Machine learning-assisted high-content analysis of pluripotent stem cell-derived embryos in vitro
Abstract
Stem cell-based embryo models by cultured pluripotent and extra-embryonic lineage stem cells are novel platforms to model early postimplantation development. We showed that induced pluripotent stem cells (iPSCs) could form ITS (iPSCs and trophectoderm stem cells) and ITX (iPSCs, trophectoderm stem cells, and XEN cells) embryos, resembling the early gastrula embryo developed in vivo. To facilitate the efficient and unbiased analysis of the stem cell-based embryo model, we set up a machine learning workflow to extract multi-dimensional features and perform quantification of ITS embryos using 3D images collected from a high-content screening system. We found that different PSC lines differ in their ability to form embryo-like structures. Through high-content screening of small molecules and cytokines, we identified that BMP4 best promoted the morphogenesis of the ITS embryo. Our study established an innovative strategy to analyze stem cell-based embryo models and uncovered new roles of BMP4 in stem cell-based embryo models.
Additional Information
© 2021 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received 20 October 2020, Revised 17 March 2021, Accepted 17 March 2021, Available online 22 April 2021. This work was supported by the National Key R&D Program of China (grants 2017YFA0102802 and 2019YFA0110001) to J.N., Wellcome Trust (098287/Z/12/Z, 108438/C/15/Z) and Curci Foundation grants to M.Z.-G., an NSFC grant (32000610) to J.G. J.G. is supported by postdoctoral fellowships from Tsinghua-Peking Center for Life Sciences. We thank Dr. P. Liu and Professor S. Ding from the School of Pharmaceutical Sciences, Tsinghua University, Beijing, China, for the mouse iPSC lines. Mingyao Cui from the Institute of Molecular Medicine, Peking University, Beijing, China, for assistance in RNA-seq experiments. Data and code availability: The RNA high-throughput sequencing data are publicly available at the National Center for Biotechnology Information with Gene Expression Omnibus, accession no. GSE 139379. The algorithms developed by this study are listed in the supplemental information. Author contributions: J.G., P.W., M.Z.-G., and J.N. conceived the study and designed experiments. J.G. performed mouse PSC, ESC, TSC, and XEN cell culture, ITX/ETX and ITS/ETS embryo assembly and characterization, HCS, and image analysis. J.G., P.W., and Y.Z. performed single iPSC, TSC, and ITS-iPSC, ITS-TSC structure collection, RNA-seq library construction, and data analysis. B.S. performed ETX and ETS embryo assembly experiments. H.Q. and X.Z. assisted with HCS data analysis and graphic presentation. J.G., P.W., and J.N. wrote the manuscript. The author declare that they have no competing interests.Attached Files
Published - 1-s2.0-S221367112100148X-main.pdf
Supplemental Material - 1-s2.0-S221367112100148X-mmc1.pdf
Supplemental Material - 1-s2.0-S221367112100148X-mmc10.mp4
Supplemental Material - 1-s2.0-S221367112100148X-mmc2.xlsx
Supplemental Material - 1-s2.0-S221367112100148X-mmc3.xlsx
Supplemental Material - 1-s2.0-S221367112100148X-mmc4.xlsx
Supplemental Material - 1-s2.0-S221367112100148X-mmc5.xlsx
Supplemental Material - 1-s2.0-S221367112100148X-mmc6.mp4
Supplemental Material - 1-s2.0-S221367112100148X-mmc7.mp4
Supplemental Material - 1-s2.0-S221367112100148X-mmc8.mp4
Supplemental Material - 1-s2.0-S221367112100148X-mmc9.mp4
Files
| Name | Size | Download all |
|---|---|---|
|
md5:27e790f803c528310ba176d73ea58133
|
2.3 MB | Download |
|
md5:8f48352ef37c77ef5130f0d5e5b3e716
|
2.3 MB | Download |
|
md5:8393d6b234f5c620b74ffc7d013cc60a
|
718.1 kB | Download |
|
md5:c63a87bf9f3e427e46ab63c258664e1a
|
372.5 kB | Download |
|
md5:ed9b8e0d6f10b122904d41d125b195d7
|
235.9 kB | Download |
|
md5:7de9631f728eedb33b994c6e8d4e2722
|
2.5 MB | Download |
|
md5:8655ae7500cf1ac03377fba6976462f2
|
616.5 kB | Download |
|
md5:d80e0c138349c2abbc71dbfa88c90164
|
6.8 MB | Preview Download |
|
md5:c82923682acf2b992db25595c3baa7f5
|
2.3 MB | Download |
|
md5:fd5ea59a2304f6d2bebd5c299e3b7c6b
|
4.9 MB | Preview Download |
|
md5:7363798505dc84486dd76038c61c7be5
|
2.9 MB | Download |
Additional details
- PMCID
- PMC8185434
- Eprint ID
- 108960
- Resolver ID
- CaltechAUTHORS:20210504-094816688
- National Key Research and Development Program of China
- 2017YFA0102802
- National Key Research and Development Program of China
- 2019YFA0110001
- Wellcome Trust
- 098287/Z/12/Z
- Wellcome Trust
- 108438/C/15/Z
- Shurl and Kay Curci Foundation
- National Natural Science Foundation of China
- 32000610
- Tsinghua-Peking Center for Life Sciences
- Created
-
2021-05-05Created from EPrint's datestamp field
- Updated
-
2021-06-21Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering (BBE)