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Kachanov A, Kostyusheva A, Brezgin S, Karandashov I, Ponomareva N, Tikhonov A, Lukashev A, Pokrovsky V, Zamyatnin AA, Parodi A, Chulanov V, Kostyushev D. The menace of severe adverse events and deaths associated with viral gene therapy and its potential solution. Med Res Rev 2024; 44:2112-2193. [PMID: 38549260 DOI: 10.1002/med.22036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 08/09/2024]
Abstract
Over the past decade, in vivo gene replacement therapy has significantly advanced, resulting in market approval of numerous therapeutics predominantly relying on adeno-associated viral vectors (AAV). While viral vectors have undeniably addressed several critical healthcare challenges, their clinical application has unveiled a range of limitations and safety concerns. This review highlights the emerging challenges in the field of gene therapy. At first, we discuss both the role of biological barriers in viral gene therapy with a focus on AAVs, and review current landscape of in vivo human gene therapy. We delineate advantages and disadvantages of AAVs as gene delivery vehicles, mostly from the safety perspective (hepatotoxicity, cardiotoxicity, neurotoxicity, inflammatory responses etc.), and outline the mechanisms of adverse events in response to AAV. Contribution of every aspect of AAV vectors (genomic structure, capsid proteins) and host responses to injected AAV is considered and substantiated by basic, translational and clinical studies. The updated evaluation of recent AAV clinical trials and current medical experience clearly shows the risks of AAVs that sometimes overshadow the hopes for curing a hereditary disease. At last, a set of established and new molecular and nanotechnology tools and approaches are provided as potential solutions for mitigating or eliminating side effects. The increasing number of severe adverse reactions and, sadly deaths, demands decisive actions to resolve the issue of immune responses and extremely high doses of viral vectors used for gene therapy. In response to these challenges, various strategies are under development, including approaches aimed at augmenting characteristics of viral vectors and others focused on creating secure and efficacious non-viral vectors. This comprehensive review offers an overarching perspective on the present state of gene therapy utilizing both viral and non-viral vectors.
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Affiliation(s)
- Artyom Kachanov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Anastasiya Kostyusheva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Sergey Brezgin
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Ivan Karandashov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Natalia Ponomareva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Andrey Tikhonov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Alexander Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Vadim Pokrovsky
- Laboratory of Biochemical Fundamentals of Pharmacology and Cancer Models, Blokhin Cancer Research Center, Moscow, Russia
- Department of Biochemistry, People's Friendship University, Russia (RUDN University), Moscow, Russia
| | - Andrey A Zamyatnin
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Research, Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alessandro Parodi
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Infectious Diseases, Sechenov University, Moscow, Russia
| | - Dmitry Kostyushev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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Boscaro D, Sikorski P. Spheroids as a 3D in vitro model to study bone and bone mineralization. BIOMATERIALS ADVANCES 2024; 157:213727. [PMID: 38101067 DOI: 10.1016/j.bioadv.2023.213727] [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: 10/10/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Traumas, fractures, and diseases can severely influence bone tissue. Insight into bone mineralization is essential for the development of therapies and new strategies to enhance bone regeneration. 3D cell culture systems, in particular cellular spheroids, have gained a lot of interest as they can recapitulate crucial aspects of the in vivo tissue microenvironment, such as the extensive cell-cell and cell-extracellular matrix (ECM) interactions found in tissue. The potential of combining spheroids and various classes of biomaterials opens also new opportunities for research within bone tissue engineering. Characterizing cellular organization, ECM structure, and ECM mineralization is a fundamental step for understanding the biological processes involved in bone tissue formation in a spheroid-based model system. Still, many experimental techniques used in this field of research are optimized for use with monolayer cell cultures. There is thus a need to develop new and improving existing experimental techniques, for applications in 3D cell culture systems. In this review, bone composition and spheroids properties are described. This is followed by an insight into the techniques that are currently used in bone spheroids research and how these can be used to study bone mineralization. We discuss the application of staining techniques used with optical and confocal fluorescence microscopy, molecular biology techniques, second harmonic imaging microscopy, Raman spectroscopy and microscopy, as well as electron microscopy-based techniques, to evaluate osteogenic differentiation, collagen production and mineral deposition. Challenges in the applications of these methods in bone regeneration and bone tissue engineering are described. STATEMENT OF SIGNIFICANCE: 3D cell cultures have gained a lot of interest in the last decades as a possible technique that can be used to recreate in vitro in vivo biological process. The importance of 3D environment during bone mineralization led scientists to use this cell culture to study this biological process, to obtain a better understanding of the events involved. New and improved techniques are also required for a proper analysis of this cell model and the process under investigation. This review summarizes the state of the art of the techniques used to study bone mineralization and how 3D cell cultures, in particular spheroids, are tested and analysed to obtain better resolved results related to this complex biological process.
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Affiliation(s)
- Diamante Boscaro
- Department of Physics, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim 7034, Norway.
| | - Pawel Sikorski
- Department of Physics, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim 7034, Norway.
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Olea AR, Jurado A, Slor G, Tevet S, Pujals S, De La Rosa VR, Hoogenboom R, Amir RJ, Albertazzi L. Reaching the Tumor: Mobility of Polymeric Micelles Inside an In Vitro Tumor-on-a-Chip Model with Dual ECM. ACS APPLIED MATERIALS & INTERFACES 2023; 15:59134-59144. [PMID: 38102079 PMCID: PMC10755695 DOI: 10.1021/acsami.3c12798] [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: 08/28/2023] [Revised: 11/20/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Degradable polymeric micelles are promising drug delivery systems due to their hydrophobic core and responsive design. When applying micellar nanocarriers for tumor delivery, one of the bottlenecks encountered in vivo is the tumor tissue barrier: crossing the dense mesh of cells and the extracellular matrix (ECM). Sometimes overlooked, the extracellular matrix can trap nanoformulations based on charge, size, and hydrophobicity. Here, we used a simple design of a microfluidic chip with two types of ECM and MCF7 spheroids to allow "high-throughput" screening of the interactions between biological interfaces and polymeric micelles. To demonstrate the applicability of the chip, a small library of fluorescently labeled polymeric micelles varying in their hydrophilic shell and hydrophobic core forming blocks was studied. Three widely used hydrophilic shells were tested and compared, namely, poly(ethylene glycol), poly(2-ethyl-2-oxazoline), and poly(acrylic acid), along with two enzymatically degradable dendritic hydrophobic cores (based on hexyl or nonyl end groups). Using ratiometric imaging of unimer:micelle fluorescence and FRAP inside the chip model, we obtained the local assembly state and dynamics inside the chip. Notably, we observed different micelle behaviors in the basal lamina ECM, from avoidance of the ECM structure to binding of the poly(acrylic acid) formulations. Binding to the basal lamina correlated with higher uptake into MCF7 spheroids. Overall, we proposed a simple microfluidic chip containing dual ECM and spheroids for the assessment of the interactions of polymeric nanocarriers with biological interfaces and evaluating nanoformulations' capacity to cross the tumor tissue barrier.
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Affiliation(s)
- Alis R. Olea
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of
Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Alicia Jurado
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of
Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Gadi Slor
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shahar Tevet
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Silvia Pujals
- Department
of Biological Chemistry, Institute for Advanced
Chemistry of Catalonia (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Victor R. De La Rosa
- Supramolecular
Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department
of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Ghent, Belgium
| | - Richard Hoogenboom
- Supramolecular
Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department
of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Ghent, Belgium
| | - Roey J. Amir
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The
ADAMA
Center for Novel Delivery Systems in Crop Protection, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of
Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute of Complex Molecular Systems
(ICMS), Eindhoven University of Technology
(TUE), Eindhoven 5612 AZ, The Netherlands
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Choi D, Gwon K, Hong HJ, Baskaran H, Calvo-Lozano O, Gonzalez-Suarez AM, Park K, de Hoyos-Vega JM, Lechuga LM, Hong J, Stybayeva G, Revzin A. Coating Bioactive Microcapsules with Tannic Acid Enhances the Phenotype of the Encapsulated Pluripotent Stem Cells. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10.1021/acsami.2c06783. [PMID: 35658394 PMCID: PMC10314364 DOI: 10.1021/acsami.2c06783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Human pluripotent stem cells (hPSCs) may be differentiated into any adult cell type and therefore hold incredible promise for cell therapeutics and disease modeling. There is increasing interest in three-dimensional (3D) hPSC culture because of improved differentiation outcomes and potential for scale up. Our team has recently described bioactive heparin (Hep)-containing core-shell microcapsules that promote rapid aggregation of stem cells into spheroids and may also be loaded with growth factors for the local and sustained delivery to the encapsulated cells. In this study, we explored the possibility of further modulating bioactivity of microcapsules through the use of an ultrathin coating composed of tannic acid (TA). Deposition of the TA film onto model substrates functionalized with Hep and poly(ethylene glycol) was characterized by ellipsometry and atomic force microscopy. Furthermore, the presence of the TA coating was observed to increase the amount of basic fibroblast growth factor (bFGF) incorporation by up to twofold and to extend its release from 5 to 7 days. Most significantly, TA-microcapsules loaded with bFGF induced higher levels of pluripotency expression compared to uncoated microcapsules containing bFGF. Engineered microcapsules described here represent a new stem cell culture approach that enables 3D cultivation and relies on local delivery of inductive cues.
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Affiliation(s)
- Daheui Choi
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Kihak Gwon
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Hye Jin Hong
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Harihara Baskaran
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBERBBN and BIST, Barcelona 08193, Spain
| | - Alan M Gonzalez-Suarez
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Kyungtae Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jose M de Hoyos-Vega
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Laura M Lechuga
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBERBBN and BIST, Barcelona 08193, Spain
| | - Jinkee Hong
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Gulnaz Stybayeva
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
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Chen Y, Xu H, Ma Y, Liu J, Zhang L. Diffusion of polymer-grafted nanoparticles with dynamical fluctuations in unentangled polymer melts. Phys Chem Chem Phys 2022; 24:11322-11335. [PMID: 35485911 DOI: 10.1039/d2cp00002d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dynamics of polymer-grafted nanoparticles (PGNPs) in melts of unentangled linear chains were investigated by means of coarse-grained molecular dynamics simulations. The results demonstrated that the graft monomers closer to the particle surface relax more slowly than those farther away due to the constraint of the grafted surface and the confinement of the neighboring chains. Such heterogeneous relaxations of the surrounding environment would perturb the particle motion, making them fluctuating around their centers before they can diffuse through the melt. During such intermediate-time stage, the dynamics is subdiffusive while the distribution of particle displacements is Gaussian, which can be described by the popular fractional Brownian motion model. For the long-time Fickian diffusion, we found that the diffusivity D decreases with increasing grafting density Σg, grafted chain length Ng, and matrix chain length Nm. This is due to the fact that the diffusivity is controlled by the viscous drag of an effective core, consisting of the NP and the non-draining layer of graft segments, and that of the free-draining graft layer outside the "core". With increasing Σg, the PGNPs become harder with greater effective size and thinner free draining layer, resulting in a reduction in D. At extremely high Σg, the diffusivity can even be estimated by the diameter-renormalized Stokes-Einstein (SE) relation. With increasing Ng, both the effective core size and the thickness of the free-draining layer increase, leading to a reduction in diffusivity by D ∼ N-γg with 0.5 < γ < 1. Increasing Nm would lead to the enlargement of the effective core size but meanwhile result in the reduction of the free-draining layer thickness due to autophobic dewetting. The counteraction between these two opposite effects leads to only a slight reduction in the diffusivity, significantly different from the typical SE behavior where D ∼ Nm-1. These findings bear significance in unraveling the fundamental physics of the anomalous dynamics of PGNPs in various polymers, including biological and synthetic.
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Affiliation(s)
- Yulong Chen
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Haohao Xu
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yangwei Ma
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Jun Liu
- Key Laboratory of Beijing City on Preparation and Processing of Novel Polymer Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Liqun Zhang
- Key Laboratory of Beijing City on Preparation and Processing of Novel Polymer Materials, Beijing University of Chemical Technology, Beijing 100029, China.
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Markiewicz R, Litowczenko J, Gapiński J, Woźniak A, Jurga S, Patkowski A. Nanomolar Nitric Oxide Concentrations in Living Cells Measured by Means of Fluorescence Correlation Spectroscopy. Molecules 2022; 27:1010. [PMID: 35164275 PMCID: PMC8838662 DOI: 10.3390/molecules27031010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023] Open
Abstract
Measurement of the nitric oxide (NO) concentration in living cells in the physiological nanomolar range is crucial in understanding NO biochemical functions, as well as in characterizing the efficiency and kinetics of NO delivery by NO-releasing drugs. Here, we show that fluorescence correlation spectroscopy (FCS) is perfectly suited for these purposes, due to its sensitivity, selectivity, and spatial resolution. Using the fluorescent indicators, diaminofluoresceins (DAFs), and FCS, we measured the NO concentrations in NO-producing living human primary endothelial cells, as well as NO delivery kinetics, by an external NO donor to the immortal human epithelial living cells. Due to the high spatial resolution of FCS, the NO concentration in different parts of the cells were also measured. The detection of nitric oxide by means of diaminofluoresceins is much more efficient and faster in living cells than in PBS solutions, even though the conversion to the fluorescent form is a multi-step reaction.
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Affiliation(s)
- Roksana Markiewicz
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
| | - Jagoda Litowczenko
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
| | - Jacek Gapiński
- Department of Molecular Biophysics, Faculty of Physics, Adam Mickiewicz University in Poznan, ul. Uniwersytetu Poznańskiego 3, 61-614 Poznan, Poland;
| | - Anna Woźniak
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland
| | - Stefan Jurga
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
| | - Adam Patkowski
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
- Department of Molecular Biophysics, Faculty of Physics, Adam Mickiewicz University in Poznan, ul. Uniwersytetu Poznańskiego 3, 61-614 Poznan, Poland;
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Karpińska A, Pilz M, Buczkowska J, Żuk PJ, Kucharska K, Magiera G, Kwapiszewska K, Hołyst R. Quantitative analysis of biochemical processes in living cells at a single-molecule level: a case of olaparib-PARP1 (DNA repair protein) interactions. Analyst 2021; 146:7131-7143. [PMID: 34726203 DOI: 10.1039/d1an01769a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Quantitative description of biochemical processes inside living cells and at single-molecule levels remains a challenge at the forefront of modern instrumentation and spectroscopy. This paper demonstrates such single-cell, single-molecule analyses performed to study the mechanism of action of olaparib - an up-to-date, FDA-approved drug for germline-BRCA mutated metastatic breast cancer. We characterized complexes formed with PARPi-FL - fluorescent analog of olaparib in vitro and in cancer cells using the advanced fluorescent-based method: Fluorescence Correlation Spectroscopy (FCS) combined with a length-scale dependent cytoplasmic/nucleoplasmic viscosity model. We determined in vitro olaparib-PARP1 equilibrium constant (6.06 × 108 mol L-1). In the cell nucleus, we distinguished three states of olaparib: freely diffusing drug (24%), olaparib-PARP1 complex (50%), and olaparib-PARP1-RNA complex (26%). We show olaparib accumulation in 3D spheroids, where intracellular concentration is twofold higher than in 2D cells. Moreover, olaparib concentration was tenfold higher (506 nmol L-1vs. 57 nmol L-1) in cervical cancer (BRCA1 high abundance) than in breast cancer cells (BRCA1 low abundance) but with a lower toxic effect. Thus we confirmed that the amount of BRCA1 protein in the cells is a better predictor of the therapeutic effect of olaparib than its penetration into cancer tissue. Our single-molecule and single-cell approach give a new perspective of drug action in living cells. FCS provides a detailed in vivo insight, valuable in drug development and targeting.
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Affiliation(s)
- Aneta Karpińska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Marta Pilz
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Joanna Buczkowska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Paweł J Żuk
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland. .,Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - Karolina Kucharska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Gaweł Magiera
- Department of Medicine, Poznan University of Medical Sciences, 60-356, Poznan, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Robert Hołyst
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
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Single Cell Gene Expression Analysis in a 3D Microtissue Liver Model Reveals Cell Type-Specific Responses to Pro-Fibrotic TGF-β1 Stimulation. Int J Mol Sci 2021; 22:ijms22094372. [PMID: 33922101 PMCID: PMC8122664 DOI: 10.3390/ijms22094372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/15/2023] Open
Abstract
3D cell culture systems are widely used to study disease mechanisms and therapeutic interventions. Multicellular liver microtissues (MTs) comprising HepaRG, hTERT-HSC and THP-1 maintain multicellular interactions and physiological properties required to mimic liver fibrosis. However, the inherent complexity of multicellular 3D-systems often hinders the discrimination of cell type specific responses. Here, we aimed at applying single cell sequencing (scRNA-seq) to discern the molecular responses of cells involved in the development of fibrosis elicited by TGF-β1. To obtain single cell suspensions from the MTs, an enzymatic dissociation method was optimized. Isolated cells showed good viability, could be re-plated and cultured in 2D, and expressed specific markers determined by scRNA-seq, qRT-PCR, ELISA and immunostaining. The three cell populations were successfully clustered using supervised and unsupervised methods based on scRNA-seq data. TGF-β1 led to a fibrotic phenotype in the MTs, detected as decreased albumin and increased αSMA expression. Cell-type specific responses to the treatment were identified for each of the three cell types. They included HepaRG damage characterized by a decrease in cellular metabolism, prototypical inflammatory responses in THP-1s and extracellular matrix remodeling in hTERT-HSCs. Furthermore, we identified novel cell-specific putative fibrosis markers in hTERT-HSC (COL15A1), and THP-1 (ALOX5AP and LAPTM5).
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