title: Identification of stable reference genes in differentiating human pluripotent stem cells.
abstract: Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells, obtained during directed differentiation toward endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled, and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by reverse transcription quantitative PCR analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs.
authors: Systems Biology Research Center, University of Skövde, Skövde, Sweden; Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden;
authors: Gustav
authors: G
authors: Holmgren
authors: Systems Biology Research Center, University of Skövde, Skövde, Sweden; Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden;
authors: Nidal
authors: N
authors: Ghosheh
authors: Buck Institute for Research on Aging, Buck Institute, Novato, California; and.
authors: Xianmin
authors: X
authors: Zeng
authors: Systems Biology Research Center, University of Skövde, Skövde, Sweden;
authors: Yalda
authors: Y
authors: Bogestål
authors: Systems Biology Research Center, University of Skövde, Skövde, Sweden; AstraZeneca Research and Development, Global Medicines Development, Cardiovascular and Metabolic Diseases Global Medicines Development Unit, Mölndal, Sweden.
authors: Peter
authors: P
authors: Sartipy
authors: Systems Biology Research Center, University of Skövde, Skövde, Sweden; jane.synnergren@his.se.
authors: Jane
authors: http://orcid.org/0000-0003-4697-0590
authors: J
authors: Synnergren
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D005796:Genes; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D039904:Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism*; D012015:Reference Standards
keywords: differentiation; endogenous controls; gene expression; housekeeping genes; human pluripotent stem cells; normalization; reference genes