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; HipSci Consortium; Richard Durbin; Franca Fraternali; Oliver Stegle; Ewan Birney; Nicholas M Luscombe; Davide Danovi; Fiona M Watt

doi:10.1016/j.celrep.2019.01.094

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Cell Rep. 2019 Feb 19;26(8):2078-2087.e3. doi: 10.1016/j.celrep.2019.01.094.

Authors

Alessandra Vigilante¹, Anna Laddach², Nathalie Moens³, Ruta Meleckyte³, Andreas Leha⁴, Arsham Ghahramani⁵, Oliver J Culley³, Annie Kathuria³, Chloe Hurling³, Alice Vickers³, Erika Wiseman³, Mukul Tewary⁶, Peter W Zandstra⁷; HipSci Consortium; Richard Durbin⁸, Franca Fraternali², Oliver Stegle⁹, Ewan Birney⁹, Nicholas M Luscombe¹⁰, Davide Danovi¹¹, Fiona M Watt¹²

Affiliations

¹ 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.
² Randall Division, King's College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK.
³ 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.
⁴ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
⁵ 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.
⁶ 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.
⁷ 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.
⁸ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
⁹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
¹⁰ 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.
¹¹ 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. Electronic address: davide.danovi@kcl.ac.uk.
¹² 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. Electronic address: fiona.watt@kcl.ac.uk.

Abstract

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.

Keywords: SNV; cell adhesion; dimensionality reduction; fibronectin; genetic variation; high content imaging; iPSC; stem cell niche; stem cells.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Biological Variation, Population*
Cell Differentiation
Cell Line
Cell Proliferation
Humans
Induced Pluripotent Stem Cells / cytology
Induced Pluripotent Stem Cells / metabolism*
Induced Pluripotent Stem Cells / physiology
Mice
Phenotype
Polymorphism, Single Nucleotide*
Transcriptome

Abstract

Publication types

MeSH terms

Grants and funding