2019 Fiscal Year Annual Research Report
心筋症関連ミトコンドリア・核内遺伝子の協奏的制御を可能にする人工転写因子の開発
| Project/Area Number |
19H03349
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| Research Institution | Kyoto University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
杉山 弘 京都大学, 理学研究科, 教授 (50183843)
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| Project Period (FY) |
2019-04-01 – 2022-03-31
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| Keywords | ピロールイミダゾールポリアミド / エピジェネティクス / 人工転写因子 / ナノテクノロジー / 心筋症 |
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| Outline of Annual Research Achievements |
In this fiscal year, we have successfully performed proof-of-concept (POC) studies to use a multi-disciplinary approach essential in constructing nanoparticle-based epigenetic codes termed SMART-TFs for mitochondrial and nuclear genes. In particular, we explored a new direction of harnessing the nanopore sequencing for epitranscriptomics and artificial intelligence for bioimaging. We have successfully created a new version of synthetic biomimetic epigenetic code for nuclear genes termed e-PIP-HoGu capable of mimicking the natural transcription factors (TFs) in terms of structure and function. This novel small molecule not only have improved design to target specific DNA nucleic acid sequences with flexible gap spacings, but also are non-toxic, cell-permeable, water-soluble, and chemically stable. We have also screened and identified a biomimetic epigenetic code capable of triggering AMPK-related genes and ensue mitochondrial biogenesis in T-cells. A synthetic TF for the mesoderm determining stemness factor SOX2 was repurposed and we demonstrated its efficacy in a mouse model to trigger targeted suppression of metastasis. Also, an image-based artificial intelligence (AI) program was developed and we performed a POC to accurately predict tumor and COVID-19 progression. We also synthesized quantum-sized pre-version of SMART-TFs and demonstrated that it can specifically localize inside the mitochondria. We published five articles and have four more under review. The outreach activity this year also was well-received and facilitated new important collaborations.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
We achieved our primary aim of successfully integrating diverse disciplines like nanotechnology, synthetic organic chemistry and molecular biology by introducing cutting-edge techniques like machine learning and nanopore sequencing. This fiscal year, we provided a strong platform with proof-of-concept studies upon which we can accelerate our future course of study to accomplish the milestones of our project to construct nanoparticle-based biomimetic epigenetic codes termed SMART-TFs for mitochondrial and nuclear genes. The successful creation of the dual-functional, epigenetically active small molecule capable of introducing targeted acetylation is an important leap for our project. We also were able to synthesize, characterize and sequentially assemble the functional and DNA-binding domains of the SMART-TFs. The incorporation of nanopore sequencing technology and artificial intelligence program further enhanced our research as we could now rapidly perform epigenome analysis. While the publication on the mitochondrial gene regulation and nanoparticle construction is still pending, our current results indicate that it is feasible to achieve SMART-TFs capable of switching ON and OFF our target gene(s) of interest. We also fostered our international collaboration with the JSPS exchange programs where Prof. Li Cai from Rutgers University, USA visited us for three months and our team member Takuya Hidaka visited AO Research Institute for two months. Taken together, we crossed the milestones mentioned in the project and may cover more new research areas this year.
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| Strategy for Future Research Activity |
Encouraged with our proof-of-concept studies, we have been creating quantum-sized nanoparticles that are sequentially assembled with mitochondrial penetrating peptide and selective DNA-binding pyrrole-imidazole polyamides. We have screened and identified biomimetic epigenetic codes capable of inducing AMPK-related gene networks associated with mitochondrial biogenesis and alter the generation of reactive oxygen species. We are screening to identify functional molecules that can be incorporated into the SMART-TFs to precisely control ROS generation. Our chemical biology approach to enhance the detection efficiency of nanopore-sequencing technology is expected to not only contribute our research but also could establish a new methodology to identify the modification in nucleic acids. The artificial intelligence program reported in our POC study is expected to precisely detect the nuclear and mitochondrial localization efficacy of SMART-TFs. We are also exploring the materials capable of substituting the small molecules that can scavenge reactive oxygen species. We aim to make good use of our international collaborations and expect to summarize the research results and publish them in high impact research journals. Our future course of study will focus on evaluating the bioefficacy of our synthetic and SMART-TFs by employing them in a step-wise manner and analyze their effect on genetic and epigenetic profiles.
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