Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors
Alessandra Vigilante,
Anna Laddach,
Nathalie Moens,
Ruta Meleckyte,
Andreas Leha,
Arsham Ghahramani,
Oliver J. Culley,
Annie Kathuria,
Chloe Hurling,
Alice Vickers,
Erika Wiseman,
Mukul Tewary,
Peter W. Zandstra,
Richard Durbin,
Franca Fraternali,
Oliver Stegle,
Ewan Birney,
Nicholas M. Luscombe,
Davide Danovi,
Fiona M. Watt
Affiliations
Alessandra Vigilante
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
Anna Laddach
Randall Division, King’s College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK
Nathalie Moens
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Ruta Meleckyte
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Andreas Leha
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
Arsham Ghahramani
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
Oliver J. Culley
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Annie Kathuria
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Chloe Hurling
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Alice Vickers
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Erika Wiseman
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
Mukul Tewary
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK; School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
Peter W. Zandstra
School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
Richard Durbin
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
Franca Fraternali
Randall Division, King’s College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK
Oliver Stegle
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Ewan Birney
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nicholas M. Luscombe
The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
Davide Danovi
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK; Corresponding author
Fiona M. Watt
Centre for Stem Cells and Regenerative Medicine, King’s College London, Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK; Corresponding author
Summary: Large cohorts of human induced pluripotent stem cells (iPSCs) from healthy donors are a potentially powerful tool for investigating the relationship between genetic variants and cellular behavior. Here, we integrate high content imaging of cell shape, proliferation, and other phenotypes with gene expression and DNA sequence datasets from over 100 human iPSC lines. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we extracted factors that captured the effects of intrinsic (genetic concordance between different cell lines from the same donor) and extrinsic (cell responses to different fibronectin concentrations) conditions. We identify genes that correlate in expression with intrinsic and extrinsic PEER factors and associate outlier cell behavior with genes containing rare deleterious non-synonymous SNVs. Our study, thus, establishes a strategy for examining the genetic basis of inter-individual variability in cell behavior. : Cell behavior reflects both the intrinsic state of the cell and extrinsic signals it receives from its microenvironment. By integrating genomic, gene expression, and cell biology datasets from a large number of human iPSCs from healthy donors, Vigilante et al. show how genetic variation contributes to phenotypic variation. Keywords: iPSC, SNV, genetic variation, high content imaging, stem cells, dimensionality reduction, fibronectin, stem cell niche, cell adhesion
