Yoav Mayshar

Characterization of human embryonic stem cell lines by the International Stem Cell Initiative

The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue-nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.

Identification and Classification of Chromosomal Aberrations in Human Induced Pluripotent Stem Cells

Because of their somatic cell origin, human induced pluripotent stem cells (HiPSCs) are assumed to carry a normal diploid genome, and adaptive chromosomal aberrations have not been fully evaluated. Here, we analyzed the chromosomal integrity of 66 HiPSC and 38 human embryonic stem cell (HESC) samples from 18 different studies by global gene expression meta-analysis. We report identification of a substantial number of cell lines carrying full and partial chromosomal aberrations, half of which were validated at the DNA level. Several aberrations resulted from culture adaptation, and others are suspected to originate from the parent somatic cell. Our classification revealed a third type of aneuploidy already evident in early passage HiPSCs, suggesting considerable selective pressure during the reprogramming process. The analysis indicated high incidence of chromosome 12 duplications, resulting in significant enrichment for cell cycle-related genes. Such aneuploidy may limit the differentiation capacity and increase the tumorigenicity of HiPSCs.

Overexpression of NANOG in human ES cells enables feeder-free growth while inducing primitive ectoderm features

Human embryonic stem cells (HESCs) are pluripotent cells derived from the ICM of blastocyst stage embryos. As the factors needed for their growth are largely undefined, they are propagated on feeder cells or with conditioned media from feeder cells. This is in contrast to mouse embryonic stem cells (MESCs) where addition of leukemia inhibitory factor (LIF) replaces the need for a feeder layer. Recently, the transcription factor Nanog was suggested to allow LIF and feeder-free growth of MESCs. Here, we show that NANOG overexpression in HESCs enables their propagation for multiple passages during which the cells remain pluripotent. NANOG overexpressing cells form colonies efficiently even at a very low density, an ability lost upon excision of the transgene. Cells overexpressing NANOG downregulate expression of markers specific to the ICM and acquire expression of a marker specific to the primitive ectoderm (the consecutive pluripotent population in the embryo). Examination of global transcriptional changes upon NANOG overexpression by DNA microarray analysis reveals new markers suggested to discriminate between these populations. These results are significant in the understanding of self-renewal and pluripotency pathways in HESCs, and of their use for modeling early development in humans.

Large-Scale Analysis Reveals Acquisition of Lineage-Specific Chromosomal Aberrations in Human Adult Stem Cells

In this study, we assessed the genetic integrity of over 400 samples of human multipotent stem cells using gene expression data sets. Our analysis reveals that neural and mesenchymal stem cells acquire characteristic large chromosomal aberrations at a similar, or somewhat lower, frequency to that seen in pluripotent stem cells, sometimes within a few passages in culture. Some of the identified chromosomal abnormalities can also be detected in human tumors of the respective tissues.

Clone‐ and Gene‐Specific Aberrations of Parental Imprinting in Human Induced Pluripotent Stem Cells

Genomic imprinting is an epigenetic phenomenon whereby genes are expressed in a monoallelic manner, which is inherited either maternally or paternally. Expression of imprinted genes has been examined in human embryonic stem (ES) cells, and the cells show a substantial degree of genomic imprinting stability. Recently, human somatic cells were reprogrammed to a pluripotent state using various defined factors. These induced pluripotent stem (iPS) cells are thought to have a great potential for studying genetic diseases and to be a source of patient‐specific stem cells. Thus, studying the expression of imprinted genes in these cells is important. We examined the allelic expression of various imprinted genes in several iPS cell lines and found polymorphisms in four genes. After analyzing parent‐specific expression of these genes, we observed overall normal monoallelic expression in the iPS cell lines. However, we found biallelic expression of the H19 gene in one iPS cell line and biallelic expression of the KCNQ10T1 gene in another iPS cell line. We further analyzed the DNA methylation levels of the promoter region of the H19 gene and found that the cell line that showed biallelic expression had undergone extensive DNA demethylation. Additionally we studied the imprinting gene expression pattern of multiple human iPS cell lines via DNA microarray analyses and divided the pattern of expression into three groups: (a) genes that showed significantly stable levels of expression in iPS cells, (b) genes that showed a substantial degree of variability in expression in both human ES and iPS cells, and (c) genes that showed aberrant expression levels in some human iPS cell lines, as compared with human ES cells. In general, iPS cells have a rather stable expression of their imprinted genes. However, we found a significant number of cell lines with abnormal expression of imprinted genes, and thus we believe that imprinted genes should be examined for each cell line if it is to be used for studying genetic diseases or for the purpose of regenerative medicine. STEM CELLS 2009;27:2686–2690

Fibroblast growth factor 4 and its novel splice isoform have opposing effects on the maintenance of human embryonic stem cell self-renewal.

Human embryonic stem cells (HESCs) are unique in their capacity to self‐renew while remaining pluripotent. This undifferentiated state must be actively maintained by secreted factors. To identify autocrine factors that may support HESC growth, we have taken a global genetic approach. Microarray analysis identified fibroblast growth factor 4 (FGF4) as a prime candidate for autocrine signaling. Furthermore, the addition of recombinant FGF4 to HESCs supports their proliferation. We show that FGF4 is produced by multiple undifferentiated HESC lines, along with a novel fibroblast growth factor 4 splice isoform (FGF4si) that codes for the amino‐terminal half of FGF4. Strikingly, although FGF4 supports the undifferentiated growth of HESCs, FGF4si effectively counters its effect. Furthermore, we show that FGF4si is an antagonist of FGF4, shutting down FGF4‐induced Erk1/2 phosphorylation. Expression analysis shows that both isoforms are expressed in HESCs and early differentiated cells. However, whereas FGF4 ceases to be expressed in mature differentiated cells, FGF4si continues to be expressed after cell differentiation. Targeted knockdown of FGF4 using small interfering RNA increased differentiation of HESCs, demonstrating the importance of endogenous FGF4 signaling in maintaining their pluripotency. Taken together, these results suggest a growth‐promoting role for FGF4 in HESCs and a putative feedback inhibition mechanism by a novel FGF4 splice isoform that may serve to promote differentiation at later stages of development.

Genetic instability in human induced pluripotent stem cells: Classification of causes and possible safeguards

Comment on: Mayshar Y, et al. Cell Stem Cell 2010; 7:521-31.

Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles

The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually performed using cytogenetic or DNA-based methods at variable sensitivities, resolutions and costs. Here we present a detailed protocol for determining the genomic integrity of pluripotent stem cells (PSCs) using their global gene expression profiles. This expression-based karyotyping (e-karyotyping) protocol uses gene expression microarray data (either originally generated or derived from the literature) and describes how to organize it properly, subject it to two complementary bioinformatic analyses and conservatively interpret the results in order to generate an accurate estimation of the chromosomal aberrations in the autosomal genome of examined stem cell lines. The experimental steps of e-karyotyping can be carried out in ∼20–30 h.

Teratogen screening using transcriptome profiling of differentiating human embryonic stem cells

Teratogens are substances that may cause defects in normal embryonic development while not necessarily being toxic in adults. Identification of possible teratogenic compounds has been historically beset by the species‐specific nature of the teratogen response. To examine teratogenic effects on early human development we performed non‐biased expression profiling of differentiating human embryonic and induced pluripotent stem cells treated with several drugs – ethanol, lithium, retinoic acid (RA), caffeine and thalidomide, which is known to be highly species specific. Our results point to the potency of specific teratogens and their affected tissues and pathways. Specifically, we could show that ethanol caused dramatic increase in endodermal differentiation, RA caused misregulation of neural development and thalidomide affected both these processes. We thus propose this method as a valuable addition to currently available animal screening approaches.

53 – Genetic Manipulation of Human Embryonic Stem Cells

This chapter focuses on recent advances in the genetic manipulation of human embryonic stem (hES) cells, the available methods of manipulation, and their possible uses. A brief description of advanced genetic manipulation techniques, not yet demonstrated in these cells, is also presented. Genetic manipulation is the process of inducing changes in gene expression, and the expression of novel genes has proved to be an indispensable tool in recent genetic research. The implementation of increasingly powerful genetic tools for mouse embryonic stem (ES) cells has led to an explosion of data concerning the specific properties of an enormous array of genes. Genetic manipulation will play a pivotal role in applying this technology to biological research as well as to the specific needs of transplantation medicine. Several gene delivery methods have been shown to be effective in human ES cells including transfection by various chemical reagents, electro oration, and viral infection.