Plating human iPSC lines on micropatterned substrates reveals role for ITGB1 nsSNV in endoderm formation

ABSTRACT: Summary Quantitative analysis of human induced pluripotent stem cell (iPSC) lines from healthy donors is a powerful tool for uncovering the relationship between genetic variants and cellular behavior. We previously identified rare, deleterious non-synonymous single nucleotide variants (nsSNVs) in cell adhesion genes that are associated with outlier iPSC phenotypes in the pluripotent state. Here, we generated micropatterned colonies of iPSCs to test whether nsSNVs influence patterning of radially ordered germ layers. Using a custom-built image analysis pipeline, we quantified the differentiation phenotypes of 13 iPSC lines that harbor nsSNVs in genes related to cell adhesion or germ layer development. All iPSC lines differentiated into the three germ layers; however, there was donor-specific variation in germ layer patterning. We identified one line that presented an outlier phenotype of expanded endodermal differentiation, which was associated with a nsSNV in ITGB1. Our study establishes a platform for investigating the impact of nsSNVs on differentiation. Graphical abstract Highlights • Healthy donor iPSCs differentiate into radial germ layers on micropatterns• Differentiation can be quantified using high-content image analysis• iPSC lines show donor-specific variation in germ layer patterning• A deleterious nsSNV in ITGB1 is associated with expanded endoderm formation In this study, Vickers and colleagues combine micropatterning and high-content image analysis of healthy donor iPSC lines to identify genetic variants that influence cellular differentiation. iPSC lines displayed donor-specific variation in germ layer patterning. Outlier cell lines were identified, including one line that displayed expanded endoderm differentiation and was associated with a deleterious nsSNV in ITGB1.

SUBMITTER: Vickers A 

PROVIDER: S-EPMC8581167 | biostudies-literature |

REPOSITORIES: biostudies-literature