatomie I - Vegetative Anatomie, Munich, Germany
| | - Jens Waschke
- Ludwig-Maximilian-Universität München, Anatomische Anstalt, Lehrstuhl Anatomie I - Vegetative Anatomie, Munich, Germany
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1596
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Garenne D, Thompson S, Brisson A, Khakimzhan A, Noireaux V. The all-E. coliTXTL toolbox 3.0: new capabilities of a cell-free synthetic biology platform. Synth Biol (Oxf) 2021; 6:ysab017. [PMID: 34712841 PMCID: PMC8546610 DOI: 10.1093/synbio/ysab017] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
The new generation of cell-free gene expression systems enables the prototyping and engineering of biological systems in vitro over a remarkable scope of applications and physical scales. As the utilization of DNA-directed in vitro protein synthesis expands in scope, developing more powerful cell-free transcription-translation (TXTL) platforms remains a major goal to either execute larger DNA programs or improve cell-free biomanufacturing capabilities. In this work, we report the capabilities of the all-E. coli TXTL toolbox 3.0, a multipurpose cell-free expression system specifically developed for synthetic biology. In non-fed batch-mode reactions, the synthesis of the fluorescent reporter protein eGFP (enhanced green fluorescent protein) reaches 4 mg/ml. In synthetic cells, consisting of liposomes loaded with a TXTL reaction, eGFP is produced at concentrations of >8 mg/ml when the chemical building blocks feeding the reaction diffuse through membrane channels to facilitate exchanges with the outer solution. The bacteriophage T7, encoded by a genome of 40 kb and ∼60 genes, is produced at a concentration of 1013 PFU/ml (plaque forming unit/ml). This TXTL system extends the current cell-free expression capabilities by offering unique strength and properties, for testing regulatory elements and circuits, biomanufacturing biologics or building synthetic cells.
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Affiliation(s)
- David Garenne
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Amaury Brisson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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1597
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Wang L, Sun X, Lu L, Marie A, Carrel D, Zhao S, Mille C, Song Q, Zhang Y, Ye S. Optoproteomics elucidates the interactome of L-type amino acid transporter 3 (LAT3). Chem Commun (Camb) 2021; 57:4734-4737. [PMID: 33977919 DOI: 10.1039/d0cc08423a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Membrane protein interactions are crucial for diverse biological processes. We report the application of genetic code expansion in combination with photo-crosslinking chemistry, as we termed "optoproteomics", to identify proteins interacting with the human L-type membrane amino acid transporter 3 (LAT3, also known as SLC43A1). The site-specifically incorporated photo-cross-linker p-azido-L-phenylalanine (AzF), which reacts with proteins in their proximity, enabled the capture of weak and transient partners of LAT3 in living cells. We identify 11 unique interacting proteins which are light-sensitive and 19 unique proteins that are site-specific, validating the approach and providing insights into the LAT3 protein-protein interaction network currently unavailable.
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Affiliation(s)
- Liquan Wang
- The Second Afiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Xiwen Sun
- The Second Afiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Linjie Lu
- INSERM U1195, Kremlin-Bicêtre Hospital, 80 Rue du Gal Leclerc, Le Kremlin-Bicêtre, 94276, France.
| | - Arul Marie
- Molécules de Communication et Adaptation des Microorganisms (MCAM), UMR 7245 CNRS, Muséum National d'Histoire Naturelle, Paris cedex 05, France
| | - Damien Carrel
- Saint-Peres Paris Institute for the Neurosciences, CNRS UMR8003, Université de Paris, Paris 75006, France
| | - Shu Zhao
- INSERM U1195, Kremlin-Bicêtre Hospital, 80 Rue du Gal Leclerc, Le Kremlin-Bicêtre, 94276, France.
| | - Clemence Mille
- INSERM U1195, Kremlin-Bicêtre Hospital, 80 Rue du Gal Leclerc, Le Kremlin-Bicêtre, 94276, France.
| | - Qiong Song
- Department of General Practice/VIP Medical Service, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Yan Zhang
- Department of Anesthesiology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, NUmber 195, Tongbai Road, Zhengzhou, Henan 450000, China
| | - Shixin Ye
- INSERM U1195, Kremlin-Bicêtre Hospital, 80 Rue du Gal Leclerc, Le Kremlin-Bicêtre, 94276, France.
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1598
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Signore MA, De Pascali C, Giampetruzzi L, Siciliano PA, Francioso L. Gut-on-Chip microphysiological systems: Latest advances in the integration of sensing strategies and adoption of mature detection mechanisms. SENSING AND BIO-SENSING RESEARCH 2021. [DOI: 10.1016/j.sbsr.2021.100443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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1599
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Olivi L, Berger M, Creyghton RNP, De Franceschi N, Dekker C, Mulder BM, Claassens NJ, Ten Wolde PR, van der Oost J. Towards a synthetic cell cycle. Nat Commun 2021; 12:4531. [PMID: 34312383 PMCID: PMC8313558 DOI: 10.1038/s41467-021-24772-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/29/2021] [Indexed: 02/08/2023] Open
Abstract
Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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1600
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Gheorghiu M, Polonschii C, Popescu O, Gheorghiu E. Advanced Optogenetic-Based Biosensing and Related Biomaterials. MATERIALS 2021; 14:ma14154151. [PMID: 34361345 PMCID: PMC8347019 DOI: 10.3390/ma14154151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
The ability to stimulate mammalian cells with light, brought along by optogenetic control, has significantly broadened our understanding of electrically excitable tissues. Backed by advanced (bio)materials, it has recently paved the way towards novel biosensing concepts supporting bio-analytics applications transversal to the main biomedical stream. The advancements concerning enabling biomaterials and related novel biosensing concepts involving optogenetics are reviewed with particular focus on the use of engineered cells for cell-based sensing platforms and the available toolbox (from mere actuators and reporters to novel multifunctional opto-chemogenetic tools) for optogenetic-enabled real-time cellular diagnostics and biosensor development. The key advantages of these modified cell-based biosensors concern both significantly faster (minutes instead of hours) and higher sensitivity detection of low concentrations of bioactive/toxic analytes (below the threshold concentrations in classical cellular sensors) as well as improved standardization as warranted by unified analytic platforms. These novel multimodal functional electro-optical label-free assays are reviewed among the key elements for optogenetic-based biosensing standardization. This focused review is a potential guide for materials researchers interested in biosensing based on light-responsive biomaterials and related analytic tools.
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Affiliation(s)
- Mihaela Gheorghiu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania;
- Correspondence: (M.G.); (E.G.)
| | - Cristina Polonschii
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania;
| | - Octavian Popescu
- Molecular Biology Center, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai-University, 400084 Cluj-Napoca, Romania;
- Institute of Biology Bucharest, Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Eugen Gheorghiu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania;
- Correspondence: (M.G.); (E.G.)
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