Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells

Abstract

We examined the gene expression and DNA methylation of 49 human induced pluripotent stem cells (hiPSCs) and 10 human embryonic stem cells and found overlapped variations in gene expression and DNA methylation in the two types of human pluripotent stem cell lines. Comparisons of the in vitro neural differentiation of 40 hiPSCs and 10 human embryonic stem cells showed that seven hiPSC clones retained a significant number of undifferentiated cells even after neural differentiation culture and formed teratoma when transplanted into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression levels of several genes, including those expressed from long terminal repeats of specific human endogenous retroviruses. These data demonstrated a subset of hiPSC lines that have aberrant gene expression and defective potential in neural differentiation, which need to be identified and eliminated before applications in regenerative medicine.

Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential

“…1D and Dataset S2), including the three previous reported genes ABHD12B, HHLA1, and C4ORF51. We also identified long intergenic non-protein coding RNA, regulator of reprogramming (lincRNA-RoR), an HERV-H LTR7-related large intergenic noncoding RNA (lincRNA), and KLF4 as DD-iPSC marker genes (3,10). Of the DD-iPSC markers, 21.5% (31 of 144) were located within 30 kb downstream of LTR7s.…”

“…S1A and Dataset S1). Based on marker-gene expression and neural differentiation potential, each DD-iPSC subclone had a normal or DD phenotype, whereas all subclones derived from ESCs and normal iPSCs exhibited a normal phenotype (3,9) (Fig. 1B and Fig.…”

“…retrotransposon | epigenetics | evolution H uman pluripotent stem cells can be generated through two paths: (i) embryonic stem cells (ESCs) can be derived from embryos (1), and (ii) induced pluripotent stem cells (iPSCs) can be generated from differentiated cells through factor-mediated reprogramming (2). Most iPSCs are highly similar to ESCs, but we recently showed that ∼10% of iPSC clones have a differentiation-defective phenotype, such that 20% of cells were undifferentiated, even after in vitro-directed neural differentiation (3). These differentiation-defective (DD)-iPSC clones exhibited high expression levels of ∼10 genes-including abhydrolase domain containing 12B (ABHD12B), HERV-H LTR-associating 1 (HHLA1) and chromosome 4 open reading frame 51 (C4ORF51)-driven by the long-terminal repeats (LTRs) of human endogenous retroviruses (HERVs).…”

In Vitro Differentiation of Human Bone Marrow Mesenchymal Stem Cells to Hair Cells Using Growth Factors

“…Genetic defects in adult or somatic cell-derived iPSCs not only cause tumorigenicity, but also lead to impairment of differentiation. Further research is required for the clinical use of these cells 9 .…”

Present and future challenges of induced pluripotent stem cells

“…Those that investigated 20-36 ESCs and 12-68 iPSCs found otherwise [74 -76]. Koyanagi-Aoi et al performed comparison analyses of gene expression, miRNA expression and DNA methylation between 10 ESCs and 49 iPSCs [77]. Although they saw no clear differences between the two cell types, they did find that some iPSCs exhibited distinguishing expression signatures that were related to defects in differentiation.…”