1
|
Fujita H, Haruki T, Sudo K, Koga Y, Nakamura Y, Abe K, Yoshida Y, Koizumi K, M Watanabe T. Yuragi biomarker concept for evaluating human induced pluripotent stem cells using heterogeneity-based Raman finger-printing. Biophys Physicobiol 2024; 21:e211016. [PMID: 39175855 PMCID: PMC11338688 DOI: 10.2142/biophysico.bppb-v21.s016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/21/2024] [Indexed: 08/24/2024] Open
Abstract
Considering the fundamental mechanism causing singularity phenomena, we performed the following abduction: Assuming that a multicellular system is driven by spontaneous fluctuation of each cell and dynamic interaction of the cells, state transition of the system would be experimentally predictable from cellular heterogeneity. This study evaluates the abductive hypothesis by analyzing cellular heterogeneity to distinguish pre-state of state transition of differentiating cells with Raman spectroscopy and human induced pluripotent stem cells (hiPSCs) technique. Herein, we investigated the time development of cellular heterogeneity in Raman spectra during cardiomyogenesis of six hiPSC lines and tested two types of analyses for heterogeneity. As expected, some spectral peaks, possibly attributed to glycogen, correctively exhibited higher heterogeneity, prior to intensity changes of the spectrum in the both analyses in the all cell-lines tested. The combination of spectral data and heterogeneity-based analysis will be an approach to the arrival of biology that uses not only signal intensity but also heterogeneity as a biological index.
Collapse
Affiliation(s)
- Hideaki Fujita
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Takayuki Haruki
- Faculty of Sustainable Design, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Kazuhiro Sudo
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, Tsukuba, Ibaragi 305-0074, Japan
| | - Yumiko Koga
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, Tsukuba, Ibaragi 305-0074, Japan
| | - Yukio Nakamura
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, Tsukuba, Ibaragi 305-0074, Japan
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, Tsukuba, Ibaragi 305-0074, Japan
| | - Yasuhiko Yoshida
- Department of Intellectual Information Engineering, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Laboratory of Drug Discovery and Development for Pre-disease, Division of Presymptomatic Disease, Department of Re-search and Development and Department of Academia-Industry-Government Collaboration, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Tomonobu M Watanabe
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan
| |
Collapse
|
2
|
Yonezawa S, Haruki T, Koizumi K, Taketani A, Oshima Y, Oku M, Wada A, Sato T, Masuda N, Tahara J, Fujisawa N, Koshiyama S, Kadowaki M, Kitajima I, Saito S. Establishing Monoclonal Gammopathy of Undetermined Significance as an Independent Pre-Disease State of Multiple Myeloma Using Raman Spectroscopy, Dynamical Network Biomarker Theory, and Energy Landscape Analysis. Int J Mol Sci 2024; 25:1570. [PMID: 38338848 PMCID: PMC10855579 DOI: 10.3390/ijms25031570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Multiple myeloma (MM) is a cancer of plasma cells. Normal (NL) cells are considered to pass through a precancerous state, such as monoclonal gammopathy of undetermined significance (MGUS), before transitioning to MM. In the present study, we acquired Raman spectra at three stages-834 NL, 711 MGUS, and 970 MM spectra-and applied the dynamical network biomarker (DNB) theory to these spectra. The DNB analysis identified MGUS as the unstable pre-disease state of MM and extracted Raman shifts at 1149 and 1527-1530 cm-1 as DNB variables. The distribution of DNB scores for each patient showed a significant difference between the mean values for MGUS and MM patients. Furthermore, an energy landscape (EL) analysis showed that the NL and MM stages were likely to become stable states. Raman spectroscopy, the DNB theory, and, complementarily, the EL analysis will be applicable to the identification of the pre-disease state in clinical samples.
Collapse
Affiliation(s)
- Shota Yonezawa
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Takayuki Haruki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Sustainable Design, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Akinori Taketani
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Yusuke Oshima
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Makito Oku
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Akinori Wada
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Tsutomu Sato
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Naoki Masuda
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY 14260-2900, USA
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, NY 14260-2200, USA
| | - Jun Tahara
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Noritaka Fujisawa
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Shota Koshiyama
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Isao Kitajima
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| |
Collapse
|
3
|
Akagi K, Koizumi K, Kadowaki M, Kitajima I, Saito S. New Possibilities for Evaluating the Development of Age-Related Pathologies Using the Dynamical Network Biomarkers Theory. Cells 2023; 12:2297. [PMID: 37759519 PMCID: PMC10528308 DOI: 10.3390/cells12182297] [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: 08/20/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is the slowest process in a living organism. During this process, mortality rate increases exponentially due to the accumulation of damage at the cellular level. Cellular senescence is a well-established hallmark of aging, as well as a promising target for preventing aging and age-related diseases. However, mapping the senescent cells in tissues is extremely challenging, as their low abundance, lack of specific markers, and variability arise from heterogeneity. Hence, methodologies for identifying or predicting the development of senescent cells are necessary for achieving healthy aging. A new wave of bioinformatic methodologies based on mathematics/physics theories have been proposed to be applied to aging biology, which is altering the way we approach our understand of aging. Here, we discuss the dynamical network biomarkers (DNB) theory, which allows for the prediction of state transition in complex systems such as living organisms, as well as usage of Raman spectroscopy that offers a non-invasive and label-free imaging, and provide a perspective on potential applications for the study of aging.
Collapse
Affiliation(s)
- Kazutaka Akagi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Isao Kitajima
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| |
Collapse
|
4
|
Oshima Y, Haruki T, Koizumi K, Yonezawa S, Taketani A, Kadowaki M, Saito S. Practices, Potential, and Perspectives for Detecting Predisease Using Raman Spectroscopy. Int J Mol Sci 2023; 24:12170. [PMID: 37569541 PMCID: PMC10418989 DOI: 10.3390/ijms241512170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Raman spectroscopy shows great potential for practical clinical applications. By analyzing the structure and composition of molecules through real-time, non-destructive measurements of the scattered light from living cells and tissues, it offers valuable insights. The Raman spectral data directly link to the molecular composition of the cells and tissues and provides a "molecular fingerprint" for various disease states. This review focuses on the practical and clinical applications of Raman spectroscopy, especially in the early detection of human diseases. Identifying predisease, which marks the transition from a healthy to a disease state, is crucial for effective interventions to prevent disease onset. Raman spectroscopy can reveal biological processes occurring during the transition states and may eventually detect the molecular dynamics in predisease conditions.
Collapse
Affiliation(s)
- Yusuke Oshima
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Takayuki Haruki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Sustainable Design, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-8555, Japan
| | - Shota Yonezawa
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Akinori Taketani
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| |
Collapse
|
5
|
Selvarajoo K, Giuliani A. Systems Biology and Omics Approaches for Complex Human Diseases. Biomolecules 2023; 13:1080. [PMID: 37509116 PMCID: PMC10377378 DOI: 10.3390/biom13071080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
For many years, there has been general interest in developing virtual cells or digital twin models [...].
Collapse
Affiliation(s)
- Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore (NUS), Singapore 117456, Singapore
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore 639798, Singapore
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| |
Collapse
|