PMC:1802744 / 6045-22350
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1802744","sourcedb":"PMC","sourceid":"1802744","source_url":"http://www.ncbi.nlm.nih.gov/pmc/1802744","text":"Results and Discussion\nStem cells have unique biological characteristics, but only a limited number of genes are currently recognized as established stem cell markers. Examples include POU domain, class 5, transcription factor 1 (Oct3/4), signal transducer and activator of transcription 3 (Stat3), teratocarcinoma-derived growth factor (Tdgf1), Enk-pending (Nanog), undifferentiated embryonic cell transcription factor 1 (Utf1) and DNA methyltransferase 3B (Dnmt3b) [20]. At the same time, hundreds of genes are suggested as candidate markers for \"stemness\", but their coupling to the undifferentiated stem cell state is not yet fully verified [21]. The concept of \"stemness\" (term introduced in 1986 by Grossman \u0026 Levine) is defined as \"core stem cell properties that underlie self-renewal and the ability to generate differentiated progeny\" [22]. Considering the complexity of the processes involved, stemness can hardly be ensured by co-operation of just a few genes. Nevertheless, three stemness genes (namely, Oct3/4, Stat3 and Nanog) are considered \"master\"-genes that control the self-renewing process [23,24]. Various types of stem cells, such as hematopoietic, mesenchymal and neural (HSCs, MSCs and NSCs, respectively), embryonic germ and embryonic carcinoma cells (EGCs and ECCs, respectively) are all characterized by variations in gene expression profiles, and only a few gene markers are associated with all these cell types [25,26]. We have aimed to embrace the most comprehensive set of those genes into a solitary array, the NeuroStem Chip. Thereby, it is possible to employ it to monitor the relative expression levels of numerous known and candidate stemness genes in a single experiment.\nSimilar to the genetic bases underlying stemness, cell differentiation is associated with altered expression levels of certain recognized or candidate genes [25]. We therefore incorporated gene markers of development and differentiation in general, and that of neuronal and dopaminergic differentiation in particular, into the NeuroStem Chip. Examples include markers for the processes of neuronal maturation, axonal branching, neural/neuronal survival, etc. Finally, we ensured that known markers for specific types of neurons, allowing identification of individual cell types, were present on the chip. We paid special attention to genes associated with the differentiation and maturation of dopaminergic neurons. In many published studies, the expression of only a single (tyrosine hydroxylase, TH) or 2–3 markers for dopaminergic neurons (e.g. amino acid decarboxylase (AADC), dopamine transporter (DAT), vesicular monoamine transporter 2 (VMAT2)) have been used to indicate dopaminergic identity of neurons. In contrast, the NeuroStem Chip includes oligonucleotide probes for 88 genes related to dopaminergic neurons, thus being more comprehensive in this sense, compared to other existing microarray platforms, including focused ones [17,18]. Those entries encompass recognized and candidate markers for dopaminergic neurons (mature and early) and progenitors, as well as markers for the maturation and differentiation of the latter (Table 1).\nTable 2 represents conditional functional breakdown of genes targeted by the NeuroStem microarray platform. A number of important gene groups that are included in the chip are not mentioned in Table 2. Among these, entries related to Dickkopf gene family, galanin-, melatonin-, vasoactive intestinal peptide (VIP)-, cAMP response element-binding protein (CREB)- and B cell leukemia 2 (Bcl2) oncogene-related are present. Many of them play potentially important, yet undefined, roles in the biology of stem cells. Additionally, we included some genes implicated in disease mechanisms of neurodegenerative disorders (most importantly, Parkinson's disease and Alzheimer's disease) in the chip. Furthermore, we incorporated a number of markers for distinct differentiation pathways (e.g. hematopoietic and pancreatic) and cell types (e.g. cancer subtypes and a range of normal cell types) to serve as essential controls. Taken together, we believe that in its present form NeuroStem Chip represents currently most comprehensive gene expression platform for studies on stem cells, neural/neuronal differentiation, human neurodegeneration and neuronal survival, both in vivo and in vitro. The complete layout of NeuroStem Chip will be disclosed to the academic community, upon request.\nThe microarray format we selected relies on long oligonucleotide molecules (69–71 nucleotides) printed over a solid surface. We spotted the synthesized oligonucleotides (Operon Biotechnologies) with a constant concentration across the slides, and evaluated the quality and consistency of spotting in a series of control experiments. We then illustrated the utility and technical reliability of the NeuroStem Chip by characterizing the gene expression profile of commonly utilized hESC line SA02 (Sahlgrenska 2; [27]), including (i) undifferentiated cells and (ii) cells committed towards neuronal/dopaminergic differentiation pathway. For the first of these, we used total RNA sample purified from hESC colonies that exhibited morphology consistent with cell proliferation and the absence of spontaneous differentiation (Figure 1A). We also evaluated the expression of the cell cycle marker Ki67 and the pluripotency marker OCT3/4 in the sample by immunocytochemistry (Figure 1B–E). Co-culturing of ESCs with murine stromal cells (including PA6 cell line) rapidly generates dopaminergic neurons from ESCs by an unexplained mechanism termed stromal cell-derived inducing activity (SDIA; [28,29]). We therefore committed hESCs toward the neuronal/dopaminergic differentiation pathway by co-culturing with PA6 cells for 16 days, resulting in appearance of cells positive for early and late neuronal markers, including nestin, β-III-tubulin, and TH, the established marker of dopaminergic neurons (Figure 2). To verify the expression of some key stem cell- and neural phenotype-associated genes we performed RT-PCR comparing RNA samples from the undifferentiated hESCs with hESCs of the same line differentiated toward neuronal/dopaminergic pathway, as described above. The expression profile outlined by RT-PCR confirmed the identity of the sample used (Figure 3). After performing RNA integrity tests, we incorporated fluorescent labels to the amplified RNA samples from hESCs (Cyanine 3-CTP (Cy3) and Cyanine 5-CTP (Cy5)), hESC-derived cells containing TH-positive neurons (Cy3 and Cy5) and human universal reference RNA (Cy5), and hybridized aliquots with NeuroStem microarray slides using the following conditions: hESC vs. reference, Cy3 : Cy5 = (i) 20:10 pmol, and (ii) 10:5 pmol; and hESC vs. hESC-derived cells, Cy3 : Cy5 = (iii) 30:20 pmol, respectively. Universal reference RNA has been previously established as a standard reference material for microarray experiments, proving an ability to effectively hybridize to a large fraction of microarray spots [30].\nWe performed two-color hybridizations (e.g. for the experiment vs. reference) following an established protocol [31], and included dye-flip technical replicates in the analysis (Figure 4). Using the online software program BASE [32] we sequentially filtered the data by background subtraction, negative flagging, negative intensities and for inconsistent data amongst replicates [33]. Figure 5A shows a comparison of the spot intensities prior to normalization (M versus A plot), with the Log2 of the expression ratio between Cy3/Cy5 being plotted as a function of the log10 of the mean of the total expression intensities for Cy3 and Cy5 channels. The deviation of the line from zero revealed a need for normalization, so prior to data analyses we normalized signals using a locally weighted scatterplot-smoothing regression (LOWESS) algorithm (Figure 5A–B; fitted line) implemented in BASE. Since the reproducibility of two-color microarray gene expression data is critically important, we calculated Pearson correlation coefficients of the reporters present in the filtered database comparing the average expression ratios (7005 for hESCs vs. universal reference; 6947 for undifferentiated vs. neuronal/dopaminergic lineage-committed hESCs). Results obtained revealed that data were consistent across technical replicates (dye-swap and amount of loaded material), showing general high reproducibility: e.g., correlation coefficients were greater than 0.96 for technical replicates and 0.78 for dye-swapping samples in hESCs vs. universal reference hybridizations (Table 3). To detect genes with high expression levels in hESC samples, we filtered data for intensity values \u003e100 in the hESC sample and performed clustering analysis using the TIGR MultiExperiment Viewer (MEV; [34]). To visualize variations of spot/reporter per technical replicate, hierarchical clustering was performed by K-means classifier based on the linear-correlation-based distance (Pearson, centred) method. The optimal number of clusters was determined empirically to produce the most balanced ratio of entries to cluster of highly expressed genes. A cluster of 101 genes up-regulated in the hESC sample [see Additional file 1], was plotted in a centroid graph (Figure 5C); the variation across technical replicates was low. We merged technical replicates to generate a list of the most up-regulated genes expressed in the hESC sample compared to the universal reference RNA (Table 4). Standard error of the mean expressed as percentage was calculated for the 4 technical replicates, and was 6.7% for the top 25 genes up-regulated in hESC samples, compared to universal reference RNA. We performed the analysis of microarray data, as described in the Methods, and spot error values were generally in the lower range, indicating high stringency of the signals and low variance.\nAs seen in Table 4 and Table 5, the NeuroStem Chip identified numerous genes associated with stem cells. In particular, homeo box expressed in ES cells 1 (Hesx1) gene was identified as the most up-regulated in the ES cell preparation, compared to universal reference RNA. Highly expressed in pluripotent ESCs, Hesx1 expression is down-regulated upon embryonic stem cell differentiation [35,36], as also clearly seen in differentiation experiment of our own (Table 4). Similarly, Gremlin 1 homolog, cysteine knot superfamily gene (Grem1, also known as Cktsf1b1 and Dand2) is a recognized factor of cell-fate determination of ESCs [37]. Many more genes highly up-regulated in the hESC sample in comparison with universal reference RNA are associated with stem cells: further examples include Gap junction protein α1 (Gja1) and Zic family member 3 heterotaxy 1 (Zic3) (Table 4) [20]. The expression of fibroblast growth factor receptor 2 (Fgfr2) is of particular interest. Basic fibroblast growth factor (FGF2, bFGF) supports hESC proliferation and their ability to maintain undifferentiated phenotype when cultured in vitro [38,39]. Moreover, in some hESC lines a very high concentration of FGF2 could substitute for the need of feeder cells [40]. At the same time, genes listed in Table 4 represent the most highly up-regulated entries in a relatively limited group of genes (Figure 5C). Many other genes involved in maintenance of ESC phenotype (i.e. established or candidate markers of stem cells) have lower levels of expression (Table 5). Examples include undifferentiated embryonic cell transcription factor 1 (Utf1), DNA methyltransferase 3B (Dnmt3b), developmental pluripotency associated 4 (Dppa4, a newly established pluripotency marker [41]) and numerous candidate markers of \"stemness\": e.g. genes for KIAA1573 protein, forkhead box O1A (Foxo1a), high-mobility group box 1 (Hmgb1), C-terminal binding protein 2 (Ctbp2) and left-right determination factor 1 (Lefty1), as well as others. For numerous established or candidate markers of stem cells the expression levels were not considerably higher (Log2 ratio \u003c 1) in the hESC sample compared to the universal reference RNA. For example, the expression of Nanog, DNA (cytosine-5-)-methyltransferase 3α (Dnmt3a), MutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli) (Msh2), Thy-1 cell surface antigen (Thy1), high-mobility group box 2 (Hmgb2), transcription factor 3 (Tcf3), Nanos homolog 1 (Nanos1), MyoD family inhibitor (Mdfi), Calumenin (Calu) and soluble thymidine kinase 1 (Tk1) was detected in hES SA02 cells with Log2 ratio value \u003c 1. Expression levels of those genes range from being inconsiderably higher to nearly equal to that in universal reference RNA sample. We believe that those findings could be explained by cellular composition of human universal reference RNA sample [42], which includes pooled RNA samples from proliferating cells (e.g., skin and testis cell lines). Thus, the relative difference between gene expression of certain markers of stem cells in undifferentiated hESCs and universal reference RNA is naturally decreased. Taken together, the gene expression signature of hES SA02 cell line profiled by NeuroStem Chip is indeed characteristic for pluripotent stem cells, providing proof-of-concept.\nNotably, comparison of expression profiles of undifferentiated hESCs and hESC-derived cells committed toward dopaminergic differentiation pathway by co-culturing with SDIA for 16 days have revealed that many of the stem cell marker genes mentioned above were down-regulated in differentiation (Table 5). Expectedly, Hesx1, Grem1, Dnmt3b, Utf1 and Nanog could be listed among these. At the same time, numerous other genes, including Pitx2, Dlk1 and Msx1 were up-regulated in the latter sample ([see Additional file 2], Figure 3). Table 1 lists 24 dopaminergic system-related entries (e.g., Ptx3, Th, Lhx1) with gene expression up-regulated by Day 16 of hESC differentiation protocol; few more genes have demonstrated less prominent up-regulation (Log2 ratio values in the range of 0.7/0.97–1.0). The gene expression profiles generated are therefore consistent with the results of earlier studies utilizing hSC-derived samples with similar characteristics [43,44]. Diversity of NeuroStem Chip entries responsive to hESC commitment toward neuronal/dopaminergic differentiation pathway clearly illustrates the complexity of that pathway. The cell population obtained after 16 day exposure to SDIA is highly heterogeneous. Only around 0.2% of the cells are TH-positive cells (Figure 2). This heterogeneity, with an apparent presence of residual pluripotent cells explains the presence of stem cell marker genes, including homeobox transcription factor Nanog, as revealed by RT-PCR data (Figure 3). It would be therefore impossible to apply the platform to identify novel genes associated with the process of differentiation; for that application, the genome-scale microarray platforms (e.g., Affymetrix) are clearly superior. Nevertheless, being based upon a moderate assay of pre-selected specific gene targets, the comparative analysis of microarray data derived from undifferentiated and dopaminergic differentiate pathway-committed hESCs provides a valuable cross-cut of complex relationship between factors driving or indicative to neuronal/dopaminergic differentiation [see Additional file 2].\nRT-PCR analyses have validated the overall reliability of NeuroStem microarray platform: all of the entries detected in the hybridization experiments have demonstrated similar trends when analyzed by RT-PCR means (Figure 3). Those entries include Sox2, En1 and Nanog (ratio of differentiated/undifferentiated hESC sample normalized spot intensity \u003c 0.75, down-regulated), Gadph, Aldh1a1, Sdha, Tubb and Nestin (ratio .1.0, unchanged), Actb, Th, Msx1 and Pitx2 (ratio \u003e1.25, up-regulated). Some of the housekeeping genes (Gapdh, Sdha, Tubb, Actb) have somewhat different expression in undifferentiated vs. differentiated cells, consistent with previous reports on certain established housekeeping genes (including Gapdh) being variable in human samples [45]. Importantly, all the observed gene expression trends were similar in both microarray and RT-PCR. Our experiment therefore confirms that the NeuroStem Chip microarray platform can still identify gene expression changes related to early stages of differentiation of hESC into dopaminergic 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