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Stem cell differentiation platform utilizing Bayesian machine learning

Research Project

Project/Area Number 20KK0160
Research Category

Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 44:Biology at cellular to organismal levels, and related fields
Research InstitutionKyoto University

Principal Investigator

Packwood Daniel  京都大学, 高等研究院, 准教授 (40640884)

Co-Investigator(Kenkyū-buntansha) 安井 孝介  京都大学, 高等研究院, 特定助教 (10877640)
ABDALKADER Rodi  立命館大学, 立命館グローバル・イノベーション研究機構, 准教授 (20839964)
Project Period (FY) 2020-10-27 – 2025-03-31
Project Status Granted (Fiscal Year 2023)
Budget Amount *help
¥18,850,000 (Direct Cost: ¥14,500,000、Indirect Cost: ¥4,350,000)
Fiscal Year 2023: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2022: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
Fiscal Year 2021: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
Fiscal Year 2020: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Keywordsstem cell / cardiomyocyte / data / machine learning / regression / descriptors / iPS / cardiomyocite / statistics / small molecule / Stem cell / Cardiomyocite / Screening / Machine learning / DFT / Data-driven / ベイズ最適化 / 材料情報 / 機械学習 / 幹細胞分化増殖 / 再生医療
Outline of Research at the Start

In order to generate tissues for clinical purposes, cells of a specific type must be created. Such cells are usually generated by adding nutrients to a stem cell culture medium. This project will develop an AI-based platform for efficient identification nutrients for inducing the target cell state.

Outline of Annual Research Achievements

This project aims to predict compounds for inducing cardiac differentiation of stem cells using data science. During FY2022, we created a series of regression models which can predict whether small organic molecules can be used as WNT inhibitors in a cardiac differentiation protocol. In FY2023, we extended this work as follows: (i) minor tweaking of model performance by introducing thermodynamically averaged descriptors; (ii) development of a new random sensitivity analysis technique for assessing model robustness to overtraining; (iii) prediction of several new compounds for use as WNT inhibitors; (iv) synthesis and experimental verification of one of these compounds when used in a real iPS stem cell differentiation protocol.

Current Status of Research Progress
Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

The project was delayed during FY2020 and FY2021 due to pandemic-related travel barriers, as well as the loss of a stem cell laboratory at our institute, which prevented us from acquiring data early in the project. However, after acquiring an existing data set in early FY2021 we could swiftly progress through the research plan, meeting all of the research goals at roughly the targeted times.

Strategy for Future Research Activity

The project has been extended by one year due to a large amount of unused budget from FY2023 (around 1M yen). The additional year will be used write a paper and attend international conferences to share the results.

Report

(4 results)
  • 2023 Research-status Report
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (12 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (1 results) Journal Article (3 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 3 results,  Open Access: 1 results) Presentation (6 results) (of which Int'l Joint Research: 2 results,  Invited: 3 results) Book (1 results) Remarks (1 results)

  • [Int'l Joint Research] University of California, Los Angeles(米国)

    • Related Report
      2023 Research-status Report
  • [Journal Article] Modeling dry eye with an air liquid interface in corneal epithelium-on-a-chip2024

    • Author(s)
      Kado Abdalkader Rodi、Chaleckis Romanas、Fujita Takuya、Kamei Ken-ichiro
    • Journal Title

      Scientific Reports

      Volume: 14 Issue: 1 Pages: 4185-4185

    • DOI

      10.1038/s41598-024-54736-z

    • Related Report
      2023 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Corneal epithelium models for safety assessment in drug development: Present and future directions2023

    • Author(s)
      Rodi Kado Abdalkader, Takuya Fujita
    • Journal Title

      Experimental Eye Research

      Volume: 237 Pages: 109697-109697

    • DOI

      10.1016/j.exer.2023.109697

    • Related Report
      2023 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] An efficient simplified method for the generation of corneal epithelial cells from human pluripotent stem cells2022

    • Author(s)
      Rodi Abdalkader and Kenichiro Kamei
    • Journal Title

      Human Cell

      Volume: 35 Issue: 4 Pages: 1016-1029

    • DOI

      10.1007/s13577-022-00713-5

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Data science for materials and chemical biology2024

    • Author(s)
      Daniel Packwood
    • Organizer
      The 9th Symposium on Theoretical and Applied Mechanics
    • Related Report
      2023 Research-status Report
    • Invited
  • [Presentation] Machine learning for materials chemistry and chemical biology2023

    • Author(s)
      Daniel Packwood
    • Organizer
      10th ICIAM (International Congress for Industrial and Applied Mathematics)
    • Related Report
      2023 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Designing bioactive materials with small data2023

    • Author(s)
      Daniel Packwood
    • Organizer
      The 1st MacDiarmid Institute-Kyoto University Workshop on Integrated Data-Material Sciences
    • Related Report
      2023 Research-status Report
  • [Presentation] データ科学・機械学習を活用する機能性分子の設計手法2022

    • Author(s)
      Daniel M. Packwood
    • Organizer
      データ科学・機械学習を活用する 機能性分子の設計研究事例(ダイキン工業主催 Webセミナー)
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] The survival and characteristics of cryopreserved human iPSC-derived corneal epithelial cells generated by SSM-CI method2022

    • Author(s)
      Rodi Abdalkader
    • Organizer
      World Ophthalmology Congress of the International Council of Ophthalmology (WOC)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Development of human cornea-on-a-chip2022

    • Author(s)
      Rodi Abdalkader
    • Organizer
      The 9th University Seeds Matching Seminar AgeTech (longevity society x technology)
    • Related Report
      2022 Research-status Report
  • [Book] Cell-Inspired Materials and Engineering2021

    • Author(s)
      D. O. Wang and D. M. Packwood (editors)
    • Total Pages
      257
    • Publisher
      Springer
    • Related Report
      2021 Research-status Report
  • [Remarks] Data science for novel molecular materials

    • URL

      https://cassyni.com/events/EAh21DVPcd5BseNzx1gs9o

    • Related Report
      2022 Research-status Report

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Published: 2020-10-29   Modified: 2024-12-25  

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