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Siquenique S, Ackerman S, Schroeder A, Sarmento B. Bioengineering lipid-based synthetic cells for therapeutic protein delivery. Trends Biotechnol 2024:S0167-7799(24)00216-6. [PMID: 39209601 DOI: 10.1016/j.tibtech.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/27/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Synthetic cells (SCs) offer a promising approach for therapeutic protein delivery, combining principles from synthetic biology and drug delivery. Engineered to mimic natural cells, SCs provide biocompatibility and versatility, with precise control over their architecture and composition. Protein production is essential in living cells, and SCs aim to replicate this process using compartmentalized cell-free protein synthesis systems within lipid bilayers. Lipid bilayers serve as favored membranes in SC design due to their similarity to the biological cell membrane. Moreover, engineering lipidic membranes enable tissue-specific targeting and immune evasion, while stimulus-responsive SCs allow for triggered protein production and release. This Review explores lipid-based SCs as platforms for therapeutic protein delivery, discussing their design principles, functional attributes, and translational challenges and potential.
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Affiliation(s)
- Sónia Siquenique
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Shanny Ackerman
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa, Israel
| | - Avi Schroeder
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa, Israel
| | - Bruno Sarmento
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Gandra, Portugal.
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2
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Ngocho K, Yang X, Wang Z, Hu C, Yang X, Shi H, Wang K, Liu J. Synthetic Cells from Droplet-Based Microfluidics for Biosensing and Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400086. [PMID: 38563581 DOI: 10.1002/smll.202400086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Synthetic cells function as biological mimics of natural cells by mimicking salient features of cells such as metabolism, response to stimuli, gene expression, direct metabolism, and high stability. Droplet-based microfluidic technology presents the opportunity for encapsulating biological functional components in uni-lamellar liposome or polymer droplets. Verified by its success in the fabrication of synthetic cells, microfluidic technology is widely replacing conventional labor-intensive, expensive, and sophisticated techniques justified by its ability to miniaturize and perform batch production operations. In this review, an overview of recent research on the preparation of synthetic cells through droplet-based microfluidics is provided. Different synthetic cells including lipid vesicles (liposome), polymer vesicles (polymersome), coacervate microdroplets, and colloidosomes, are systematically discussed. Efforts are then made to discuss the design of a variety of microfluidic chips for synthetic cell preparation since the combination of microfluidics with bottom-up synthetic biology allows for reproductive and tunable construction of batches of synthetic cell models from simple structures to higher hierarchical structures. The recent advances aimed at exploiting them in biosensors and other biomedical applications are then discussed. Finally, some perspectives on the challenges and future developments of synthetic cell research with microfluidics for biomimetic science and biomedical applications are provided.
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Affiliation(s)
- Kleins Ngocho
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Xilei Yang
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Zefeng Wang
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Cunjie Hu
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Xiaohai Yang
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Hui Shi
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Kemin Wang
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Jianbo Liu
- State key laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
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3
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Kim H, Jung SO, Lee S, Lee Y. Bioluminescent Systems for Theranostic Applications. Int J Mol Sci 2024; 25:7563. [PMID: 39062805 PMCID: PMC11277111 DOI: 10.3390/ijms25147563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Bioluminescence, the light produced by biochemical reactions involving luciferases in living organisms, has been extensively investigated for various applications. It has attracted particular interest as an internal light source for theranostic applications due to its safe and efficient characteristics that overcome the limited penetration of conventional external light sources. Recent advancements in protein engineering technologies and protein delivery platforms have expanded the application of bioluminescence to a wide range of theranostic areas, including bioimaging, biosensing, photodynamic therapy, and optogenetics. This comprehensive review presents the fundamental concepts of bioluminescence and explores its recent applications across diverse fields. Moreover, it discusses future research directions based on the current status of bioluminescent systems for further expansion of their potential.
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Affiliation(s)
- Hyemin Kim
- Department of Cosmetics Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.O.J.); (S.L.); (Y.L.)
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4
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Valente S, Galanti A, Maghin E, Najdi N, Piccoli M, Gobbo P. Matching Together Living Cells and Prototissues: Will There Be Chemistry? Chembiochem 2024:e202400378. [PMID: 39031571 DOI: 10.1002/cbic.202400378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/22/2024]
Abstract
Scientific advancements in bottom-up synthetic biology have led to the development of numerous models of synthetic cells, or protocells. To date, research has mainly focused on increasing the (bio)chemical complexity of these bioinspired micro-compartmentalized systems, yet the successful integration of protocells with living cells remains one of the major challenges in bottom-up synthetic biology. In this review, we aim to summarize the current state of the art in hybrid protocell/living cell and prototissue/living cell systems. Inspired by recent breakthroughs in tissue engineering, we review the chemical, bio-chemical, and mechano-chemical aspects that hold promise for achieving an effective integration of non-living and living matter. The future production of fully integrated protocell/living cell systems and increasingly complex prototissue/living tissue systems not only has the potential to revolutionize the field of tissue engineering, but also paves the way for new technologies in (bio)sensing, personalized therapy, and drug delivery.
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Affiliation(s)
- Stefano Valente
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Agostino Galanti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Edoardo Maghin
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Corso Stati Uniti 4, 35127, Padova, Italy
| | - Nahid Najdi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Martina Piccoli
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Corso Stati Uniti 4, 35127, Padova, Italy
| | - Pierangelo Gobbo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
- National Interuniversity Consortium of Materials Science and Technology, Unit of Trieste, Via G. Giusti 9, 50121, Firenze, Italy
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5
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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Westensee IN, Paffen LJMM, Pendlmayr S, De Dios Andres P, Ramos Docampo MA, Städler B. Artificial Cells and HepG2 Cells in 3D-Bioprinted Arrangements. Adv Healthc Mater 2024; 13:e2303699. [PMID: 38277695 DOI: 10.1002/adhm.202303699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Artificial cells are engineered units with cell-like functions for different purposes including acting as supportive elements for mammalian cells. Artificial cells with minimal liver-like function are made of alginate and equipped with metalloporphyrins that mimic the enzyme activity of a member of the cytochrome P450 family namely CYP1A2. The artificial cells are employed to enhance the dealkylation activity within 3D bioprinted structures composed of HepG2 cells and these artificial cells. This enhancement is monitored through the conversion of resorufin ethyl ether to resorufin. HepG2 cell aggregates are 3D bioprinted using an alginate/gelatin methacryloyl ink, resulting in the successful proliferation of the HepG2 cells. The composite ink made of an alginate/gelatin liquid phase with an increasing amount of artificial cells is characterized. The CYP1A2-like activity of artificial cells is preserved over at least 35 days, where 6 nM resorufin is produced in 8 h. Composite inks made of artificial cells and HepG2 cell aggregates in a liquid phase are used for 3D bioprinting. The HepG2 cells proliferate over 35 days, and the structure has boosted CYP1A2 activity. The integration of artificial cells and their living counterparts into larger 3D semi-synthetic tissues is a step towards exploring bottom-up synthetic biology in tissue engineering.
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Affiliation(s)
- Isabella N Westensee
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Lars J M M Paffen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Stefan Pendlmayr
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Paula De Dios Andres
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Miguel A Ramos Docampo
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
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Wang K, Liu X, Hu KKY, Haritos VS. Artificial Methylotrophic Cells via Bottom-Up Integration of a Methanol-Utilizing Pathway. ACS Synth Biol 2024; 13:888-900. [PMID: 38359048 DOI: 10.1021/acssynbio.3c00683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Methanol has gained substantial attention as a substrate for biomanufacturing due to plentiful stocks and nonreliance on agriculture, and it can be sourced renewably. However, due to inevitable complexities in cell metabolism, microbial methanol conversion requires further improvement before industrial applicability. Here, we present a novel, parallel strategy using artificial cells to provide a simplified and well-defined environment for methanol utilization as artificial methylotrophic cells. We compartmentalized a methanol-utilizing enzyme cascade, including NAD-dependent methanol dehydrogenase (Mdh) and pyruvate-dependent aldolase (KHB aldolase), in cell-sized lipid vesicles using the inverted emulsion method. The reduction of cofactor NAD+ to NADH was used to quantify the conversion of methanol within individual artificial methylotrophic cells via flow cytometry. Compartmentalization of the reaction cascade in liposomes led to a 4-fold higher NADH production compared with bulk enzyme experiments, and the incorporation of KHB aldolase facilitated another 2-fold increase above the Mdh-only reaction. This methanol-utilizing platform can serve as an alternative route to speed up methanol biological conversion, eventually shifting sugar-based bioproduction toward a sustainable methanol bioeconomy.
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Affiliation(s)
- Ke Wang
- Department of Chemical and Biological Engineering, Monash University, Clayton 3800, Australia
| | - Xueqing Liu
- Department of Chemical and Biological Engineering, Monash University, Clayton 3800, Australia
| | - Kevin K Y Hu
- Department of Chemical and Biological Engineering, Monash University, Clayton 3800, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton 3800, Australia
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8
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Andersen DG, Pedersen AB, Jørgensen MH, Montasell MC, Søgaard AB, Chen G, Schroeder A, Andersen GR, Zelikin AN. Chemical Zymogens and Transmembrane Activation of Transcription in Synthetic Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309385. [PMID: 38009384 DOI: 10.1002/adma.202309385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/17/2023] [Indexed: 11/28/2023]
Abstract
In this work, synthetic cells equipped with an artificial signaling pathway that connects an extracellular trigger event to the activation of intracellular transcription are engineered. Learning from nature, this is done via an engineering of responsive enzymes, such that activation of enzymatic activity can be triggered by an external biochemical stimulus. Reversibly deactivated creatine kinase to achieve triggered production of adenosine triphosphate, and a reversibly deactivated nucleic acid polymerase for on-demand synthesis of RNA are engineered. An extracellular, enzyme-activated production of a diffusible zymogen activator is also designed. The key achievement of this work is that the importance of cellularity is illustrated whereby the separation of biochemical partners is essential to resolve their incompatibility, to enable transcription within the confines of a synthetic cell. The herein designed biochemical pathway and the engineered synthetic cells are arguably primitive compared to their natural counterpart. Nevertheless, the results present a significant step toward the design of synthetic cells with responsive behavior, en route from abiotic to life-like cell mimics.
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Affiliation(s)
| | | | | | | | | | - Gal Chen
- Department of Chemical Engineering, Technion, Haifa, 32000, Israel
| | - Avi Schroeder
- Department of Chemical Engineering, Technion, Haifa, 32000, Israel
| | - Gregers Rom Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Alexander N Zelikin
- iNano Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, 8000, Denmark
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
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Maffeis V, Heuberger L, Nikoletić A, Schoenenberger C, Palivan CG. Synthetic Cells Revisited: Artificial Cells Construction Using Polymeric Building Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305837. [PMID: 37984885 PMCID: PMC10885666 DOI: 10.1002/advs.202305837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
The exponential growth of research on artificial cells and organelles underscores their potential as tools to advance the understanding of fundamental biological processes. The bottom-up construction from a variety of building blocks at the micro- and nanoscale, in combination with biomolecules is key to developing artificial cells. In this review, artificial cells are focused upon based on compartments where polymers are the main constituent of the assembly. Polymers are of particular interest due to their incredible chemical variety and the advantage of tuning the properties and functionality of their assemblies. First, the architectures of micro- and nanoscale polymer assemblies are introduced and then their usage as building blocks is elaborated upon. Different membrane-bound and membrane-less compartments and supramolecular structures and how they combine into advanced synthetic cells are presented. Then, the functional aspects are explored, addressing how artificial organelles in giant compartments mimic cellular processes. Finally, how artificial cells communicate with their surrounding and each other such as to adapt to an ever-changing environment and achieve collective behavior as a steppingstone toward artificial tissues, is taken a look at. Engineering artificial cells with highly controllable and programmable features open new avenues for the development of sophisticated multifunctional systems.
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Affiliation(s)
- Viviana Maffeis
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- NCCR‐Molecular Systems EngineeringBPR 1095, Mattenstrasse 24aBaselCH‐4058Switzerland
| | - Lukas Heuberger
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
| | - Anamarija Nikoletić
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- Swiss Nanoscience InstituteUniversity of BaselKlingelbergstrasse 82BaselCH‐4056Switzerland
| | | | - Cornelia G. Palivan
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- NCCR‐Molecular Systems EngineeringBPR 1095, Mattenstrasse 24aBaselCH‐4058Switzerland
- Swiss Nanoscience InstituteUniversity of BaselKlingelbergstrasse 82BaselCH‐4056Switzerland
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10
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Ji Y, Heidari A, Nzigou Mombo B, Wegner SV. Photoactivation of LOV domains with chemiluminescence. Chem Sci 2024; 15:1027-1038. [PMID: 38239695 PMCID: PMC10793642 DOI: 10.1039/d3sc04815b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024] Open
Abstract
Optogenetics has opened new possibilities in the remote control of diverse cellular functions with high spatiotemporal precision using light. However, delivering light to optically non-transparent systems remains a challenge. Here, we describe the photoactivation of light-oxygen-voltage-sensing domains (LOV domains) with in situ generated light from a chemiluminescence reaction between luminol and H2O2. This activation is possible due to the spectral overlap between the blue chemiluminescence emission and the absorption bands of the flavin chromophore in LOV domains. All four LOV domain proteins with diverse backgrounds and structures (iLID, BcLOV4, nMagHigh/pMagHigh, and VVDHigh) were photoactivated by chemiluminescence as demonstrated using a bead aggregation assay. The photoactivation with chemiluminescence required a critical light-output below which the LOV domains reversed back to their dark state with protein characteristic kinetics. Furthermore, spatially confined chemiluminescence produced inside giant unilamellar vesicles (GUVs) was able to photoactivate proteins both on the membrane and in solution, leading to the recruitment of the corresponding proteins to the GUV membrane. Finally, we showed that reactive oxygen species produced by neutrophil like cells can be converted into sufficient chemiluminescence to recruit the photoswitchable protein BcLOV4-mCherry from solution to the cell membrane. The findings highlight the utility of chemiluminescence as an endogenous light source for optogenetic applications, offering new possibilities for studying cellular processes in optically non-transparent systems.
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Affiliation(s)
- Yuhao Ji
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster 48149 Münster Germany
| | - Ali Heidari
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster 48149 Münster Germany
| | - Brice Nzigou Mombo
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster 48149 Münster Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster 48149 Münster Germany
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11
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Powers J, Jang Y. Advancing Biomimetic Functions of Synthetic Cells through Compartmentalized Cell-Free Protein Synthesis. Biomacromolecules 2023; 24:5539-5550. [PMID: 37962115 DOI: 10.1021/acs.biomac.3c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Synthetic cells are artificial constructs that mimic the structures and functions of living cells. They are attractive for studying diverse biochemical processes and elucidating the origins of life. While creating a living synthetic cell remains a grand challenge, researchers have successfully synthesized hundreds of unique synthetic cell platforms. One promising approach to developing more sophisticated synthetic cells is to integrate cell-free protein synthesis (CFPS) mechanisms into vesicle platforms. This makes it possible to create synthetic cells with complex biomimetic functions such as genetic circuits, autonomous membrane modifications, sensing and communication, and artificial organelles. This Review explores recent advances in the use of CFPS to impart advanced biomimetic structures and functions to bottom-up synthetic cell platforms. We also discuss the potential applications of synthetic cells in biomedicine as well as the future directions of synthetic cell research.
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Affiliation(s)
- Jackson Powers
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, United States
| | - Yeongseon Jang
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, United States
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12
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Peruzzi JA, Vu TQ, Gunnels TF, Kamat NP. Rapid Generation of Therapeutic Nanoparticles Using Cell-Free Expression Systems. SMALL METHODS 2023; 7:e2201718. [PMID: 37116099 PMCID: PMC10611898 DOI: 10.1002/smtd.202201718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/06/2023] [Indexed: 05/05/2023]
Abstract
The surface modification of membrane-based nanoparticles, such as liposomes, polymersomes, and lipid nanoparticles, with targeting molecules, such as binding proteins, is an important step in the design of therapeutic materials. However, this modification can be costly and time-consuming, requiring cellular hosts for protein expression and lengthy purification and conjugation steps to attach proteins to the surface of nanocarriers, which ultimately limits the development of effective protein-conjugated nanocarriers. Here, the use of cell-free protein synthesis systems to rapidly create protein-conjugated membrane-based nanocarriers is demonstrated. Using this approach, multiple types of functional binding proteins, including affibodies, computationally designed proteins, and scFvs, can be cell-free expressed and conjugated to liposomes in one-pot. The technique can be expanded further to other nanoparticles, including polymersomes and lipid nanoparticles, and is amenable to multiple conjugation strategies, including surface attachment to and integration into nanoparticle membranes. Leveraging these methods, rapid design of bispecific artificial antigen presenting cells and enhanced delivery of lipid nanoparticle cargo in vitro is demonstrated. It is envisioned that this workflow will enable the rapid generation of membrane-based delivery systems and bolster our ability to create cell-mimetic therapeutics.
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Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Timothy Q. Vu
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F. Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Neha P. Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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13
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Ivanov T, Cao S, Bohra N, de Souza Melchiors M, Caire da Silva L, Landfester K. Polymeric Microreactors with pH-Controlled Spatial Localization of Cascade Reactions. ACS APPLIED MATERIALS & INTERFACES 2023; 15:50755-50764. [PMID: 37903081 PMCID: PMC10636718 DOI: 10.1021/acsami.3c09196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023]
Abstract
Lipid and polymer vesicles provide versatile means of creating systems that mimic the architecture of cells. However, these constructs cannot mimic the adaptive compartmentalization observed in cells, where the assembly and disassembly of subcompartments are dynamically modulated by environmental cues. Here, we describe a fully polymeric microreactor with a coacervate-in-vesicle architecture that exhibits an adaptive response to pH. The system was fabricated by microfluidic generation of semipermeable biomimetic polymer vesicles within 1 min using oleyl alcohol as the oil phase. The polymersomes allowed for the diffusion of protons and substrates acting as external signals. Using this method, we were able to construct adaptive microreactors containing internal polyelectrolyte-based catalytic organelles capable of sequestering and localizing enzymes and reaction products in a dynamic process driven by an external stimulus. This approach provides a platform for the rapid and efficient construction of robust adaptive microreactors that can be used in catalysis, biosensing, and cell mimicry.
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Affiliation(s)
- Tsvetomir Ivanov
- Department of Physical Chemistry
of Polymers, Max Planck Institute for Polymer
Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Shoupeng Cao
- Department of Physical Chemistry
of Polymers, Max Planck Institute for Polymer
Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Nitin Bohra
- Department of Physical Chemistry
of Polymers, Max Planck Institute for Polymer
Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marina de Souza Melchiors
- Department of Physical Chemistry
of Polymers, Max Planck Institute for Polymer
Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Lucas Caire da Silva
- Department of Physical Chemistry
of Polymers, Max Planck Institute for Polymer
Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Katharina Landfester
- Department of Physical Chemistry
of Polymers, Max Planck Institute for Polymer
Research, Ackermannweg 10, 55128 Mainz, Germany
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14
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Westensee IN, Städler B. Artificial cells eavesdropping on HepG2 cells. Interface Focus 2023; 13:20230007. [PMID: 37577001 PMCID: PMC10415741 DOI: 10.1098/rsfs.2023.0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/17/2023] [Indexed: 08/15/2023] Open
Abstract
Cellular communication is a fundamental feature to ensure the survival of cellular assemblies, such as multicellular tissue, via coordinated adaption to changes in their surroundings. Consequently, the development of integrated semi-synthetic systems consisting of artificial cells (ACs) and mammalian cells requires feedback-based interactions. Here, we illustrate that ACs can eavesdrop on HepG2 cells focusing on the activity of cytochrome P450 1A2 (CYP1A2), an enzyme from the cytochrome P450 enzyme family. Specifically, d-cysteine is sent as a signal from the ACs via the triggered reduction of disulfide bonds. Simultaneously, HepG2 cells enzymatically convert 2-cyano-6-methoxybenzothiazole into 2-cyano-6-hydroxybenzothiazole that is released in the extracellular space. d-Cysteine and 2-cyano-6-hydroxybenzothiazole react to form d-luciferin. The ACs respond to this signal by converting d-luciferin into luminescence due to the presence of encapsulated luciferase in the ACs. As a result, the ACs can eavesdrop on the mammalian cells to evaluate the level of hepatic CYP1A2 function.
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Affiliation(s)
- Isabella Nymann Westensee
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
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15
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Somathilaka SS, Balasubramaniam S, Martins DP, Li X. Revealing gene regulation-based neural network computing in bacteria. BIOPHYSICAL REPORTS 2023; 3:100118. [PMID: 37649578 PMCID: PMC10462848 DOI: 10.1016/j.bpr.2023.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Bacteria are known to interpret a range of external molecular signals that are crucial for sensing environmental conditions and adapting their behaviors accordingly. These external signals are processed through a multitude of signaling transduction networks that include the gene regulatory network (GRN). From close observation, the GRN resembles and exhibits structural and functional properties that are similar to artificial neural networks. An in-depth analysis of gene expression dynamics further provides a new viewpoint of characterizing the inherited computing properties underlying the GRN of bacteria despite being non-neuronal organisms. In this study, we introduce a model to quantify the gene-to-gene interaction dynamics that can be embedded in the GRN as weights, converting a GRN to gene regulatory neural network (GRNN). Focusing on Pseudomonas aeruginosa, we extracted the GRNN associated with a well-known virulence factor, pyocyanin production, using an introduced weight extraction technique based on transcriptomic data and proving its computing accuracy using wet-lab experimental data. As part of our analysis, we evaluated the structural changes in the GRNN based on mutagenesis to determine its varying computing behavior. Furthermore, we model the ecosystem-wide cell-cell communications to analyze its impact on computing based on environmental as well as population signals, where we determine the impact on the computing reliability. Subsequently, we establish that the individual GRNNs can be clustered to collectively form computing units with similar behaviors to single-layer perceptrons with varying sigmoidal activation functions spatio-temporally within an ecosystem. We believe that this will lay the groundwork toward molecular machine learning systems that can see artificial intelligence move toward non-silicon devices, or living artificial intelligence, as well as giving us new insights into bacterial natural computing.
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Affiliation(s)
- Samitha S. Somathilaka
- VistaMilk Research Centre, Walton Institute for Information and Communication Systems Science, South East Technological University, Waterford, Ireland
- School of Computing, University of Nebraska-Lincoln, Lincoln, Nebraska
| | | | - Daniel P. Martins
- VistaMilk Research Centre, Walton Institute for Information and Communication Systems Science, South East Technological University, Waterford, Ireland
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska
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16
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Allen ME, Hindley JW, O’Toole N, Cooke HS, Contini C, Law RV, Ces O, Elani Y. Biomimetic behaviors in hydrogel artificial cells through embedded organelles. Proc Natl Acad Sci U S A 2023; 120:e2307772120. [PMID: 37603747 PMCID: PMC10466294 DOI: 10.1073/pnas.2307772120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/23/2023] Open
Abstract
Artificial cells are biomimetic structures formed from molecular building blocks that replicate biological processes, behaviors, and architectures. Of these building blocks, hydrogels have emerged as ideal, yet underutilized candidates to provide a gel-like chassis in which to incorporate both biological and nonbiological componentry which enables the replication of cellular functionality. Here, we demonstrate a microfluidic strategy to assemble biocompatible cell-sized hydrogel-based artificial cells with a variety of different embedded functional subcompartments, which act as engineered synthetic organelles. The organelles enable the recreation of increasingly biomimetic behaviors, including stimulus-induced motility, content release through activation of membrane-associated proteins, and enzymatic communication with surrounding bioinspired compartments. In this way, we showcase a foundational strategy for the bottom-up construction of hydrogel-based artificial cell microsystems which replicate fundamental cellular behaviors, paving the way for the construction of next-generation biotechnological devices.
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Affiliation(s)
- Matthew E. Allen
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - James W. Hindley
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Nina O’Toole
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Hannah S. Cooke
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Claudia Contini
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Robert V. Law
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
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17
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Lin AJ, Sihorwala AZ, Belardi B. Engineering Tissue-Scale Properties with Synthetic Cells: Forging One from Many. ACS Synth Biol 2023; 12:1889-1907. [PMID: 37417657 PMCID: PMC11017731 DOI: 10.1021/acssynbio.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
In metazoans, living cells achieve capabilities beyond individual cell functionality by assembling into multicellular tissue structures. These higher-order structures represent dynamic, heterogeneous, and responsive systems that have evolved to regenerate and coordinate their actions over large distances. Recent advances in constructing micrometer-sized vesicles, or synthetic cells, now point to a future where construction of synthetic tissue can be pursued, a boon to pressing material needs in biomedical implants, drug delivery systems, adhesives, filters, and storage devices, among others. To fully realize the potential of synthetic tissue, inspiration has been and will continue to be drawn from new molecular findings on its natural counterpart. In this review, we describe advances in introducing tissue-scale features into synthetic cell assemblies. Beyond mere complexation, synthetic cells have been fashioned with a variety of natural and engineered molecular components that serve as initial steps toward morphological control and patterning, intercellular communication, replication, and responsiveness in synthetic tissue. Particular attention has been paid to the dynamics, spatial constraints, and mechanical strengths of interactions that drive the synthesis of this next-generation material, describing how multiple synthetic cells can act as one.
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Affiliation(s)
- Alexander J Lin
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ahmed Z Sihorwala
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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18
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Ji Y, Chakraborty T, Wegner SV. Self-Regulated and Bidirectional Communication in Synthetic Cell Communities. ACS NANO 2023; 17:8992-9002. [PMID: 37156507 DOI: 10.1021/acsnano.2c09908] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cell-to-cell communication is not limited to a sender releasing a signaling molecule and a receiver perceiving it but is often self-regulated and bidirectional. Yet, in communities of synthetic cells, such features that render communication efficient and adaptive are missing. Here, we report the design and implementation of adaptive two-way signaling with lipid-vesicle-based synthetic cells. The first layer of self-regulation derives from coupling the temporal dynamics of the signal, H2O2, production in the sender to adhesions between sender and receiver cells. This way the receiver stays within the signaling range for the duration sender produces the signal and detaches once the signal fades. Specifically, H2O2 acts as both a forward signal and a regulator of the adhesions by activating photoswitchable proteins at the surface for the duration of the chemiluminescence. The second layer of self-regulation arises when the adhesions render the receiver permeable and trigger the release of a backward signal, resulting in bidirectional exchange. These design rules provide a concept for engineering multicellular systems with adaptive communication.
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Affiliation(s)
- Yuhao Ji
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Taniya Chakraborty
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
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19
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Porta-de-la-Riva M, Gonzalez AC, Sanfeliu-Cerdán N, Karimi S, Malaiwong N, Pidde A, Morales-Curiel LF, Fernandez P, González-Bolívar S, Hurth C, Krieg M. Neural engineering with photons as synaptic transmitters. Nat Methods 2023; 20:761-769. [PMID: 37024651 DOI: 10.1038/s41592-023-01836-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Neuronal computation is achieved through connections of individual neurons into a larger network. To expand the repertoire of endogenous cellular communication, we developed a synthetic, photon-assisted synaptic transmission (PhAST) system. PhAST is based on luciferases and channelrhodopsins that enable the transmission of a neuronal state across space, using photons as neurotransmitters. PhAST overcomes synaptic barriers and rescues the behavioral deficit of a glutamate mutant with conditional, calcium-triggered photon emission between two neurons of the Caenorhabditis elegans nociceptive avoidance circuit. To demonstrate versatility and flexibility, we generated de novo synaptic transmission between two unconnected cells in a sexually dimorphic neuronal circuit, suppressed endogenous nocifensive response through activation of an anion channelrhodopsin and switched attractive to aversive behavior in an olfactory circuit. Finally, we applied PhAST to dissect the calcium dynamics of the temporal pattern generator in a motor circuit for ovipositioning. In summary, we established photon-based synaptic transmission that facilitates the modification of animal behavior.
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Affiliation(s)
| | | | | | - Shadi Karimi
- Institut de Ciències Fotòniques, Castelldefels, Spain
| | | | | | | | | | | | - Cedric Hurth
- Institut de Ciències Fotòniques, Castelldefels, Spain
| | - Michael Krieg
- Institut de Ciències Fotòniques, Castelldefels, Spain.
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20
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Di Iorio D, Bergmann J, Higashi SL, Hoffmann A, Wegner SV. A disordered tether to iLID improves photoswitchable protein patterning on model membranes. Chem Commun (Camb) 2023; 59:4380-4383. [PMID: 36946614 DOI: 10.1039/d3cc00709j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Reversible protein patterning on model membranes is important to reproduce spatiotemporal protein dynamics in vitro. An engineered version of iLID, disiLID, with a disordered domain as a membrane tether improves the recruitment of Nano under blue light and the reversibility in the dark, which enables protein patterning on membranes with higher spatiotemporal precision.
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Affiliation(s)
- Daniele Di Iorio
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Johanna Bergmann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Sayuri L Higashi
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Arne Hoffmann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany.
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21
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Jiang T, Song J, Zhang Y. Coelenterazine-Type Bioluminescence-Induced Optical Probes for Sensing and Controlling Biological Processes. Int J Mol Sci 2023; 24:ijms24065074. [PMID: 36982148 PMCID: PMC10049153 DOI: 10.3390/ijms24065074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Bioluminescence-based probes have long been used to quantify and visualize biological processes in vitro and in vivo. Over the past years, we have witnessed the trend of bioluminescence-driven optogenetic systems. Typically, bioluminescence emitted from coelenterazine-type luciferin–luciferase reactions activate light-sensitive proteins, which induce downstream events. The development of coelenterazine-type bioluminescence-induced photosensory domain-based probes has been applied in the imaging, sensing, and control of cellular activities, signaling pathways, and synthetic genetic circuits in vitro and in vivo. This strategy can not only shed light on the mechanisms of diseases, but also promote interrelated therapy development. Here, this review provides an overview of these optical probes for sensing and controlling biological processes, highlights their applications and optimizations, and discusses the possible future directions.
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Affiliation(s)
- Tianyu Jiang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, China
- Correspondence: (T.J.); (Y.Z.)
| | - Jingwen Song
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Correspondence: (T.J.); (Y.Z.)
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22
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Li H, Yan Y, Chen J, Shi K, Song C, Ji Y, Jia L, Li J, Qiao Y, Lin Y. Artificial receptor-mediated phototransduction toward protocellular subcompartmentalization and signaling-encoded logic gates. SCIENCE ADVANCES 2023; 9:eade5853. [PMID: 36857444 PMCID: PMC9977178 DOI: 10.1126/sciadv.ade5853] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Engineering artificial cellular systems capable of perceiving and transmitting external signals across membranes to activate downstream targets and coordinate protocellular responses is key to build cell-cell communications and protolife. Here, we report a synthetic photoreceptor-mediated signaling pathway with the integration of light harvesting, photo-to-chemical energy conversion, signal transmission, and amplification in synthetic cells, which ultimately resulted in protocell subcompartmentalization. Key to our design is a ruthenium-bipyridine complex that acts as a membrane-anchored photoreceptor to convert visible light into chemical information and transduce signals across the lipid membrane via flip-flop motion. By coupling receptor-mediated phototransduction with biological recognition and enzymatic cascade reactions, we further develop protocell signaling-encoded Boolean logic gates. Our results illustrate a minimal cell model to mimic the photoreceptor cells that can transduce the energy of light into intracellular responses and pave the way to modular control over the flow of information for complex metabolic and signaling pathways.
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Affiliation(s)
- He Li
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Yan
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jing Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ke Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chuwen Song
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yanglimin Ji
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyan Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianming Li
- Research Center of New Energy, Research Institute of Petroleum Exploration and Development (RIPED), PetroChina, Beijing 100083, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiyang Lin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
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23
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Heidari A, Sentürk OI, Yang S, Joesaar A, Gobbo P, Mann S, de Greef TFA, Wegner SV. Orthogonal Light-Dependent Membrane Adhesion Induces Social Self-Sorting and Member-Specific DNA Communication in Synthetic Cell Communities. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206474. [PMID: 36599623 DOI: 10.1002/smll.202206474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Developing orthogonal chemical communication pathways in diverse synthetic cell communities is a considerable challenge due to the increased crosstalk and interference associated with large numbers of different types of sender-receiver pairs. Herein, the authors control which sender-receiver pairs communicate in a three-membered community of synthetic cells through red and blue light illumination. Semipermeable protein-polymer-based synthetic cells (proteinosomes) with complementary membrane-attached protein adhesion communicate through single-stranded DNA oligomers and synergistically process biochemical information within a community consisting of one sender and two different receiver populations. Different pairs of red and blue light-responsive protein-protein interactions act as membrane adhesion mediators between the sender and receivers such that they self-assemble and socially self-sort into different multicellular structures under red and blue light. Consequently, distinct sender-receiver pairs come into the signaling range depending on the light illumination and are able to communicate specifically without activation of the other receiver population. Overall, this work shows how photoswitchable membrane adhesion gives rise to different self-sorting protocell patterns that mediate member-specific DNA-based communication in ternary populations of synthetic cells and provides a step towards the design of orthogonal chemical communication networks in diverse communities of synthetic cells.
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Affiliation(s)
- Ali Heidari
- Institute of Physiological Chemistry and Pathobiochemistry University of Münster, Waldeyerstr. 15, 48149, Münster, Germany
| | - Oya I Sentürk
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Shuo Yang
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands
| | - Alex Joesaar
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands
| | - Pierangelo Gobbo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, 34127, Italy
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, Max Planck Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Tom F A de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry University of Münster, Waldeyerstr. 15, 48149, Münster, Germany
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24
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Gonzales DT, Suraritdechachai S, Tang TYD. Compartmentalized Cell-Free Expression Systems for Building Synthetic Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:77-101. [PMID: 37306700 DOI: 10.1007/10_2023_221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
One of the grand challenges in bottom-up synthetic biology is the design and construction of synthetic cellular systems. One strategy toward this goal is the systematic reconstitution of biological processes using purified or non-living molecular components to recreate specific cellular functions such as metabolism, intercellular communication, signal transduction, and growth and division. Cell-free expression systems (CFES) are in vitro reconstitutions of the transcription and translation machinery found in cells and are a key technology for bottom-up synthetic biology. The open and simplified reaction environment of CFES has helped researchers discover fundamental concepts in the molecular biology of the cell. In recent decades, there has been a drive to encapsulate CFES reactions into cell-like compartments with the aim of building synthetic cells and multicellular systems. In this chapter, we discuss recent progress in compartmentalizing CFES to build simple and minimal models of biological processes that can help provide a better understanding of the process of self-assembly in molecularly complex systems.
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Affiliation(s)
- David T Gonzales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | | | - T -Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, Cluster of Excellence, TU Dresden, Dresden, Germany.
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25
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Morales-Curiel LF, Gonzalez AC, Castro-Olvera G, Lin LCL, El-Quessny M, Porta-de-la-Riva M, Severino J, Morera LB, Venturini V, Ruprecht V, Ramallo D, Loza-Alvarez P, Krieg M. Volumetric imaging of fast cellular dynamics with deep learning enhanced bioluminescence microscopy. Commun Biol 2022; 5:1330. [PMID: 36463346 PMCID: PMC9719505 DOI: 10.1038/s42003-022-04292-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Bioluminescence microscopy is an appealing alternative to fluorescence microscopy, because it does not depend on external illumination, and consequently does neither produce spurious background autofluorescence, nor perturb intrinsically photosensitive processes in living cells and animals. The low photon emission of known luciferases, however, demands long exposure times that are prohibitive for imaging fast biological dynamics. To increase the versatility of bioluminescence microscopy, we present an improved low-light microscope in combination with deep learning methods to image extremely photon-starved samples enabling subsecond exposures for timelapse and volumetric imaging. We apply our method to image subcellular dynamics in mouse embryonic stem cells, epithelial morphology during zebrafish development, and DAF-16 FoxO transcription factor shuttling from the cytoplasm to the nucleus under external stress. Finally, we concatenate neural networks for denoising and light-field deconvolution to resolve intracellular calcium dynamics in three dimensions of freely moving Caenorhabditis elegans.
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Affiliation(s)
| | | | | | | | | | | | - Jacqueline Severino
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Battle Morera
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valeria Venturini
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Verena Ruprecht
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain
| | - Diego Ramallo
- ICFO, Institut de Ciencies Fotòniques, Castelldefels, Spain
| | | | - Michael Krieg
- ICFO, Institut de Ciencies Fotòniques, Castelldefels, Spain.
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26
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Staufer O, Gantner G, Platzman I, Tanner K, Berger I, Spatz JP. Bottom-up assembly of viral replication cycles. Nat Commun 2022; 13:6530. [PMID: 36323671 PMCID: PMC9628313 DOI: 10.1038/s41467-022-33661-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Bottom-up synthetic biology provides new means to understand living matter by constructing minimal life-like systems. This principle can also be applied to study infectious diseases. Here we summarize approaches and ethical considerations for the bottom-up assembly of viral replication cycles.
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Affiliation(s)
- Oskar Staufer
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, OX3 7FY, UK.
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany.
| | - Gösta Gantner
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Theological Seminary, Heidelberg University, Kisselgasse 1, 69117, Heidelberg, Germany
| | - Ilia Platzman
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), University of Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
| | - Klaus Tanner
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Theological Seminary, Heidelberg University, Kisselgasse 1, 69117, Heidelberg, Germany
| | - Imre Berger
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol, BS8 1TQ, UK
| | - Joachim P Spatz
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), University of Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
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27
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Chen G, Levin R, Landau S, Kaduri M, Adir O, Ianovici I, Krinsky N, Doppelt-Flikshtain O, Shklover J, Shainsky-Roitman J, Levenberg S, Schroeder A. Implanted synthetic cells trigger tissue angiogenesis through de novo production of recombinant growth factors. Proc Natl Acad Sci U S A 2022; 119:e2207525119. [PMID: 36095208 PMCID: PMC9499519 DOI: 10.1073/pnas.2207525119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
Progress in bottom-up synthetic biology has stimulated the development of synthetic cells (SCs), autonomous protein-manufacturing particles, as dynamic biomimetics for replacing diseased natural cells and addressing medical needs. Here, we report that SCs genetically encoded to produce proangiogenic factors triggered the physiological process of neovascularization in mice. The SCs were constructed of giant lipid vesicles and were optimized to facilitate enhanced protein production. When introduced with the appropriate genetic code, the SCs synthesized a recombinant human basic fibroblast growth factor (bFGF), reaching expression levels of up to 9⋅106 protein copies per SC. In culture, the SCs induced endothelial cell proliferation, migration, tube formation, and angiogenesis-related intracellular signaling, confirming their proangiogenic activity. Integrating the SCs with bioengineered constructs bearing endothelial cells promoted the remodeling of mature vascular networks, supported by a collagen-IV basement membrane-like matrix. In vivo, prolonged local administration of the SCs in mice triggered the infiltration of blood vessels into implanted Matrigel plugs without recorded systemic immunogenicity. These findings emphasize the potential of SCs as therapeutic platforms for activating physiological processes by autonomously producing biological drugs inside the body.
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Affiliation(s)
- Gal Chen
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
- The Interdisciplinary Program for Biotechnology, Technion, Haifa 32000, Israel
| | - Rotem Levin
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
| | - Shira Landau
- Department of Biomedical Engineering, Technion, Haifa 32000, Israel
| | - Maya Kaduri
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
| | - Omer Adir
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion, Haifa 32000, Israel
| | - Iris Ianovici
- Department of Biomedical Engineering, Technion, Haifa 32000, Israel
| | - Nitzan Krinsky
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
| | - Ofri Doppelt-Flikshtain
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Jeny Shklover
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
| | - Janna Shainsky-Roitman
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
| | | | - Avi Schroeder
- The Luis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion, Haifa 32000, Israel
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