Comparison of Liberality Between Melanocyte Stem Cells and Differentiated Cells in Mice

緒方, 法親

doi:10.51094/jxiv.909

##article.authors##

緒方, 法親株式会社日本バイオデータ; 大阪大学大学院工学研究科生物工学専攻; 次世代バイオ医薬品製造技術研究組合 https://orcid.org/0000-0002-6856-6655 https://researchmap.jp/n0rr

DOI:

https://doi.org/10.51094/jxiv.909

キーワード:

Liberality、 Transcriptome、 Melanocyte、 differentiation、 dedifferentiation、 single-cell RNA-seq

抄録

Liberality refers to the degree of cellular dedifferentiation/differentiation, quantified through the estimation of information entropy from numeric transcriptome data and Lempel-Ziv complexity from transcriptome sequence data. In a previous study, single-cell RNA-seq data for melanocyte stem cells (McSCs) and melanocytes were obtained. Based on the definition of liberality, McSCs are expected to exhibit higher liberality than differentiated melanocytes. In this study, we estimated and compared the liberality between these two cell types.

利益相反に関する開示

The authors have no competing interests to disclose

ダウンロード *前日までの集計結果を表示します

ダウンロード実績データは、公開の翌日以降に作成されます。

著者の経歴

緒方, 法親、株式会社日本バイオデータ; 大阪大学大学院工学研究科生物工学専攻; 次世代バイオ医薬品製造技術研究組合

2008年　東京農工大学農学部応用生物科学科卒業
2010年　東京農工大学農学府生物制御科学専攻　修了
2013年　株式会社日本バイオデータ設立
2013年　東京農工大学大学院連合農学研究科修了博士（農学）取得
2013年　株式会社ネオ・モルガン研究所開発研究員（2015年迄）
2014年　次世代バイオ医薬品製造技術研究組合　事務局顧問（ゲノム技術）
2015年　東北大学　研究員 (2020年迄)
2015年　千葉大学　非常勤講師
2015年　Chitose Bio Evolution Pte. Ltd. General Manager （2020年迄）
2018年　Medicale Meccanica Inc., CEO （2023年迄）
2022年　東京農工大学客員准教授 (2023年迄)
2023年　大阪大学大学院工学研究科生物工学専攻招へい教授

引用文献

Champy C. NOTES DE BIOLOGIE CYTOLOGIQUE. QUELQUES RÉSULTATS DE LA MÉTHODE DE CULTURE DES TISSUS. Archives de zoologie expérimentale et générale. 1913; 42–46. Available: https://archive.org/details/archivesdezoolog53cent/page/n55/mode/2up

Sun Q, Lee W, Hu H, Ogawa T, De Leon S, Katehis I, et al. Dedifferentiation maintains melanocyte stem cells in a dynamic niche. Nature. 2023;616: 774–782. doi:10.1038/s41586-023-05960-6

Ogata N, Yokoyama T, Iwabuchi K. Transcriptome responses of insect fat body cells to tissue culture environment. PLoS One. 2012;7: e34940. doi:10.1371/journal.pone.0034940

Ogata N. Transcriptome dedifferentiation observed in animal primary cultures is essential to plant reprogramming. J Bioinform Syst Biol. 2022;5: 116–118. doi:10.26502/jbsb.5107039

Seekaki P, Ogata N. Calculating kolmogorov complexity from the transcriptome data. Intelligent Computing Theories and Application. Cham: Springer International Publishing; 2017. pp. 529–540. doi:10.1007/978-3-319-63312-1_46

Ogata N, Konishi S, Yokoyama T. In vivo-like Culture of Monophagous Animal Organ using Dietary Components. J Biotechnol Biomed. 2023;6: 42–48. doi:10.26502/jbb.2642-91280070

Sakamoto T, Kozaki T, Ogata N. Synergic Interaction between Permethrin and Bt Toxin Discovered Using RNA-seq. Journal of Clinical Toxicology. 2022;12: 1–9. doi:10.35248/2161-0495.22.12.519

Ogata N, Kozaki T, Yokoyama T, Hata T, Iwabuchi K. Comparison between the Amount of Environmental Change and the Amount of Transcriptome Change. PLoS One. 2015;10: e0144822. doi:10.1371/journal.pone.0144822

Wiesner K, Teles J, Hartnor M, Peterson C. Haematopoietic stem cells: entropic landscapes of differentiation. Interface Focus. 2018;8: 20180040. doi:10.1098/rsfs.2018.0040

Kannan S, Farid M, Lin BL, Miyamoto M, Kwon C. Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level. PLoS Comput Biol. 2021;17: e1009305. doi:10.1371/journal.pcbi.1009305

Guo M, Bao EL, Wagner M, Whitsett JA, Xu Y. SLICE: determining cell differentiation and lineage based on single cell entropy. Nucleic Acids Res. 2017;45: e54. doi:10.1093/nar/gkw1278

Ogata N. The growing liberality observed in primary animal and plant cultures is common to the social amoeba. J Bioinform Syst Biol. 2023;6: 10–17. doi:10.26502/jbsb.5107045

Ogata N, Hosaka A. Cellular liberality is measurable as Lempel-Ziv complexity of fastq files. 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (BIBE). IEEE; 2022. pp. 321–326. doi:10.1109/BIBE55377.2022.00072

Sun Q, Lee W, Mohri Y, Takeo M, Lim CH, Xu X, et al. A novel mouse model demonstrates that oncogenic melanocyte stem cells engender melanoma resembling human disease. Nat Commun. 2019;10: 5023. doi:10.1038/s41467-019-12733-1

R Core Team. R: A Language and Environment for Statistical Computing. 2024. Available: https://www.R-project.org/