Elucidation of renal disease onset and progression mechanism using single cell RNA-sequence

Research Project

Project/Area Number	19K22621
Research Category	Grant-in-Aid for Challenging Research (Exploratory)
Allocation Type	Multi-year Fund
Review Section	Medium-sized Section 53:Organ-based internal medicine and related fields
Research Institution	Osaka University
Principal Investigator	ISAKA YOSHITAKA 大阪大学, 医学系研究科, 教授 (00379166)
Co-Investigator(Kenkyū-buntansha)	井上和則大阪大学, 医学系研究科, 助教 (10631301) 水井理之大阪大学, 医学系研究科, 講師 (30423106) 松井功大阪大学, 医学系研究科, 助教 (60456986)
Project Period (FY)	2019-06-28 – 2021-03-31
Project Status	Completed (Fiscal Year 2020)
Budget Amount *help	¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000) Fiscal Year 2020: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000) Fiscal Year 2019: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Keywords	single cell RNA解析 / 腎発生 / Single cell RNA seq
Outline of Research at the Start	本研究で我々はscRNA-seq、spatial transcriptomics、AIという3つの新しい技術を組み合わせて、腎疾患の発症・進展に関わる変化を一細胞レベルで捉え、新規腎疾患治療法開発に資する基盤を提供する。疾病腎のscRNA-seqはこれまでほとんど行われていないため、疾病腎scRNA-seq解析のみでも挑戦的研究としての意義を有するが、本研究ではその一歩先を行き、scRNA-seqで得られた一細胞レベルの遺伝子発現情報をspatial transcriptomicsおよびAIと組み合わせて、組織平面上の位置情報を含んだ形で俯瞰できる技術を開発する。
Outline of Final Research Achievements	In this study, single-cell RNA sequencing data obtained from embryonic mouse kidney were re-analyzed. Manifold learning based on partition-based graph-abstraction coordinated cells, reflecting their expected lineage relationships. Consequently, the coordination in combination with ForceAtlas2 enabled the inference of parietal epithelial cells of Bowman's capsule and the inference of cells involved in the developmental process from the S-shaped body to each nephron segment. RNA velocity suggested developmental sequences of proximal tubules and podocytes. In combination with a Markov chain algorithm, RNA velocity suggested the self-renewal processes of nephron progenitors. NicheNet analyses suggested that not only cells belonging to ureteric bud and stroma, but also endothelial cells, macrophages, and pericytes may contribute to the differentiation of cells from nephron progenitors.
Academic Significance and Societal Importance of the Research Achievements	シングルセルRNA-seq解析では、trajectory解析やRNA velocity解析などを用いることで、従来のbulk RNA sequenceとは異なった側面から生命現象を捉えることが可能です。シングルセルRNA-seq解析技術は日々進化しており、今後益々有用なツールとなると考えられる。