RIKEN Center for Biosystems Dynamics Research Laboratory for the Stem Cell Zoo

Team Director: Miki Ebisuya (Ph.D.)

Japanese Page

Research Summary

The gestation period is about 9 months in humans, only 20 days in mice, and nearly 2 years in elephants. Yet the molecular and biophysical principles underlying such species-specific differences in biological timing and morphology remain largely unknown. We have established a “stem cell zoo,” inducing defined cell types and organoids from pluripotent stem cells of diverse mammals to quantitatively compare developmental tempo, heart rate, and morphogenesis across species. By identifying and manipulating the key regulatory factors, we aim to engineer human tissues that recapitulate the characteristics of other species.

Main Research Fields

Biology

Related Research Fields

Developmental biology
Synthetic biology
Biophysics

Keywords

Comparative stem cell biology
Synthetic developmental biology
Quantitative biology
Mathematical modeling
Organoids

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
A hash(#) denotes corresponding authors of a paper.

1. *Matsuda M, Hammarén H, Lázaro J, #Savitski M & #Ebisuya M.
"Systematic differences in protein stability underlie species-specific developmental tempo."
Dev. Cell, in press (2026). doi: 10.1016/j.devcel.2026.07.012
2. *#Sanaki-Matsumiya M, Sanaki Y, Villava C, Rappez L, Gritti N, Nakaki F, Shapre J, Haase K, Wu J & #Ebisuya M.
"Self-organization of vascularized muscle from bovine embryonic stem cells."
Nat. Commun., in press (2026). doi: 10.1038/s41467-026-76569-2
3. *Korbmacher F, Long R, Fleckenstein H, Polinski P, Crusius D, Piatti L, Lopez-Gutierrez B, Batzilla A, Trivedi V, #Ebisuya M & #Bernabeu M.
"ETS-guided iPSC-endothelial models recapitulate malaria pathogenesis."
EMBO Mol. Med., 18, 3389-3418 (2026). doi: 10.1038/s44321-026-00467-9
4. *#Stapornwongkul K, Hahn E, Poliński P, Salamo Palau L, Arato K, Yao L, Williamson K, Gritti N, Anlas K, Osuna Lopez M, Patil KR, Heemskerk I, #Ebisuya M & #Trivedi V.
"Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling."
Cell Stem Cell, 32, 1-15 (2025). doi: 10.1016/j.stem.2025.03.011
5. *#Matsuda M, Lázaro J, & #Ebisuya M.
"Metabolic activities are selective modulators for individual segmentation clock processes."
Nat. Commun., 16, 845 (2025). doi: 10.1038/s41467-025-56120-5
6. *Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, #Trivedi V, #Matsuda M & #Ebisuya M.
"A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals."
Cell Stem Cell, 30, 938-949 (2023). doi: 10.1016/j.stem.2023.05.014
7. *Martínez-Ara G, Taberner N, Takayama M, Sandaltzopoulou E, Villava C, Bosch-Padrós M, Takata N, Trepat X, Eiraku M & #Ebisuya M.
"Optogenetic control of apical constriction induces synthetic morphogenesis in mammalian tissues."
Nat. Commun., 13, 5400 (2022). doi: 10.1038/s41467-022-33115-0
8. *#Sanaki-Matsumiya M, Matsuda M, Gritti N, Nakaki F, Sharpe J, Trivedi V & #Ebisuya M.
"Periodic formation of epithelial somites from human pluripotent stem cells."
Nat. Commun., 13, 2325 (2022). doi: 10.1038/s41467-022-29967-1
9. *Matsuda M, Yamanaka Y, Uemura M, Osawa M, Saito MK, Nagahashi A, Nishio M, Guo L, Ikegawa S, Sakurai S, Kihara S, Maurissen TL, Nakamura M, Matsumoto T, Yoshitomi H, Ikeya M, Kawakami N, Yamamoto T, Woltjen K, #Ebisuya M, Toguchida J & #Alev C.
"Recapitulating the human segmentation clock with pluripotent stem cells."
Nature, 580, 124-129 (2020). doi: 10.1038/s41586-020-2144-9
10. *Matsuda M, Hayashi H, Garcia-Ojalvo J, Yoshioka-Kobayashi K, Kageyama R, Yamanaka Y, Ikeya M, Toguchida J, Alev C & #Ebisuya M.
"Species-specific segmentation clock periods are due to differential biochemical reaction speeds."
Science, 369, 1450-1455 (2020). doi: 10.1126/science.aba7668

Lab Members

Principal investigator

Miki Ebisuya: Team Director

Contact Information

Building A
2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe,
Hyogo, 650-0047, Japan
Email: miki.ebisuya@riken.jp