Skip to main content

Advertisement

Log in

Soliton Dynamics and DDMC/sncRNAs Complex for Epigenetic Change to Normal Cells in TME

  • Published:
BioNanoScience Aims and scope Submit manuscript

Abstract

Complex by DDMC/sncRNAs(a-miR-155, piR-30074, and miR-125b) have shown the full recovery of mice from virus-induced sarcoma after treatment by changing to normal cells from cancer cells. With kinetic of inhibiting tumor growth, the difference from control \(\varvec{(mm^2)}\) of one intravenous injection and two intravenous injections is the same curvature and rate so that this is a soliton wave having a permanent form (velocity, shape) such as one faster soliton overcoming another one without any changing shape in the case of two intravenous injections. Signal transduction for this DDS must be Hill-type sigmoids following the nonlinear Schrödinger model by transfer of energy, sine-Gordon soliton model by momentum, and Fisher KPP soliton model by mass transfer. We find out that the cell outlet/inlet response of DDMC/sncRNAs is more dependent on the soliton signal not losing energy and shape without jamming communication. The endoplasmic reticulum-mitochondrial \(\varvec{Ca^{2+}}\) fluxes induced by soliton to Chromosome in nuclear will take place epigenetic modifications on 5-position of cytosine (5mC) by TET enzymes and thymine DNA glycosylase (TDG) as an overall intracellular reaction. By soliton flow, the result shows the equations of quantum mechanics can be related to the epigenetic control with \(\varvec{Ca^{2+}}\) fluxes followed by “induced fit model” Hill equation S-shaped.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Data Availability

The data that support the findings of this study are available within the article.

References

  1. Doi, T., Kuroda, S., Michikawa, T., et al. (2005). Inositol 1,4,5-trisphosphate-dependent Ca2+ threshold dynamics detect spike timing in cerebellar Purkinje cells. The Journal of Neuroscience, 25, 950–961.

    Article  Google Scholar 

  2. Englander, S. W., Kallenbach, J. A., & Litwin, S. (1980). Nature of the open state in long polynucleotide double helices: Possibility of soliton excitations. PNAS, 77, 7222–7226.

    Article  Google Scholar 

  3. Onishi, Y., Ji, R., Kobayashi, T., et al. (2022). Soliton-based signaling communication and supermolecular nano-complex by ddmc/ptx in tumor micro-environment. BioNanoScience

  4. Onishi, Y., Eshitai, Y., Ji, R. C., et al. (2018). A robust control system for targeting melanoma by a supermolecular DDMC/paclitaxel complex. Integrative Biology, 10, 549–554.

    Article  Google Scholar 

  5. Klimenko, O. V., & Sidorov, A. (2019). The full recovery of mice (Mus Musculus c57bl/6 strain) from virus-induced sarcoma after treatment with a complex of DDMC delivery system and sncRNAs. Non-coding RNA Research, 4, 69–78.

    Article  Google Scholar 

  6. Li, B. Q., Ma, Y. L., Li-Po, et al. (2017). Computers and mathematics with applications the n-loop soliton solutions for-dimensional Vakhnenko equation. Computers and Mathematics with Applications, 74, 504–512.

    Article  MathSciNet  Google Scholar 

  7. Onorato, M., Proment, D., Clauss, G., et al. (2013). Rogue waves from nonlinear Schrödinger breather solutions to sea-keeping test. PLOS ONE, 8, e54,629.

    Article  Google Scholar 

  8. Onishi, Y., Eshita, Y., Murashita, A., et al. (2005). Synthesis and characterization of 2-diethylaminoethyl(DEAE)-dextran-MMA graft copolymer for non-viral gene delivery vector. Journal of Applied Polymer Science, 98, 9–14.

    Article  Google Scholar 

  9. Onishi, Y., Eshita, Y., Murashita, A., et al. (2007). Characteristics of 2-diethylaminoethyl(DEAE)-dextran-MMA graft copolymer as a non-viral gene carrier. Nanomedicine: Nanotech, Biology and Medicine, 3, 184–191.

    Article  Google Scholar 

  10. Zhang, M., Wang, J., Zhang, K., et al. (2021). Ten-eleven translocation 1 mediated-DNA hydroxymethylation is required for myelination and remyelination in the mouse brain. Nature Communications, 12, 5091.

    Article  Google Scholar 

  11. Zhang, M., Wang, J., Zhang, K., et al. (2019). Homeostasis regulates myelination and synaptic functions. bioRxiv preprint.

  12. Kohli, R. M., & Zhang, Y. (2013). TET enzymes, TDG and the dynamics of DNA demethylation. Nature, 502, 472–479.

    Article  Google Scholar 

  13. Luan, F., Guerrero, R. C., Zhong, N., et al. (2014). Tetmediated formation of 5-hydroxymethylcytosine in RNA. Journal of the American Chemical Society, 136, 11582–11585.

    Article  Google Scholar 

  14. Pecorino, L. (2017). Molecular biology of cancer: Mechanisms, targets, and therapeutics. Tokyo: Medical Sciences International.

    Google Scholar 

  15. Craig, J. M. (2011). Epigenetics: A reference manual. Caister Academic Press, Victoria.

  16. Yomosa, S. (1974). Theory of the excited state of molecular complex in solution. Journal of the Physical Society of Japan, 36, 1655–1660.

    Article  Google Scholar 

  17. Klimenko, O. V., & Onishi, Y. (2018). Disappeared cancer cell by sncRNAs: Application of DDMC vector/sncRNAs complex for transformation of cancer cells into non-cancerous cells. Journal of Nanomedicine and Biotherapeutic Discovery, 8, 1.

    Article  Google Scholar 

  18. Matsumura, Y., & Maeda, H. (1986). A new concept for macromolecular therapeutics in cancer chemotherapy: Mechanism of tumoritropic accumulation of proteins and the antitumor agent smancs. Cancer Research, 12 Pt 1, 6387–6392.

    Google Scholar 

  19. Allen, T. M., & Chonn, A. (1987). Large unilamellar liposomes with low uptake into the reticuloendothelial system. FEBS Letters, 223, 42–46.

    Article  Google Scholar 

  20. Oku, N., Namba, Y., & Okada, S. (1992). Tumor accumulation of novel res-avoiding liposomes. Biochimica et Biophysica, 1126, 255–260.

    Article  Google Scholar 

  21. Barros, M. T. (2017). Ca2+-signaling-based molecular communication systems: Design and future research directions. Nano Communication Networks, 11, 103–113.

    Article  Google Scholar 

  22. Huang, X., Schwind, S., Yu, B., et al. (2013). Targeted delivery of microrna-29b by transferrin-conjugated anionic lipopolyplex nanoparticles: A novel therapeutic strategy in acute myeloid leukemia. Clinical Cancer Research, 19, 2355–23,567.

    Article  Google Scholar 

  23. Singh, R., & Saini, N. X. (2012). Downregulation of bcl2 by miRNAs augments druginduced apoptosis-a combined computational and experimental approach. Journal of Cell Science, 125, 1568–1578.

    Google Scholar 

  24. Cimmino, A., Calin, G. A., Fabbri, M., et al. (2005). miR-15 and miR-16 induce apoptosis by targeting bcl2. Proceedings of the National Academy of Sciences of the United States of America, 102, 13,944-13,949.

    Article  Google Scholar 

  25. Bouchie, A. (2013). First microRNA mimic enters clinic. Nature Biotechnology, 31, 577.

    Article  Google Scholar 

  26. Daige, C. L., Wiggins, J. F., Priddy, L., et al. (2014). Systemic delivery of a mir34a mimic as a potential therapeutic for liver cancer. Molecular Cancer Therapeutics, 13, 2352–2360.

    Article  Google Scholar 

  27. Agostini, M., & Knight, R. A. (2014). miR-34: From bench to bedside. Oncotarget, 5, 872–881.

    Article  Google Scholar 

  28. Pileczki, V., Cojocneanu-Petric, R., Maralani, M., et al. (2016). Sandulescu, r. micrornas as regulators of apoptosis mechanisms in cancer. Clujul Medical, 89, 50–55.

    Google Scholar 

  29. Klimenko, O. V. (2017). Joint action of the nano-sized system of small noncoding RNAs with DDMC vector and recombinant IL-7 reprograms A-549 lung adenocarcinoma cells into cd4+ cells. Immunotherapy (Los Angel), 3, 137.

    Article  Google Scholar 

  30. Liu, X., Li, J., Qin, F., et al. (2016). miR-152 as a tumor suppressor microRNA: Target recognition and regulation in cancer. Oncology Letters, 11, 3911–3916.

    Article  Google Scholar 

  31. Zhang, Y. J., Liu, X. C., Du, J., et al. (2015). miR-152 regulates metastases of non-small cell lung cancer cells by targeting neuropilin-1. International Journal of Clinical and Experimental Pathology, 8, 14,235-1424.

    Google Scholar 

  32. Klimenko, O. V. (2017). Small non-coding RNAs as regulators of structural evolution and carcinogenesis. Non-coding RNA Research, 2, 88–92.

    Article  Google Scholar 

  33. Pal-Bhadra, M., Leibovitch, B. A., Gandhi, S. G., et al. (2004). Heterochromatic silencing and HP1 localization in drosophila are dependent on the RNAi machinery. Science, 303, 669–672.

    Article  Google Scholar 

  34. Brower-Toland, B., Findley, S. D., Jiang, L., et al. (2007). Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes and Development, 21, 2300–2310.

    Article  Google Scholar 

  35. Yin, H., & Lin, H. (2007). An epigenetic activation role of PIWI and a PIWI-associated piRNA in Drosophila melanogaster. Nature, 450, 304–308.

    Article  Google Scholar 

  36. Tian, Y., Guo, R., Shi, B., et al. (2016). MicroRNA-30a promotes chondrogenic differentiation of mesenchymal stem cells through inhibiting delta-like 4 expression. Life Sciences, 148, 220–228.

    Article  Google Scholar 

  37. Otto, T., Candido, S. V., Pilarz, M. S., et al. (2017). Cell cycle-targeting microRNAs promote differentiation by enforcing cell-cycle exit. Proceedings of the National Academy of Sciences of the United States of America, 114, 10,660-10,665.

    Article  Google Scholar 

  38. Jin, M., Wu, Y., Wang, Y., et al. (2016). MicroRNA-29a promotes smooth muscle cell differentiation by targeting YY1. Stem Cell Research, 17, 277–284.

    Article  Google Scholar 

  39. Chen, C. H., Lu, H. T., Tsuang, Y. H., et al. (2017). MicroRNA-215 promotes proliferation and differentiation of osteoblasts by regulation of c-fos. International Journal of Clinical and Experimental Pathology, 10, 6536–6543.

    Google Scholar 

  40. Le, M. T. N., Xie, H., Zhou, B., et al. (2009). MicroRNA-125b promotes neuronal differentiation in human cells by repressing multiple targets. Molecular Cell Biology, 29, 5290–5305.

    Article  Google Scholar 

  41. Fujii, T., Shimada, K., Tatsumi, Y., et al. (2015). MicroRNA-145 promotes differentiation in human urothelial carcinoma through down-regulation of syndecan-1. BMC Cancer, 15, 818.

    Article  Google Scholar 

  42. Mai, H., Lini, Y., Zhaoi, Z. A., et al. (2016). MicroRNA-127 promotes mesendoderm differentiation of mouse embryonic stem cells by targeting leftright determination factor 2. Journal of Biological Chemistry, 291, 12,126-12,135.

    Article  Google Scholar 

  43. Klimenko, O. V., & Shtilman, M. I. (2013). Transfection of Kasumi-1 cells with a new type of polymer carriers loaded with miR-155 and antago-miR-155. Cancer Gene Therapy, 20, 237–241.

    Article  Google Scholar 

  44. Yoshikawa, Y., Tsumoto, K., & Yoshikawa, K. (2002). Switching of higher-order structure of DNA and gene expression. Seibutsu Butsuri, 42, 179–184.

    Article  Google Scholar 

  45. Klimenko, O. V. (2017). Toxicity and transfection efficiency of new non-viral delivery systems for small non-coding RNAs: Amphiphilic poly(n-vinylpyrrolidone) and diethylaminoethyl-dextran-methacrylic acid methyl ester copolymer. Advanced Science, Engineering and Medicine, 9, 426–431.

    Article  Google Scholar 

  46. Suzuki, H., Yamagata, K., Sugimoto, K., et al. (2009). Modulation of microRNA processing by p53. Nature, 460, 529–533.

    Article  Google Scholar 

  47. Filippov, A. (2000). The versatile soliton: Modern Birkhauser classics. Boston: Birkhauser.

    Google Scholar 

  48. Braun, O. M., & Kivshar, Y. (2004). The Frenkel-Kontorova model: Concepts, methods, and applications. Berlin: Springer-Verlag.

    Book  Google Scholar 

  49. Novikov, S. P., Manakov, S. V., Pitaevskiii, L. P., et al. (1984). Theory of solitons: The inverse scattering method. Berlin: Springer-Verlag.

    Google Scholar 

  50. Helmholtz, H. (1850). Messungen uber den zeitlichen verlauf der zuchung animalisher muskeln und die fortplanzungsgeschwindig-keit der reizung in der nerven. Archives of Anatomy and Physiology, 276, 71–73.

    Google Scholar 

  51. Hodgkin, A. L., & Huxley, A. F. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. Journal of Physiology, 117, 500–544.

    Article  Google Scholar 

  52. Fitzhugh, R. (1969). Biological engineering. New York: McGraw-Hill.

    Google Scholar 

  53. Nagumo, J., Arimoto, S., & Yoshizawa, S. (1962). An active pulse transmission line simulating nerve axon. Proceedings of the IRE, 50, 2061–2070.

    Article  Google Scholar 

  54. Scott, A. (1979). Sine-gordon breather dynamics. Physica Scripta, 20, 395–401.

    Article  MathSciNet  Google Scholar 

  55. Frank, S. A. (2013). Input-output relations in biological systems: Measurement, information and the hill equation. Biology Direct, 8, 1–25.

    Article  Google Scholar 

  56. Toda, M. (1967). Vibration of a chain with a non-linear interaction. Journal of the Physical Society of Japan, 22, 431–436.

    Article  Google Scholar 

  57. Warburg, O., Wind, F., & Negelein, E. (1927). The metabolism of tumors in the body. Journal of General Physiology, 8, 519–530.

  58. Avalle, L., Camporeale, A., Morciano, G., et al. (2019). Stat3 localizes to the er, acting as a gatekeeper for er-mitochondrion ca2+ fluxes and apoptotic responses. Cell Death and Differentiation, 26, 932–942.

    Article  Google Scholar 

  59. Berridge, M. J., Bootman, M. D., & Roderick, H. L. (2003). Calcium signalling: Dynamics, homeostasis and remodelling. Nature Reviews. Molecular Cell Biology, 4, 517–529.

  60. Hideshima, T., & Kato, Y. (2006). Oscillatory reaction of catalase wrapped by liposome. Biophysical Chemistry, 124, 100–105.

  61. Savic, R., Luo, L., Eisenberg, A., et al. (2003). Micellar nanocontainers distribute to defined cytoplasmic organelles. Science, 300, 615–618.

    Article  Google Scholar 

  62. Nagahama, K., Sano, Y., Inui, M., et al. (2020). Bioinspired cell nuclear nanotransporters generated by self-assembly of amphiphilic polysaccharide-amino acid derivatives conjugates. Advanced Biosystems, 4, e1900,189.

    Article  Google Scholar 

Download references

Acknowledgements

We are deeply grateful to the late Prof. Terukiyo Hanafusa of Hiroshima University for his discussion of DDMC.

Funding

Not applicable

Author information

Authors and Affiliations

Authors

Contributions

YO designed and performed the data analysis, and wrote the manuscript. OK conducted the experiments, performed the data analysis, and wrote the manuscript. RJ, TK, MM, JY, Nk, and UE reviewed the manuscript. MO supervised the project.

Corresponding author

Correspondence to Yasuhiko Onishi.

Ethics declarations

Informed Consent

Not applicable

Conflict of Interest

The authors declare no competing interests.

Research Involving Humans and Animals Statement

Not applicable

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Klimenko, O.V., Ji, RC., Kobayashi, T. et al. Soliton Dynamics and DDMC/sncRNAs Complex for Epigenetic Change to Normal Cells in TME. BioNanoSci. (2023). https://doi.org/10.1007/s12668-023-01258-z

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12668-023-01258-z

Keywords

Navigation