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Roy L, Chatterjee O, Bose D, Roy A, Chatterjee S. Noncoding RNA as an influential epigenetic modulator with promising roles in cancer therapeutics. Drug Discov Today 2023; 28:103690. [PMID: 37379906 DOI: 10.1016/j.drudis.2023.103690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/11/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
The epigenetic landscape has an important role in cellular homeostasis and its deregulation leads to cancer. Noncoding (nc)RNA networks function as major regulators of cellular epigenetic hallmarks via regulation of vital processes, such as histone modification and DNA methylation. They are integral intracellular components affecting multiple oncogenic pathways. Thus, it is important to elucidate the effects of ncRNA networks on epigenetic programming that lead to the initiation and progression of cancer. In this review, we summarize the effects of epigenetic modification influenced by ncRNA networks and crosstalk between diverse classes of ncRNA, which could aid the development of patient-specific cancer therapeutics targeting ncRNAs, thereby altering cellular epigenetics.
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Affiliation(s)
- Laboni Roy
- Department of Biophysics, Bose Institute, Kolkata 700091, India
| | | | - Debopriya Bose
- Department of Biophysics, Bose Institute, Kolkata 700091, India
| | - Ananya Roy
- Department of Biophysics, Bose Institute, Kolkata 700091, India
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Zhdanov VP. Lipid nanoparticles with ionizable lipids: Statistical aspects. Phys Rev E 2022; 105:044405. [PMID: 35590555 DOI: 10.1103/physreve.105.044405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Lipid nanoparticles (LNPs) with size ∼100 nm are now used for fabrication of a new generation of drugs and antiviral vaccines. To optimize their function or, more specifically, interaction with cell membranes, their composition often includes ionizable lipids which are neutral or cationic (after association with H^{+}). Physically, such LNPs represent an interesting example of mesoscopic nanosystems with complex and far from understood properties. Experimentally, they can be studied at cell-membrane mimics. Herein, I analyze theoretically three related aspects. (i) I describe how the extent of protonation of ionizable lipids located at the surface of LNPs depends on the H^{+} concentration by using the phenomenological Langmuir-Stern and Poisson-Boltzmann models with continuum distribution of charges and the dipole model with discrete charges. In these frameworks, the H^{+} adsorption isotherms are predicted to be close to Langmuirian provided the fraction of ionizable lipids is smaller than 0.5. (ii) I scrutinize the interaction between charged LNPs and their interaction with a supported lipid bilayer (SLB) by using the phenomenological theory and lattice-gas model. The long-term association or attachment is predicted provided the charges are opposite. The models make it possible to estimate the size of the contact region (provided a LNP is not deformed) and the number of lipid-lipid bonds in this region. (iii) I briefly discuss denaturation of a LNP during interaction with the SLB and argue that it may occur via a few stepwise transitions.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden and Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia
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Deng XJ, Zheng HL, Ke XQ, Deng M, Ma ZZ, Zhu Y, Cui YY. Hsa-miR-34a-5p reverses multidrug resistance in gastric cancer cells by targeting the 3'-UTR of SIRT1 and inhibiting its expression. Cell Signal 2021; 84:110016. [PMID: 33894312 DOI: 10.1016/j.cellsig.2021.110016] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022]
Abstract
Multidrug resistance (MDR) is a major obstacle to chemotherapy, which leads to ineffective chemotherapy, an important treatment strategy for gastric cancer (GC). The abnormality of microRNAs (miRNAs) is critical to the occurrence and progression of MDR in various tumors. In this study, hsa-miR-34a-5p was found to be decreased in multidrug resistant GC cells SGC-7901/5-Fluorouracil (SGC-7901/5-Fu) compared to the parental SGC-7901 cells. Overexpression of hsa-miR-34a-5p in SGC-7901/5-Fu cells promoted apoptosis and decreased migration and invasiveness after chemotherapy. In addition, overexpression of hsa-miR-34a-5p suppressed the growth of drug-resistant tumor in vivo. The mechanism of the effects of hsa-miR-34a-5p could include the regulation of the expression of Sirtuin 1 (SIRT1), P-glycoprotein (P-gp) or Multidrug resistance-related protein 1 (MRP1) through direct binding to the 3'-untranslated region (UTR) of SIRT1. Functional gain-and-loss experiments indicated that hsa-miR-34a-5p enhances the chemotherapy sensitivity of MDR GC cells by inhibiting SIRT1, P-gp and MRP1. In conclusion, hsa-miR-34a-5p can reverse the MDR of GC cells by inhibiting the expression of SIRT1, P-gp or MRP1.
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Affiliation(s)
- X J Deng
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China; Department of Gastroenterology, The First Affiliated Hospital of Jinan University, China.
| | - H L Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China
| | - X Q Ke
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China
| | - M Deng
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China
| | - Z Z Ma
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China
| | - Y Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China
| | - Y Y Cui
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, China
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Chauhan N, Jaggi M, Chauhan SC, Yallapu MM. COVID-19: fighting the invisible enemy with microRNAs. Expert Rev Anti Infect Ther 2020; 19:137-145. [PMID: 32814446 DOI: 10.1080/14787210.2020.1812385] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The novel coronavirus (CoV) disease 2019 (COVID-19) is a viral infection that causes severe acute respiratory syndrome (SARS). It is believed that early reports of COVID-19 cases were noticed in December 2019 and soon after it became a global public health emergency. It is advised that COVID-19 transmits through human to human contact and in most cases, it remains asymptomatic. Several approaches are being utilized to control the outbreak of this fatal viral disease. microRNAs (miRNAs) are known signature therapeutic tool for the viral diseases; they are small non-coding RNAs that target the mRNAs to inhibit their post-transcriptional expression, therefore, impeding their functions, can serve as watchdogs or micromanagers in the cells. AREAS COVERED This review work delineated COVID-19 and its association with SARS and Middle East respiratory syndrome (MERS), the possible role of miRNAs in the pathogenesis of COVID-19, and therapeutic potential of miRNAs and their effective delivery to treat COVID-19. EXPERT OPINION This review highlighted the importance of various miRNAs and their potential role in fighting with this pandemic as therapeutic molecules utilizing nanotechnology.
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Affiliation(s)
- Neeraj Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA.,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA.,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA
| | - Subhash C Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA.,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA
| | - Murali M Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA.,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley , McAllen, Texas, USA
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The role of cooperativity in a p53-miR34 dynamical mathematical model. J Theor Biol 2020; 495:110252. [PMID: 32199858 DOI: 10.1016/j.jtbi.2020.110252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 01/07/2023]
Abstract
The objective of this study is to evaluate the role of cooperativity, captured by the Hill coefficient, in a minimal mathematical model describing the interactions between p53 and miR-34a. The model equations are analyzed for negative, none and normal cooperativity using a specific version of bifurcation theory and they are solved numerically. Special attention is paid to the sign of so-called first Lyapunov value. Interpretations of the results are given, both according to dynamic theory and in biological terms. In terms of cell signaling, we propose the hypothesis that when the outgoing signal of a system spends a physiologically significant amount of time outside of its equilibrium state, then the value of that signal can be sampled at any point along the trajectory towards that equilibrium and indeed, at multiple points. Coupled with non-linear behavior, such as that caused by cooperativity, this feature can account for a complex and varied response, which p53 is known for. From dynamical point of view, we found that when cooperativity is negative, the system has only one stable equilibrium point. In the absence of cooperativity, there is a single unstable equilibrium point with a critical boundary of stability. In the case with normal cooperativity, the system can have one, two, or three steady states with both, bi-stability and bi-instability occurring.
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Zhdanov VP. Intracellular RNA delivery by lipid nanoparticles: Diffusion, degradation, and release. Biosystems 2019; 185:104032. [PMID: 31563119 DOI: 10.1016/j.biosystems.2019.104032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 07/15/2019] [Indexed: 01/09/2023]
Abstract
Various RNAs (siRNAs, miRNAs, or mRNAs) can be delivered into cells by lipid nanoparticles (LNPs) of 50-150 nm in diameter. The subsequent RNA release from LNPs may occur via various scenarios. Herein, two related kinetic models are proposed. The first model takes into account that LNPs are often porous so that RNA molecules diffuse in and detach from nanopores. The analysis is focused on RNA diffusion from a pore. The analytical expression obtained for the RNA escape rate constant is used to identify the difference in the release of siRNAs, miRNAs, and mRNAs. The key message here is that the mRNA diffusion from pores appears to be too slow, and accordingly the mRNA release seems to occur primarily via degradation of LNPs. The second coarse-grained model describes the diffusion-mediated release of RNA from a LNP in the situation when this process is accompanied by the LNP degradation at the lipid-solution interface. The corresponding kinetics are shown in detail at different relative rates of the RNA diffusion and LNP degradation. Potentially, this can help to interpret drug plasma levels after various dosing regimens.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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Zhdanov VP. Slow relaxation during and after perturbation of bistable kinetics of gene expression. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:297-302. [PMID: 30903265 DOI: 10.1007/s00249-019-01358-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/27/2018] [Accepted: 03/09/2019] [Indexed: 01/09/2023]
Abstract
After a short perturbation of a bistable genetic network, it returns to its initial steady state or transits to another steady state. The time scale characterizing such transient regimes can be appreciably longer compared to those of the degradation of the perturbed mRNAs and proteins. The author shows in detail the specifics of this slowdown of the transient kinetics using mean-field kinetic equations and Monte Carlo simulations. Attention is focused on nanocarrier-mediated delivery and release of short non-coding RNA (e.g., miRNA or siRNA) into cells with subsequent suppression of the populations of the targeted mRNA and corresponding protein.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden.
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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