1
|
Rassomakhina NV, Ryazanova AY, Likhov AR, Bruskin SA, Maloshenok LG, Zherdeva VV. Tumor Organoids: The Era of Personalized Medicine. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S127-S147. [PMID: 38621748 DOI: 10.1134/s0006297924140086] [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: 10/03/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 04/17/2024]
Abstract
The strategies of future medicine are aimed to modernize and integrate quality approaches including early molecular-genetic profiling, identification of new therapeutic targets and adapting design for clinical trials, personalized drug screening (PDS) to help predict and individualize patient treatment regimens. In the past decade, organoid models have emerged as an innovative in vitro platform with the potential to realize the concept of patient-centered medicine. Organoids are spatially restricted three-dimensional clusters of cells ex vivo that self-organize into complex functional structures through genetically programmed determination, which is crucial for reconstructing the architecture of the primary tissue and organs. Currently, there are several strategies to create three-dimensional (3D) tumor systems using (i) surgically resected patient tissue (PDTOs, patient-derived tumor organoids) or (ii) single tumor cells circulating in the patient's blood. Successful application of 3D tumor models obtained by co-culturing autologous tumor organoids (PDTOs) and peripheral blood lymphocytes have been demonstrated in a number of studies. Such models simulate a 3D tumor architecture in vivo and contain all cell types characteristic of this tissue, including immune system cells and stem cells. Components of the tumor microenvironment, such as fibroblasts and immune system cells, affect tumor growth and its drug resistance. In this review, we analyzed the evolution of tumor models from two-dimensional (2D) cell cultures and laboratory animals to 3D tissue-specific tumor organoids, their significance in identifying mechanisms of antitumor response and drug resistance, and use of these models in drug screening and development of precision methods in cancer treatment.
Collapse
Affiliation(s)
- Natalia V Rassomakhina
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Astemir R Likhov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| |
Collapse
|
2
|
Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
Collapse
Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| |
Collapse
|
3
|
Konovalov AB, Vlasov VV, Samarin SI, Soloviev ID, Savitsky AP, Tuchin VV. Reconstruction of fluorophore absorption and fluorescence lifetime using early photon mesoscopic fluorescence molecular tomography: a phantom study. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:126001. [PMID: 36519075 PMCID: PMC9743783 DOI: 10.1117/1.jbo.27.12.126001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
SIGNIFICANCE Fluorescence molecular lifetime tomography (FMLT) plays an increasingly important role in experimental oncology. The article presents and experimentally verifies an original method of mesoscopic time domain FMLT, based on an asymptotic approximation to the fluorescence source function, which is valid for early arriving photons. AIM The aim was to justify the efficiency of the method by experimental scanning and reconstruction of a phantom with a fluorophore. The experimental facility included the TCSPC system, the pulsed supercontinuum Fianium laser, and a three-channel fiber probe. Phantom scanning was done in mesoscopic regime for three-dimensional (3D) reflectance geometry. APPROACH The sensitivity functions were simulated with a Monte Carlo method. A compressed-sensing-like reconstruction algorithm was used to solve the inverse problem for the fluorescence parameter distribution function, which included the fluorophore absorption coefficient and fluorescence lifetime distributions. The distributions were separated directly in the time domain with the QR-factorization least square method. RESULTS 3D tomograms of fluorescence parameters were obtained and analyzed using two strategies for the formation of measurement data arrays and sensitivity matrices. An algorithm is developed for the flexible choice of optimal strategy in view of attaining better reconstruction quality. Variants on how to improve the method are proposed, specifically, through stepped extraction and further use of a posteriori information about the object. CONCLUSIONS Even if measurement data are limited, the proposed method is capable of giving adequate reconstructions but their quality depends on available a priori (or a posteriori) information. Further research aims to improve the method by implementing the variants proposed.
Collapse
Affiliation(s)
- Alexander B. Konovalov
- Federal State Unitary Enterprise “Russian Federal Nuclear Center – Zababakhin All-Russia Research Institute of Technical Physics,” Snezhinsk, Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Vitaly V. Vlasov
- Federal State Unitary Enterprise “Russian Federal Nuclear Center – Zababakhin All-Russia Research Institute of Technical Physics,” Snezhinsk, Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Sergei I. Samarin
- Federal State Unitary Enterprise “Russian Federal Nuclear Center – Zababakhin All-Russia Research Institute of Technical Physics,” Snezhinsk, Russia
| | - Ilya D. Soloviev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander P. Savitsky
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Valery V. Tuchin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Saratov State University, Saratov, Russia
| |
Collapse
|
4
|
Application of Genetically Encoded Photoconvertible Protein SAASoti for the Study of Enzyme Activity in a Single Live Cell by Fluorescence Correlation Microscopy. MATERIALS 2022; 15:ma15144962. [PMID: 35888428 PMCID: PMC9316514 DOI: 10.3390/ma15144962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/07/2022]
Abstract
Fluorescent Correlation Spectroscopy (FCS) allows us to determine interactions of labeled proteins or changes in the oligomeric state. The FCS method needs a low amount of fluorescent dye, near nanomolar concentrations. To control the amount of fluorescent dye, we used new photoconvertible FP SAASoti. This work is devoted to the proof of principle of using photoconvertible proteins to measure caspase enzymatic activity in a single live cell. The advantage of this approach is that partial photoconversion of the FP makes FCS measurements possible when studying enzymatic reactions. To investigate the process, in vivo we used HeLa cell line expressing the engineered FRET sensor, SAASoti-23-KFP. This FRET sensor has a cleavable (DEVD) sequence in the linker between two FPs for the detection of one of the key enzymes of apoptosis, caspase-3. Caspase-3 activity was detected by registering the increase in the fluorescent lifetimes of the sensor, whereas the diffusion coefficient of SAASoti decreased. This can be explained by an increase in the total cell viscosity during apoptosis. We can suppose that in the moment of detectible caspase-3 activity, cell structure already has crucial changes in viscosity.
Collapse
|
5
|
Yuzhakova D, Kiseleva E, Shirmanova M, Shcheslavskiy V, Sachkova D, Snopova L, Bederina E, Lukina M, Dudenkova V, Yusubalieva G, Belovezhets T, Matvienko D, Baklaushev V. Highly Invasive Fluorescent/Bioluminescent Patient-Derived Orthotopic Model of Glioblastoma in Mice. Front Oncol 2022; 12:897839. [PMID: 35912166 PMCID: PMC9326400 DOI: 10.3389/fonc.2022.897839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Development of the novel diagnostic and therapeutic approaches in neuro-oncology requires tumor models that closely reproduce the biological features of patients’ tumors. Patient-derived xenografts (PDXs) are recognized as a valuable and the most “close-to-patient” tool for preclinical studies. However, their establishment is complicated by the factors related to both the surgical material and technique of the orthotopic implantation. The aim of this work was to develop a patient-derived glioblastoma multiform (GBM) model that stably co-expresses luciferase and a far-red fluorescent protein for monitoring of tumor progression in the brain and, using this model, to validate new diagnostic methods—macroscopic fluorescence lifetime imaging (macro-FLIM) and cross-polarization optical coherence tomography (CP OCT). The established model was similar to the original patient’s GBM in terms of histological and immunohistochemical features and possessed reproducible growth in nude mice, which could be observed by both fluorescence and bioluminescence imaging. Our results demonstrated the high potential of macro-FLIM and CP OCT for intraoperative differentiation of GBM from the white matter. Thus, the dual-labeled PDX model of GBM proved to be an excellent approach for observation of tumor development by optical methods.
Collapse
Affiliation(s)
- Diana Yuzhakova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- *Correspondence: Diana Yuzhakova, ; Vladislav Shcheslavskiy,
| | - Elena Kiseleva
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Marina Shirmanova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Vladislav Shcheslavskiy
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- R&D Department, Becker&Hickl GmbH, Berlin, Germany
- *Correspondence: Diana Yuzhakova, ; Vladislav Shcheslavskiy,
| | - Daria Sachkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ludmila Snopova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Evgeniya Bederina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria Lukina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Laboratory of Molecular Oncology, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Varvara Dudenkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Gaukhar Yusubalieva
- Biomedical Research Center, Federal Research and Clinical Center, Federal Medical and Biological Agency, Moscow, Russia
- Laboratory of Molecular Mechanisms of Regeneration and Aging, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Tatyana Belovezhets
- Department of Molecular Immunology, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Daria Matvienko
- Department of Molecular Immunology, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Vladimir Baklaushev
- Biomedical Research Center, Federal Research and Clinical Center, Federal Medical and Biological Agency, Moscow, Russia
- Laboratory of Molecular Mechanisms of Regeneration and Aging, Engelhardt Institute of Molecular Biology, Moscow, Russia
| |
Collapse
|
6
|
Dmitriev RI, Intes X, Barroso MM. Luminescence lifetime imaging of three-dimensional biological objects. J Cell Sci 2021; 134:1-17. [PMID: 33961054 PMCID: PMC8126452 DOI: 10.1242/jcs.254763] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.
Collapse
Affiliation(s)
- Ruslan I. Dmitriev
- Tissue Engineering and Biomaterials Group, Department of
Human Structure and Repair, Faculty of Medicine and Health Sciences,
Ghent University, Ghent 9000,
Belgium
| | - Xavier Intes
- Department of Biomedical Engineering, Center for
Modeling, Simulation and Imaging for Medicine (CeMSIM),
Rensselaer Polytechnic Institute, Troy, NY
12180-3590, USA
| | - Margarida M. Barroso
- Department of Molecular and Cellular
Physiology, Albany Medical College,
Albany, NY 12208, USA
| |
Collapse
|
7
|
Buschhaus JM, Humphries B, Luker KE, Luker GD. A Caspase-3 Reporter for Fluorescence Lifetime Imaging of Single-Cell Apoptosis. Cells 2018; 7:cells7060057. [PMID: 30720785 PMCID: PMC6025355 DOI: 10.3390/cells7060057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 11/16/2022] Open
Abstract
Fluorescence lifetime imaging (FLIM) is a powerful imaging modality used to gather fluorescent reporter data independent of intracellular reporter intensity or imaging depth. We applied this technique to image real-time activation of a reporter for the proteolytic enzyme, caspase-3, in response to apoptotic cell death. This caspase-3 reporter activity provides valuable insight into cancer cell responsiveness to therapy and overall viability at a single-cell scale. Cleavage of a aspartate-glutamate-valine-aspartate (DEVD) linkage sequence alters Förster resonance energy transfer (FRET) within the reporter, affecting its lifetime. Cellular apoptosis was quantified in multiple environments ranging from 2D flat and 3D spheroid cell culture systems to in vivo murine mammary tumor xenografts. We evaluated cell-by-cell apoptotic responses to multiple pharmacological and genetic methods of interest involved in cancer cell death. Within this article, we describe methods for measuring caspase-3 activation at single-cell resolution in various complex environments using FLIM.
Collapse
Affiliation(s)
- Johanna M Buschhaus
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48190, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48190, USA.
| | - Brock Humphries
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48190, USA.
| | - Kathryn E Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48190, USA.
| | - Gary D Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48190, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48190, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48190, USA.
| |
Collapse
|