379-Okubo-bilaminoid

Project

Title
3D images of bilaminar organoid generated from co-culture of human pluripotent stem cells (hPSC) and hPSC-derived hypoblast-like cells
Description
Recently, several studies using cultures of human embryos together with single-cell RNA-seq analyses have revealed differences between humans and mice, necessitating the study of human embryos. Despite the importance of human embryology, ethical and legal restrictions have limited post-implantation-stage studies. Thus, recent efforts have focused on developing in vitro self-organizing models using human stem cells. In this paper, the authors report genetic and non-genetic approaches to generate authentic hypoblast cells (naive hPSC-derived hypoblast-like cells (nHyCs))-known to give rise to one of the two extraembryonic tissues essential for embryonic development-from naive human pluripotent stem cells (hPSCs). Their nHyCs spontaneously assemble with naive hPSCs to form a three-dimensional bilaminar structure (bilaminoids) with a pro-amniotic-like cavity. In the presence of additional naive hPSC-derived analogues of the second extraembryonic tissue, the trophectoderm, the efficiency of bilaminoid formation increases from 20% to 40%, and the epiblast within the bilaminoids continues to develop in response to trophectoderm-secreted IL-6. Furthermore, they show that bilaminoids robustly recapitulate the patterning of the anterior-posterior axis and the formation of cells reflecting the pregastrula stage, the emergence of which can be shaped by genetically manipulating the DKK1/OTX2 hypoblast-like domain.
License
CC BY
Released at
Oct. 20, 2025, midnight
Updated at
Funding
This work was supported by MEXT KAKENHI (grant numbers: JP16H02465, JP15H02360, JP20H05361, JP20H05762, JP21K19189, JP23K18340) and AMED (grant numbers: JP21bm0704035, JP21bm0104001, JP21gm1310011, JP23bm1323001) to Y.T.; MEXT KAKENHI (grant number: JP19H03418) and the JST FOREST Program (grant number: JPMJFR206C), JST CREST (grant number: JPMJCR2023) and AMED (grant numbers: JP17gm1110004, JP19gm1310002, JP19bm0704032, JP21bm0104001, JP21gm1310011) to T.Y.; MEXT KAKENHI (grant numbers: JP15H02360, JP19H05759) to E.S.; AMED (grant number: JP22bm1004002) to H.N.; the Takeda Science Foundation to Y.T.; the Naito Foundation to Y.T.; the Mochida Memorial Foundation for Medical and Pharmaceutical Research to Y.T.; and the Astellas Foundation for Research on Metabolic Disorders to Y.T.
# of image datasets
8

Papers

Papers
Paper information: Okubo T, Rivron N, Kabata M, Masaki H, Kishimoto K, Semi K, Nakajima-Koyama M, Kunitomi H, Kaswandy B, Sato H, Nakauchi H, Woltjen K, Saitou M, Sasaki E, Yamamoto T, Takashima Y. Hypoblast from human pluripotent stem cells regulates epiblast development. Nature. 2024 Feb;626(7998):357-366.,
Pubmed ID: 38052228,
PMCID: PMC10849967,
DOI: https://doi.org/10.1038/s41586-023-06871-2,
URL: https://pubmed.ncbi.nlm.nih.gov/38052228/

Contacts

Contacts
Takuya Yamamoto (Contact) , Center for iPS Cell Research and Application , Kyoto University
Yasuhiro Takashima (Contact) , Center for iPS Cell Research and Application , Kyoto University
Takumi Okubo (Imaging Contributor) , Center for iPS Cell Research and Application , Kyoto University

Biosamples

Organisms
Homo sapiens (NCBI:txid9606)
Strains

Cells
pluripotent stem cell (CL_0002248)
Cell lines

Ontologies

UBERON
pluripotent stem cell (CL_0002248)
Anatomical entities
GO: Biological processes
embryo development (GO:0009790)
GO: Cellular components
GO: Molecular functions

Genetics

Gene names
Protein names
T-box transcription factor T (O15178)
Insulin gene enhancer protein ISL-1 (P61371)
Partitioning defective 6 homolog alpha (Q9NPB6)
Transcription factor GATA-6 (Q92908)
Partitioning defective 6 homolog alpha (Q9NPB8)
Transcription factor GATA-4 (P43694)
Trans-acting T-cell-specific transcription factor GATA-3 (P23771)
Homeobox protein OTX2 (P32243)
POU domain, class 5, transcription factor 1 (Q01860)
Partitioning defective 6 homolog alpha (Q9NPB7)
Genetic methods
transfection (EFO_0000726)
labelling protocol (EFO_0003810)
Protein tags
Alexa Fluor 647 (FBbi:00000447)
GFP (FBbi:00000437)
Alexa Fluor 488 (FBbi:00000440)
Alexa Fluor 555 (FBbi:00000443)
Probes
Antibody (FBbi:00000401)
DAPI (FBbi:00000058)
DAPI (FBbi:00000057)
DAPI (FBbi:00000059)
DAPI (FBbi:00000060)
DAPI (FBbi:00000056)
Oligo Primer
Genotype

Treatments

Reagent or Compound
Concentration
Fold Dilution
doxycycline (CHEBI:50845)
1 micromolar (UO_0000064)
doxycycline (CHEBI:50845)
1 micromolar (UO_0000064)
doxycycline (CHEBI:50845)
1 micromolar (UO_0000064)
doxycycline (CHEBI:50845)
1 micromolar (UO_0000064)
doxycycline (CHEBI:50845)
1 micromolar (UO_0000064)
doxycycline (CHEBI:50845)
1 micromolar (UO_0000064)

Imaging Methods

Dimensions
1024x1024x28x4x1, 971x967x36x4x1, NA, 1024x1024x26x4x1, 1024x1024x47x4x1, 1024x1024x23x4x1,
X scales
0.104 micrometer, 0.24 micrometer, 0.194 micrometer, NA, 0.181 micrometer, 0.26 micrometer,
Y scales
0.104 micrometer, 0.24 micrometer, 0.194 micrometer, NA, 0.181 micrometer, 0.26 micrometer,
Z scales
NA, 5.00 micrometer, 3.00 micrometer,
T scales
NA,
Channels
NA, 4 channel,
Microscopy types
fluorescence microscopy (FBbi:00000246)
confocal microscopy (FBbi:00000251)
Detection methods
Visualization methods
Illumination methods
Sources of contrast
Contrast enhancing methods
Resolution enhancing methods
Imaged parameters
Sample preparation methods

Instruments

Body
Celldiscover7 (Zeiss)
Model
Light source
Detector
Objective
Zeiss Plan-Apochromat 50x/1.2
Filter set
Dichroic
Body
LSM710 (Zeiss)
Model
Light source
Detector
Objective
Zeiss Plan-Apochromat 20x/0.95
Filter set
Dichroic
Body
LSM710 (Zeiss)
Model
Light source
Detector
Objective
Zeiss Plan-Apochromat 40x/1.4 Oil
Filter set
Dichroic
Body
LSM710 (Zeiss)
Model
Light source
Detector
Objective
Zeiss Plan-Apochromat 40x/1.3 Oil
Filter set
Dichroic
Body
Model
Light source
Detector
Objective
Filter set
Dichroic
Body
LSM710 (Zeiss)
Model
Light source
Detector
Objective
Zeiss Plan-Apochromat 20x/0.8
Filter set
Dichroic

Datasets

Dataset name
Organism
Gene / Protein
Dimensions
File size
SSBD:OMERO
Download
Homo sapiens (NCBI:txid9606)
NA / Transcription factor GATA-6 (Q92908) / Partitioning defective 6 homolog alpha (Q9NPB6) / POU domain, class 5, transcription factor 1 (Q01860)
1024x1024x26x4x1
208MB
zip
Homo sapiens (NCBI:txid9606)
NA / Transcription factor GATA-6 (Q92908) / Partitioning defective 6 homolog alpha (Q9NPB7)
1024x1024x28x4x1
224MB
zip
Homo sapiens (NCBI:txid9606)
/ Partitioning defective 6 homolog alpha (Q9NPB7)
NA
207MB
zip
Homo sapiens (NCBI:txid9606)
NA / Transcription factor GATA-6 (Q92908) / Partitioning defective 6 homolog alpha (Q9NPB8)
1024x1024x28x4x1
224MB
zip
Homo sapiens (NCBI:txid9606)
/ Partitioning defective 6 homolog alpha (Q9NPB8)
NA
240MB
zip
Homo sapiens (NCBI:txid9606)
NA / Transcription factor GATA-6 (Q92908) / Homeobox protein OTX2 (P32243) / T-box transcription factor T (O15178) / Transcription factor GATA-4 (P43694)
971x967x36x4x1
258MB
zip
Homo sapiens (NCBI:txid9606)
NA / Transcription factor GATA-6 (Q92908) / Insulin gene enhancer protein ISL-1 (P61371) / Trans-acting T-cell-specific transcription factor GATA-3 (P23771)
1024x1024x23x4x1
184MB
zip
Homo sapiens (NCBI:txid9606)
NA / Transcription factor GATA-6 (Q92908) / POU domain, class 5, transcription factor 1 (Q01860) / Trans-acting T-cell-specific transcription factor GATA-3 (P23771)
1024x1024x47x4x1
376MB
zip