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Niraula D, El Naqa I, Tuszynski JA, Gatenby RA. Modeling non-genetic information dynamics in cells using reservoir computing. iScience 2024; 27:109614. [PMID: 38632985 PMCID: PMC11022048 DOI: 10.1016/j.isci.2024.109614] [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: 01/10/2024] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Virtually all cells use energy-driven, ion-specific membrane pumps to maintain large transmembrane gradients of Na+, K+, Cl-, Mg++, and Ca++, but the corresponding evolutionary benefit remains unclear. We propose that these gradients enable a dynamic and versatile biological system that acquires, analyzes, and responds to environmental information. We hypothesize that environmental signals are transmitted into the cell by ion fluxes along pre-existing gradients through gated ion-specific membrane channels. The consequent changes in cytoplasmic ion concentration can generate a local response or orchestrate global/regional cellular dynamics through wire-like ion fluxes along pre-existing and self-assembling cytoskeleton to engage the endoplasmic reticulum, mitochondria, and nucleus.
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Affiliation(s)
- Dipesh Niraula
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | - Issam El Naqa
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | - Jack Adam Tuszynski
- Departments of Physics and Oncology, University of Alberta, Edmonton, AB, Canada
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
| | - Robert A. Gatenby
- Departments of Radiology and Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
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2
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Di Gregorio E, Israel S, Staelens M, Tankel G, Shankar K, Tuszyński JA. The distinguishing electrical properties of cancer cells. Phys Life Rev 2022; 43:139-188. [PMID: 36265200 DOI: 10.1016/j.plrev.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
In recent decades, medical research has been primarily focused on the inherited aspect of cancers, despite the reality that only 5-10% of tumours discovered are derived from genetic causes. Cancer is a broad term, and therefore it is inaccurate to address it as a purely genetic disease. Understanding cancer cells' behaviour is the first step in countering them. Behind the scenes, there is a complicated network of environmental factors, DNA errors, metabolic shifts, and electrostatic alterations that build over time and lead to the illness's development. This latter aspect has been analyzed in previous studies, but how the different electrical changes integrate and affect each other is rarely examined. Every cell in the human body possesses electrical properties that are essential for proper behaviour both within and outside of the cell itself. It is not yet clear whether these changes correlate with cell mutation in cancer cells, or only with their subsequent development. Either way, these aspects merit further investigation, especially with regards to their causes and consequences. Trying to block changes at various levels of occurrence or assisting in their prevention could be the key to stopping cells from becoming cancerous. Therefore, a comprehensive understanding of the current knowledge regarding the electrical landscape of cells is much needed. We review four essential electrical characteristics of cells, providing a deep understanding of the electrostatic changes in cancer cells compared to their normal counterparts. In particular, we provide an overview of intracellular and extracellular pH modifications, differences in ionic concentrations in the cytoplasm, transmembrane potential variations, and changes within mitochondria. New therapies targeting or exploiting the electrical properties of cells are developed and tested every year, such as pH-dependent carriers and tumour-treating fields. A brief section regarding the state-of-the-art of these therapies can be found at the end of this review. Finally, we highlight how these alterations integrate and potentially yield indications of cells' malignancy or metastatic index.
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Affiliation(s)
- Elisabetta Di Gregorio
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, Corso Duca degli Abruzzi, 24, Torino, 10129, TO, Italy; Autem Therapeutics, 35 South Main Street, Hanover, 03755, NH, USA
| | - Simone Israel
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, Corso Duca degli Abruzzi, 24, Torino, 10129, TO, Italy; Autem Therapeutics, 35 South Main Street, Hanover, 03755, NH, USA
| | - Michael Staelens
- Department of Physics, University of Alberta, 11335 Saskatchewan Drive NW, Edmonton, T6G 2E1, AB, Canada
| | - Gabriella Tankel
- Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, ON, Canada
| | - Karthik Shankar
- Department of Electrical & Computer Engineering, University of Alberta, 9211 116 Street NW, Edmonton, T6G 1H9, AB, Canada
| | - Jack A Tuszyński
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, Corso Duca degli Abruzzi, 24, Torino, 10129, TO, Italy; Department of Physics, University of Alberta, 11335 Saskatchewan Drive NW, Edmonton, T6G 2E1, AB, Canada; Department of Oncology, University of Alberta, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada.
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3
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Wu R, Guzman-Sepulveda J, Kalra A, Tuszynski J, Dogariu A. Thermal hysteresis in microtubule assembly/disassembly dynamics: The aging-induced degradation of tubulin dimers. Biochem Biophys Rep 2022; 29:101199. [PMID: 35036585 PMCID: PMC8749447 DOI: 10.1016/j.bbrep.2021.101199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 11/08/2022] Open
Abstract
The assembly/disassembly of biological macromolecules plays an important role in their biological functionalities. Although the dynamics of tubulin polymers and their super-assembly into microtubule structures is critical for many cellular processes, details of their cyclical polymerization/depolymerization are not fully understood. Here, we use a specially designed light scattering technique to continuously examine the effects of temperature cycling on the process of microtubule assembly/disassembly. We observe a thermal hysteresis loop during tubulin assembly/disassembly, consistently with earlier reports on the coexistence of tubulin and microtubules as a phase transition. In a cyclical process, the structural hysteresis has a kinetic component that depends on the rate of temperature change but also an intrinsic thermodynamic component that depends on the protein topology, possibly related to irreversible processes. Analyzing the evolution of such thermal hysteresis loops over successive cycles, we found that the assembly/disassembly ceases after some time, which is indicative of protein aging leading to its inability to self-assemble after a finite number of temperature cycles. The emergence of assembly-incompetent tubulin could have major consequences for human pathologies related to microtubules, including aging, neurodegenerative diseases and cancer.
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Affiliation(s)
- R. Wu
- CREOL, College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816, USA
| | - J.R. Guzman-Sepulveda
- CREOL, College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816, USA
| | - A.P. Kalra
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta, T6G 2M9, Canada
| | - J.A. Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta, T6G 2M9, Canada
- DIMEAS, Polytechnic di Torino, Turin, I-10129, Italy
| | - A. Dogariu
- CREOL, College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816, USA
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Havelka D, Zhernov I, Teplan M, Lánský Z, Chafai DE, Cifra M. Lab-on-chip microscope platform for electro-manipulation of a dense microtubules network. Sci Rep 2022; 12:2462. [PMID: 35165315 PMCID: PMC8844285 DOI: 10.1038/s41598-022-06255-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/18/2022] [Indexed: 12/20/2022] Open
Abstract
Pulsed electric field (PEF) technology is promising for the manipulation of biomolecular components and has potential applications in biomedicine and bionanotechnology. Microtubules, nanoscopic tubular structures self-assembled from protein tubulin, serve as important components in basic cellular processes as well as in engineered biomolecular nanosystems. Recent studies in cell-based models have demonstrated that PEF affects the cytoskeleton, including microtubules. However, the direct effects of PEF on microtubules are not clear. In this work, we developed a lab-on-a-chip platform integrated with a total internal reflection fluorescence microscope system to elucidate the PEF effects on a microtubules network mimicking the cell-like density of microtubules. The designed platform enables the delivery of short (microsecond-scale), high-field-strength (\documentclass[12pt]{minimal}
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\begin{document}$$\le$$\end{document}≤ 25 kV/cm) electric pulses far from the electrode/electrolyte interface. We showed that microsecond PEF is capable of overcoming the non-covalent microtubule bonding force to the substrate and translocating the microtubules. This microsecond PEF effect combined with macromolecular crowding led to aggregation of microtubules. Our results expand the toolbox of bioelectronics technologies and electromagnetic tools for the manipulation of biomolecular nanoscopic systems and contribute to the understanding of microsecond PEF effects on a microtubule cytoskeleton.
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5
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Bell CJ, Potts KG, Hitt MM, Pink D, Tuszynski JA, Lewis JD. Novel colchicine derivative CR42-24 demonstrates potent anti-tumor activity in urothelial carcinoma. Cancer Lett 2022; 526:168-179. [PMID: 34838691 DOI: 10.1016/j.canlet.2021.11.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023]
Abstract
Bladder cancers, and specifically urothelial carcinoma, have few effective treatment options, and tumors typically develop resistance against standard of care chemotherapies leading to significant mortality. The development of alternative therapies with increased selectivity and improved tolerability would significantly impact this patient population. Here, we investigate a novel colchicine derivative, CR42-24, with increased selectivity for the βIII tubulin subtype as a treatment for urothelial carcinoma. βIII tubulin is a promising target due to its low expression in healthy tissues and its clinical association with poor prognosis. This study demonstrated that CR42-24 is selectively cytotoxic to several cancer cell lines at low nanomolar IC50, with high activity in bladder cancer cell lines both in vitro and in vivo. CR42-24 monotherapy in an aggressive urothelial carcinoma xenograft model results in effective control when treated early. We observed significant ablation of large tumors and patient-derived xenografts at low doses with excellent tolerability. CR42-24 was highly synergistic in combination with the standard of care chemotherapies gemcitabine and cisplatin, further increasing its therapeutic potential as a novel treatment for urothelial carcinoma.
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Affiliation(s)
- Clayton J Bell
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Kyle G Potts
- Department Microbiology, Immunology & Infectious Diseases, Alberta Children's Hospital Research Institute, T2N-4N1, Canada
| | - Mary M Hitt
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Desmond Pink
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - John D Lewis
- Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada.
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Kalra AP, Eakins BB, Vagin SI, Wang H, Patel SD, Winter P, Aminpour M, Lewis JD, Rezania V, Shankar K, Scholes GD, Tuszynski JA, Rieger B, Meldrum A. A Nanometric Probe of the Local Proton Concentration in Microtubule-Based Biophysical Systems. NANO LETTERS 2022; 22:517-523. [PMID: 34962401 DOI: 10.1021/acs.nanolett.1c04487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We show a double-functional fluorescence sensing paradigm that can retrieve nanometric pH information on biological structures. We use this method to measure the extent of protonic condensation around microtubules, which are protein polymers that play many roles crucial to cell function. While microtubules are believed to have a profound impact on the local cytoplasmic pH, this has been hard to show experimentally due to the limitations of conventional sensing techniques. We show that subtle changes in the local electrochemical surroundings cause a double-functional sensor to transform its spectrum, thus allowing a direct measurement of the protonic concentration at the microtubule surface. Microtubules concentrate protons by as much as one unit on the pH scale, indicating a charge storage role within the cell via the localized ionic condensation. These results confirm the bioelectrical significance of microtubules and reveal a sensing concept that can deliver localized biochemical information on intracellular structures.
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Affiliation(s)
- Aarat P Kalra
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States of America
| | - Boden B Eakins
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Sergei I Vagin
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85747 Garching bei München, Germany
| | - Hui Wang
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2E1, Canada
| | - Sahil D Patel
- Electrical and Computer Engineering Department, University of California, Santa Barbara, California 93106, United States of America
| | - Philip Winter
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Maral Aminpour
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - John D Lewis
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University, Edmonton, Alberta T5J 4S2, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States of America
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2E1, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino 10129, Italy
| | - Bernhard Rieger
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85747 Garching bei München, Germany
| | - Alkiviathes Meldrum
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2E1, Canada
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7
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Eakins BB, Patel SD, Kalra AP, Rezania V, Shankar K, Tuszynski JA. Modeling Microtubule Counterion Distributions and Conductivity Using the Poisson-Boltzmann Equation. Front Mol Biosci 2021; 8:650757. [PMID: 33842549 PMCID: PMC8027483 DOI: 10.3389/fmolb.2021.650757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Microtubules are highly negatively charged proteins which have been shown to behave as bio-nanowires capable of conducting ionic currents. The electrical characteristics of microtubules are highly complicated and have been the subject of previous work; however, the impact of the ionic concentration of the buffer solution on microtubule electrical properties has often been overlooked. In this work we use the non-linear Poisson Boltzmann equation, modified to account for a variable permittivity and a Stern Layer, to calculate counterion concentration profiles as a function of the ionic concentration of the buffer. We find that for low-concentration buffers ([KCl] from 10 μM to 10 mM) the counterion concentration is largely independent of the buffer's ionic concentration, but for physiological-concentration buffers ([KCl] from 100 to 500 mM) the counterion concentration varies dramatically with changes in the buffer's ionic concentration. We then calculate the conductivity of microtubule-counterion complexes, which are found to be more conductive than the buffer when the buffer's ionic concentrations is less than ≈100 mM and less conductive otherwise. These results demonstrate the importance of accounting for the ionic concentration of the buffer when analyzing microtubule electrical properties both under laboratory and physiological conditions. We conclude by calculating the basic electrical parameters of microtubules over a range of ionic buffer concentrations applicable to nanodevice and medical applications.
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Affiliation(s)
- Boden B Eakins
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Sahil D Patel
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Aarat P Kalra
- Department of Chemistry, Princeton University, Princeton, NJ, United States
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University, Edmonton, AB, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB, Canada.,Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
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