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

Stem Cell Reports. 2021 Nov 9;16(11):2628-2641. doi: 10.1016/j.stemcr.2021.09.017. Epub 2021 Oct 21.


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.

Keywords: cell adhesion; differentiation; genomics; high-content imaging.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Adhesion / genetics
  • Cell Differentiation / genetics*
  • Cell Line
  • Endoderm / cytology
  • Endoderm / metabolism*
  • Fetal Proteins / genetics
  • Fetal Proteins / metabolism
  • Gene Expression Profiling / methods
  • Germ Layers / cytology
  • Germ Layers / metabolism
  • Humans
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism*
  • Integrin beta1 / genetics*
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Proteomics / methods
  • SOXB1 Transcription Factors / genetics
  • SOXB1 Transcription Factors / metabolism
  • SOXF Transcription Factors / genetics
  • SOXF Transcription Factors / metabolism
  • T-Box Domain Proteins / genetics
  • T-Box Domain Proteins / metabolism


  • Fetal Proteins
  • Integrin beta1
  • Itgb1 protein, human
  • SOX17 protein, human
  • SOX2 protein, human
  • SOXB1 Transcription Factors
  • SOXF Transcription Factors
  • T-Box Domain Proteins
  • Brachyury protein

Associated data

  • figshare/10.6084/m9.figshare.14497725