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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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2
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Poniewierski A, Hołyst R. Analytical Form of the Fluorescence Correlation Spectroscopy Autocorrelation Function in Chemically Reactive Systems. J Chem Theory Comput 2024; 20:2830-2841. [PMID: 38518174 PMCID: PMC11008109 DOI: 10.1021/acs.jctc.3c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024]
Abstract
Fluorescence correlation spectroscopy (FCS) applied to chemically reactive systems provides information about chemical reaction equilibrium constants and diffusion coefficients of reactants. These physical quantities are determined from the FCS-measured autocorrelation function, G(t), as a function of time, t. In most of the studied cases, the analytical form of G(t) is well-known for reactions that are much faster than the diffusion time of reactants across the focal volume probed by FCS or when they are much slower than the diffusion time. Here, we develop an analytical form of G(t) for reactions occurring at an intermediate time scale comparable to the diffusion time. G(t) depends on the reaction rates in such reactions. We focus on reversibly binding a fluorescently labeled small molecule to a macromolecule in a diluted solution in thermodynamic equilibrium. Our approach allows the analysis of FCS data over a wide range of diffusion coefficients, reaction rate constants, and brightness levels of fluorescent labels. Our G(t) is valid even when the fluorescent label changes its brightness upon binding. The easy-to-implement analytical form of the autocorrelation function greatly helps experimentalists study chemical reactions, determining the equilibrium constants of reactions and the reaction rates.
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Affiliation(s)
- Andrzej Poniewierski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
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3
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Shibru MG, Ali ZM, Almansoori AS, Paunovic J, Pantic IV, Corridon PR. Slaughterhouse waste: a unique and sustainable source for dECM-based bioinks. Regen Med 2024; 19:113-118. [PMID: 38356397 DOI: 10.2217/rme-2023-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Affiliation(s)
- Meklit G Shibru
- Department of Biomedical Engineering & Biotechnology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Zehara M Ali
- Department of Biomedical Engineering & Biotechnology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Aliyaa S Almansoori
- Department of Biomedical Engineering & Biotechnology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Jovana Paunovic
- University of Belgrade, Faculty of Medicine, Department of Pathophysiology, Dr. Subotica 9, RS-11129, Belgrade, Serbia
| | - Igor V Pantic
- University of Belgrade, Faculty of Medicine, Department of Medical Physiology, Laboratory for Cellular Physiology, Visegradska 26/II, RS-11129, Belgrade, Serbia
- University of Haifa, 199 Abba Hushi Blvd, Mount Carmel, Haifa, IL, 3498838, Israel
- Department of Pharmacology, College of Medicine & Health Sciences, Khalifa University of Science & Technology
| | - Peter R Corridon
- Department of Biomedical Engineering & Biotechnology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
- Biomedical Engineering & Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
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4
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Shibru MG, Ali ZM, Alali S, Alkhoori H, Corridon PR. Keeping an eye on sustainable regeneration. Regen Med 2023; 18:891-895. [PMID: 37554104 DOI: 10.2217/rme-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Affiliation(s)
- Meklit G Shibru
- Department of Immunology & Physiology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Zehara M Ali
- Department of Immunology & Physiology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Sumayya Alali
- Department of Immunology & Physiology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Hessa Alkhoori
- Department of Immunology & Physiology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
| | - Peter R Corridon
- Department of Immunology & Physiology, College of Medicine & Health Sciences, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science & Technology, Abu Dhabi, United Arab Emirates
- Biomedical Engineering & Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
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5
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Wang X, Elbahrawi RT, Abdukadir AM, Ali ZM, Chan V, Corridon PR. A proposed model of xeno-keratoplasty using 3D printing and decellularization. Front Pharmacol 2023; 14:1193606. [PMID: 37799970 PMCID: PMC10548234 DOI: 10.3389/fphar.2023.1193606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023] Open
Abstract
Corneal opacity is a leading cause of vision impairment and suffering worldwide. Transplantation can effectively restore vision and reduce chronic discomfort. However, there is a considerable shortage of viable corneal graft tissues. Tissue engineering may address this issue by advancing xeno-keratoplasty as a viable alternative to conventional keratoplasty. In particular, livestock decellularization strategies offer the potential to generate bioartificial ocular prosthetics in sufficient supply to match existing and projected needs. To this end, we have examined the best practices and characterizations that have supported the current state-of-the-art driving preclinical and clinical applications. Identifying the challenges that delimit activities to supplement the donor corneal pool derived from acellular scaffolds allowed us to hypothesize a model for keratoprosthesis applications derived from livestock combining 3D printing and decellularization.
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Affiliation(s)
- Xinyu Wang
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Rawdah Taha Elbahrawi
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Azhar Mohamud Abdukadir
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Zehara Mohammed Ali
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Vincent Chan
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Peter R. Corridon
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
- Hleathcare, Engineering and Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
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6
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Kenworthy AK. What's past is prologue: FRAP keeps delivering 50 years later. Biophys J 2023; 122:3577-3586. [PMID: 37218127 PMCID: PMC10541474 DOI: 10.1016/j.bpj.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) has emerged as one of the most widely utilized techniques to quantify binding and diffusion kinetics of biomolecules in biophysics. Since its inception in the mid-1970s, FRAP has been used to address an enormous array of questions including the characteristic features of lipid rafts, how cells regulate the viscosity of their cytoplasm, and the dynamics of biomolecules inside condensates formed by liquid-liquid phase separation. In this perspective, I briefly summarize the history of the field and discuss why FRAP has proven to be so incredibly versatile and popular. Next, I provide an overview of the extensive body of knowledge that has emerged on best practices for quantitative FRAP data analysis, followed by some recent examples of biological lessons learned using this powerful approach. Finally, I touch on new directions and opportunities for biophysicists to contribute to the continued development of this still-relevant research tool.
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Affiliation(s)
- Anne K Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
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7
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Prindle JR, de Cuba OIC, Gahlmann A. Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects. J Chem Phys 2023; 159:071002. [PMID: 37589409 PMCID: PMC10908566 DOI: 10.1063/5.0155638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/06/2023] [Indexed: 08/18/2023] Open
Abstract
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
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Affiliation(s)
- Joshua Robert Prindle
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Olivia Isabella Christiane de Cuba
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
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8
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Pantic IV, Cumic J, Valjarevic S, Shakeel A, Wang X, Vurivi H, Daoud S, Chan V, Petroianu GA, Shibru MG, Ali ZM, Nesic D, Salih AE, Butt H, Corridon PR. Computational approaches for evaluating morphological changes in the corneal stroma associated with decellularization. Front Bioeng Biotechnol 2023; 11:1105377. [PMID: 37304146 PMCID: PMC10250676 DOI: 10.3389/fbioe.2023.1105377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/11/2023] [Indexed: 06/13/2023] Open
Abstract
Decellularized corneas offer a promising and sustainable source of replacement grafts, mimicking native tissue and reducing the risk of immune rejection post-transplantation. Despite great success in achieving acellular scaffolds, little consensus exists regarding the quality of the decellularized extracellular matrix. Metrics used to evaluate extracellular matrix performance are study-specific, subjective, and semi-quantitative. Thus, this work focused on developing a computational method to examine the effectiveness of corneal decellularization. We combined conventional semi-quantitative histological assessments and automated scaffold evaluations based on textual image analyses to assess decellularization efficiency. Our study highlights that it is possible to develop contemporary machine learning (ML) models based on random forests and support vector machine algorithms, which can identify regions of interest in acellularized corneal stromal tissue with relatively high accuracy. These results provide a platform for developing machine learning biosensing systems for evaluating subtle morphological changes in decellularized scaffolds, which are crucial for assessing their functionality.
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Affiliation(s)
- Igor V. Pantic
- Department of Medical Physiology, Faculty of Medicine, Visegradska 26/II, University of Belgrade, Belgrade, Serbia
- University of Haifa, Haifa, Israel
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jelena Cumic
- Faculty of Medicine, University of Belgrade, University Clinical Center of Serbia, Belgrade, Serbia
| | - Svetlana Valjarevic
- Faculty of Medicine, Clinical Hospital Center Zemun, University of Belgrade, Belgrade, Serbia
| | - Adeeba Shakeel
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Xinyu Wang
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Biomedical Engineering, Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Sayel Daoud
- Anatomical Pathology Laboratory, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vincent Chan
- Biomedical Engineering, Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Georg A. Petroianu
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Meklit G. Shibru
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Zehara M. Ali
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dejan Nesic
- Department of Medical Physiology, Faculty of Medicine, Visegradska 26/II, University of Belgrade, Belgrade, Serbia
| | - Ahmed E. Salih
- Department of Mechanical Engineering, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Haider Butt
- Department of Mechanical Engineering, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Peter R. Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Biomedical Engineering, Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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9
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Wang X, Shakeel A, Salih AE, Vurivi H, Daoud S, Desidery L, Khan RL, Shibru MG, Ali ZM, Butt H, Chan V, Corridon PR. A scalable corneal xenograft platform: simultaneous opportunities for tissue engineering and circular economic sustainability by repurposing slaughterhouse waste. Front Bioeng Biotechnol 2023; 11:1133122. [PMID: 37180037 PMCID: PMC10168539 DOI: 10.3389/fbioe.2023.1133122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Introduction: Corneal disease is a leading cause of blindness globally that stems from various etiologies. High-throughput platforms that can generate substantial quantities of corneal grafts will be invaluable in addressing the existing global demand for keratoplasty. Slaughterhouses generate substantial quantities of underutilized biological waste that can be repurposed to reduce current environmentally unfriendly practices. Such efforts to support sustainability can simultaneously drive the development of bioartificial keratoprostheses. Methods: Scores of discarded eyes from the prominent Arabian sheep breeds in our surrounding region of the United Arab Emirates (UAE) were repurposed to generate native and acellular corneal keratoprostheses. Acellular corneal scaffolds were created using a whole-eye immersion/agitation-based decellularization technique with a widely available, eco-friendly, and inexpensive 4% zwitterionic biosurfactant solution (Ecover, Malle, Belgium). Conventional approaches like DNA quantification, ECM fibril organization, scaffold dimensions, ocular transparency and transmittance, surface tension measurements, and Fourier-transform infrared (FTIR) spectroscopy were used to examine corneal scaffold composition. Results: Using this high-throughput system, we effectively removed over 95% of the native DNA from native corneas while retaining the innate microarchitecture that supported substantial light transmission (over 70%) after reversing opacity, a well-established hallmark of decellularization and long-term native corneal storage, with glycerol. FTIR data revealed the absence of spectral peaks in the frequency range 2849 cm-1 to 3075 cm-1, indicating the effective removal of the residual biosurfactant post-decellularization. Surface tension studies confirmed the FTIR data by capturing the surfactant's progressive and effectual removal through tension measurements ranging from approximately 35 mN/m for the 4% decellularizing agent to 70 mN/m for elutes highlighting the effective removal of the detergent. Discussion: To our knowledge, this is the first dataset to be generated outlining a platform that can produce dozens of ovine acellular corneal scaffolds that effectively preserve ocular transparency, transmittance, and ECM components using an eco-friendly surfactant. Analogously, decellularization technologies can support corneal regeneration with attributes comparable to native xenografts. Thus, this study presents a simplified, inexpensive, and scalable high-throughput corneal xenograft platform to support tissue engineering, regenerative medicine, and circular economic sustainability.
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Affiliation(s)
- Xinyu Wang
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Adeeba Shakeel
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed E. Salih
- Department of Mechanical Engineering, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Sayel Daoud
- Anatomical Pathology Laboratory, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Luca Desidery
- Department of Civil Infrastructure and Environmental Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Raheema L. Khan
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Meklit G. Shibru
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Zehara M. Ali
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Haider Butt
- Department of Mechanical Engineering, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Vincent Chan
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Peter R. Corridon
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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10
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Corridon PR. Capturing effects of blood flow on the transplanted decellularized nephron with intravital microscopy. Sci Rep 2023; 13:5289. [PMID: 37002341 PMCID: PMC10066218 DOI: 10.1038/s41598-023-31747-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 04/04/2023] Open
Abstract
Organ decellularization creates cell-free, collagen-based extracellular matrices that can be used as scaffolds for tissue engineering applications. This technique has recently gained much attention, yet adequate scaffold repopulation and implantation remain a challenge. Specifically, there still needs to be a greater understanding of scaffold responses post-transplantation and ways we can improve scaffold durability to withstand the in vivo environment. Recent studies have outlined vascular events that limit organ decellularization/recellularization scaffold viability for long-term transplantation. However, these insights have relied on in vitro/in vivo approaches that need enhanced spatial and temporal resolutions to investigate such issues at the microvascular level. This study uses intravital microscopy to gain instant feedback on their structure, function, and deformation dynamics. Thus, the objective of this study was to capture the effects of in vivo blood flow on the decellularized glomerulus, peritubular capillaries, and tubules after autologous and allogeneic orthotopic transplantation into rats. Large molecular weight dextran molecules labeled the vasculature. They revealed substantial degrees of translocation from glomerular and peritubular capillary tracks to the decellularized tubular epithelium and lumen as early as 12 h after transplantation, providing real-time evidence of the increases in microvascular permeability. Macromolecular extravasation persisted for a week, during which the decellularized microarchitecture was significantly and comparably compromised and thrombosed in both autologous and allogeneic approaches. These results indicate that in vivo multiphoton microscopy is a powerful approach for studying scaffold viability and identifying ways to promote scaffold longevity and vasculogenesis in bioartificial organs.
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Affiliation(s)
- Peter R Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, UAE.
- Healthcare Engineering Innovation Center, Biomedical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, UAE.
- Center for Biotechnology, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, UAE.
- Wake Forest Institute for Regenerative Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157-1083, USA.
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11
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Corridon PR. Enhancing the expression of a key mitochondrial enzyme at the inception of ischemia-reperfusion injury can boost recovery and halt the progression of acute kidney injury. Front Physiol 2023; 14:1024238. [PMID: 36846323 PMCID: PMC9945300 DOI: 10.3389/fphys.2023.1024238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Hydrodynamic fluid delivery has shown promise in influencing renal function in disease models. This technique provided pre-conditioned protection in acute injury models by upregulating the mitochondrial adaptation, while hydrodynamic injections of saline alone have improved microvascular perfusion. Accordingly, hydrodynamic mitochondrial gene delivery was applied to investigate the ability to halt progressive or persistent renal function impairment following episodes of ischemia-reperfusion injuries known to induce acute kidney injury (AKI). The rate of transgene expression was approximately 33% and 30% in rats with prerenal AKI that received treatments 1 (T1hr) and 24 (T24hr) hours after the injury was established, respectively. The resulting mitochondrial adaptation via exogenous IDH2 (isocitrate dehydrogenase 2 (NADP+) and mitochondrial) significantly blunted the effects of injury within 24 h of administration: decreased serum creatinine (≈60%, p < 0.05 at T1hr; ≈50%, p < 0.05 at T24hr) and blood urea nitrogen (≈50%, p < 0.05 at T1hr; ≈35%, p < 0.05 at T24hr) levels, and increased urine output (≈40%, p < 0.05 at T1hr; ≈26%, p < 0.05 at T24hr) and mitochondrial membrane potential, Δψm, (≈ by a factor of 13, p < 0.001 at T1hr; ≈ by a factor of 11, p < 0.001 at T24hr), despite elevated histology injury score (26%, p < 0.05 at T1hr; 47%, p < 0.05 at T24hr). Therefore, this study identifies an approach that can boost recovery and halt the progression of AKI at its inception.
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Affiliation(s)
- Peter R. Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates,Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates,Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates,*Correspondence: Peter R. Corridon,
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12
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Khan RL, Khraibi AA, Dumée LF, Corridon PR. From waste to wealth: Repurposing slaughterhouse waste for xenotransplantation. Front Bioeng Biotechnol 2023; 11:1091554. [PMID: 36815880 PMCID: PMC9935833 DOI: 10.3389/fbioe.2023.1091554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Slaughterhouses produce large quantities of biological waste, and most of these materials are underutilized. In many published reports, the possibility of repurposing this form of waste to create biomaterials, fertilizers, biogas, and feeds has been discussed. However, the employment of particular offal wastes in xenotransplantation has yet to be extensively uncovered. Overall, viable transplantable tissues and organs are scarce, and developing bioartificial components using such discarded materials may help increase their supply. This perspective manuscript explores the viability and sustainability of readily available and easily sourced slaughterhouse waste, such as blood vessels, eyes, kidneys, and tracheas, as starting materials in xenotransplantation derived from decellularization technologies. The manuscript also examines the innovative use of animal stem cells derived from the excreta to create a bioartificial tissue/organ platform that can be translated to humans. Institutional and governmental regulatory approaches will also be outlined to support this endeavor.
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Affiliation(s)
- Raheema L. Khan
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ali A. Khraibi
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ludovic F. Dumée
- Department of Chemical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates,Research and Innovation Center on CO2 and Hydrogen (RICH), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Peter R. Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates,Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates,*Correspondence: Peter R. Corridon,
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Artificial neural networks in contemporary toxicology research. Chem Biol Interact 2023; 369:110269. [PMID: 36402212 DOI: 10.1016/j.cbi.2022.110269] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/04/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Artificial neural networks (ANNs) have a huge potential in toxicology research. They may be used to predict toxicity of various chemical compounds or classify the compounds based on their toxic effects. Today, numerous ANN models have been developed, some of which may be used to detect and possibly explain complex chemico-biological interactions. Fully connected multilayer perceptrons may in some circumstances have high classification accuracy and discriminatory power in separating damaged from intact cells after exposure to a toxic substance. Regularized and not fully connected convolutional neural networks can detect and identify discrete changes in patterns of two-dimensional data associated with toxicity. Bayesian neural networks with weight marginalization sometimes may have better prediction performance when compared to traditional approaches. With the further development of artificial intelligence, it is expected that ANNs will in the future become important parts of various accurate and affordable biosensors for detection of various toxic substances and evaluation of their biochemical properties. In this concise review article, we discuss the recent research focused on the scientific value of ANNs in evaluation and prediction of toxicity of chemical compounds.
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Corridon PR. Still finding ways to augment the existing management of acute and chronic kidney diseases with targeted gene and cell therapies: Opportunities and hurdles. Front Med (Lausanne) 2023; 10:1143028. [PMID: 36960337 PMCID: PMC10028138 DOI: 10.3389/fmed.2023.1143028] [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: 01/12/2023] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
The rising global incidence of acute and chronic kidney diseases has increased the demand for renal replacement therapy. This issue, compounded with the limited availability of viable kidneys for transplantation, has propelled the search for alternative strategies to address the growing health and economic burdens associated with these conditions. In the search for such alternatives, significant efforts have been devised to augment the current and primarily supportive management of renal injury with novel regenerative strategies. For example, gene- and cell-based approaches that utilize recombinant peptides/proteins, gene, cell, organoid, and RNAi technologies have shown promising outcomes primarily in experimental models. Supporting research has also been conducted to improve our understanding of the critical aspects that facilitate the development of efficient gene- and cell-based techniques that the complex structure of the kidney has traditionally limited. This manuscript is intended to communicate efforts that have driven the development of such therapies by identifying the vectors and delivery routes needed to drive exogenous transgene incorporation that may support the treatment of acute and chronic kidney diseases.
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Affiliation(s)
- Peter R. Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
- Biomedical Engineering, Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
- *Correspondence: Peter R. Corridon,
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Wang X, Chan V, Corridon PR. Acellular Tissue-Engineered Vascular Grafts from Polymers: Methods, Achievements, Characterization, and Challenges. Polymers (Basel) 2022; 14:polym14224825. [PMID: 36432950 PMCID: PMC9695055 DOI: 10.3390/polym14224825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Extensive and permanent damage to the vasculature leading to different pathogenesis calls for developing innovative therapeutics, including drugs, medical devices, and cell therapies. Innovative strategies to engineer bioartificial/biomimetic vessels have been extensively exploited as an effective replacement for vessels that have seriously malfunctioned. However, further studies in polymer chemistry, additive manufacturing, and rapid prototyping are required to generate highly engineered vascular segments that can be effectively integrated into the existing vasculature of patients. One recently developed approach involves designing and fabricating acellular vessel equivalents from novel polymeric materials. This review aims to assess the design criteria, engineering factors, and innovative approaches for the fabrication and characterization of biomimetic macro- and micro-scale vessels. At the same time, the engineering correlation between the physical properties of the polymer and biological functionalities of multiscale acellular vascular segments are thoroughly elucidated. Moreover, several emerging characterization techniques for probing the mechanical properties of tissue-engineered vascular grafts are revealed. Finally, significant challenges to the clinical transformation of the highly promising engineered vessels derived from polymers are identified, and unique perspectives on future research directions are presented.
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Affiliation(s)
- Xinyu Wang
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Vincent Chan
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence: (V.C.); (P.R.C.)
| | - Peter R. Corridon
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence: (V.C.); (P.R.C.)
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Corridon PR. Intravital microscopy datasets examining key nephron segments of transplanted decellularized kidneys. Sci Data 2022; 9:561. [PMID: 36088356 PMCID: PMC9464233 DOI: 10.1038/s41597-022-01685-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/07/2022] [Indexed: 12/28/2022] Open
Abstract
AbstractThis study contains intravital microscopy (IVM) data examining the microarchitecture of acellular kidney scaffolds. Acellular scaffolds are cell-free collagen-based matrices derived from native organs that can be used as templates for regenerative medicine applications. This data set contains in vivo assays that evaluate the effectiveness of decellularization and how these acellular nephron compartments perform in the post-transplantation environment. Qualitative and quantitative assessments of scaffold DNA concentrations, tissue fluorescence signals, and structural and functional integrities of decellularized tubular and peritubular capillary segments were acquired and compared to the native (non-transplanted) organ. Cohorts of 2–3-month-old male Sprague Dawley rats were used: non-transplanted (n = 4), transplanted day 0 (n = 4), transplanted day 1 (n = 4), transplanted day 2 (n = 4), and transplanted day 7 (n = 4). Micrographs and supporting measurements are provided to illustrate IVM processes used to perform this study and are publicly available in a data repository to assist scientific reproducibility and extend the use of this powerful imaging application to analyze other scaffold systems.
Measurements(s)
DNA quantification • tissue fluorescence • microvascular leakage • tubular and peritubular capillary integrity
Technology Type(s)
intravital microscopy • multiphoton microscopy • UV-visible spectroscopy
Sample Characterization(s)
rats • native and decellularized kidneys
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