| Title: |
A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids |
| Authors: |
Sockell, Alexandra; Wong, Wing; Longwell, Scott; Vu, Thy; Karlsson, Kasper; Mokhtari, Daniel; Schaepe, Julia; Lo, Yuan-Hung; Cornelius, Vincent; Kuo, Calvin; Van Valen, David; Curtis, Christina; Fordyce, Polly M. |
| Publication Year: |
2022 |
| Collection: |
Caltech Authors (California Institute of Technology) |
| Description: |
Organoids are powerful experimental models for studying the ontogeny and progression of diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, organoids in bulk culture physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or microenvironment variability. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can be retrieved from their microwells for sequencing and molecular profiling. Coupled with a deep-learning image processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity. ; The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. The authors thank the Cell Sciences Imaging Facility and Genetics Bioinformatics Service Center at Stanford University for assistance in confocal microscopy and computational resources respectively. This work was supported by the NIH Director's Pioneer Award (DP1CA238296) to C.C. and the NIH Director's New Innovator Award (DP2GM123641) to P.M.F. C.C and P.M.F are Chan Zuckerberg Biohub Investigators. We thank members of the Curtis and Fordyce lab for helpful feedback on this manuscript. Author Contributions. A.S., W.W, K.K., C.C., and P.M.F. conceptualized the initial research idea. A.S. and W.W. performed the microwell experiments. A.S. tested and made the ... |
| Document Type: |
report |
| Language: |
unknown |
| Relation: |
https://osf.io/r4s3m/; https://authors.library.caltech.edu/records/49xd1-6wb05; https://authors.library.caltech.edu/communities/caltechauthors/; https://doi.org/10.1101/2022.11.01.514733; eprintid:120180 |
| DOI: |
10.1101/2022.11.01.514733 |
| Availability: |
https://doi.org/10.1101/2022.11.01.514733 |
| Rights: |
info:eu-repo/semantics/openAccess ; Other |
| Accession Number: |
edsbas.7B285A2F |
| Database: |
BASE |