Lab-Specific Gene Expression Signatures in Pluripotent Stem Cells

• Published in: Cell stem cell Vol. 7; no. 2; pp. 258 - 262
• Main Authors: Newman, Aaron M., Cooper, James B.
• Format: Journal Article
• Language: English
• Published: Cambridge, MA Elsevier Inc 06-08-2010; Cell Press
• Subjects: Biological and medical sciences; Cell differentiation, maturation, development, hematopoiesis; Cell physiology; Cluster Analysis; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Gene Expression Regulation, Developmental; Humans; Laboratories; Molecular and cellular biology; Pluripotent Stem Cells - metabolism; STEMCELL; STEMCELL; Gene expression; Pluripotent cell; Stem cell; Gene expression profile
• ISSN: 1934-5909; 1875-9777
• DOI: 10.1016/j.stem.2010.06.016

Pluripotent stem cells derived from both embryonic and reprogrammed somatic cells have significant potential for human regenerative medicine. Despite similarities in developmental potential, however, several groups have found fundamental differences between embryonic stem cell (ESC) and induced-pluripotent stem cell (iPSC) lines that may have important implications for iPSC-based medical therapies. Using an unsupervised clustering algorithm, we further studied the genetic homogeneity of iPSC and ESC lines by reanalyzing microarray gene expression data from seven different laboratories. Unexpectedly, this analysis revealed a strong correlation between gene expression signatures and specific laboratories in both ESC and iPSC lines. Nearly one-third of the genes with lab-specific expression signatures are also differentially expressed between ESCs and iPSCs. These data are consistent with the hypothesis that in vitro microenvironmental context differentially impacts the gene expression signatures of both iPSCs and ESCs.
► iPSC and ESC gene expression correlates with lab of origin ► Lab-specific signatures overshadow iPSC and ESC expression differences