PMC:1523200 / 22001-25778 JSONTXT

{"project":"CellFinder","denotations":[{"id":"T202","span":{"begin":1737,"end":1748},"obj":"CellType"},{"id":"T203","span":{"begin":3274,"end":3277},"obj":"GeneProtein"},{"id":"T204","span":{"begin":656,"end":661},"obj":"CellLine"},{"id":"T205","span":{"begin":55,"end":59},"obj":"CellLine"},{"id":"T206","span":{"begin":2371,"end":2376},"obj":"CellLine"},{"id":"T207","span":{"begin":3294,"end":3298},"obj":"GeneProtein"},{"id":"T208","span":{"begin":3658,"end":3664},"obj":"CellLine"},{"id":"T209","span":{"begin":3107,"end":3112},"obj":"CellLine"},{"id":"T210","span":{"begin":2486,"end":2492},"obj":"CellLine"},{"id":"T211","span":{"begin":2694,"end":2698},"obj":"GeneProtein"},{"id":"T212","span":{"begin":2881,"end":2887},"obj":"CellLine"},{"id":"T213","span":{"begin":2836,"end":2840},"obj":"GeneProtein"},{"id":"T214","span":{"begin":2687,"end":2692},"obj":"GeneProtein"},{"id":"T215","span":{"begin":2457,"end":2472},"obj":"Anatomy"},{"id":"T216","span":{"begin":443,"end":448},"obj":"CellType"},{"id":"T217","span":{"begin":2006,"end":2010},"obj":"GeneProtein"},{"id":"T218","span":{"begin":362,"end":366},"obj":"CellLine"},{"id":"T219","span":{"begin":273,"end":278},"obj":"CellLine"},{"id":"T220","span":{"begin":150,"end":155},"obj":"CellType"},{"id":"T221","span":{"begin":1528,"end":1534},"obj":"CellLine"},{"id":"T222","span":{"begin":2703,"end":2707},"obj":"GeneProtein"},{"id":"T223","span":{"begin":2616,"end":2620},"obj":"GeneProtein"},{"id":"T224","span":{"begin":586,"end":592},"obj":"CellLine"},{"id":"T225","span":{"begin":2663,"end":2669},"obj":"GeneProtein"},{"id":"T226","span":{"begin":2638,"end":2642},"obj":"GeneProtein"},{"id":"T227","span":{"begin":2656,"end":2661},"obj":"GeneProtein"},{"id":"T228","span":{"begin":1829,"end":1834},"obj":"GeneProtein"},{"id":"T229","span":{"begin":2671,"end":2677},"obj":"GeneProtein"},{"id":"T230","span":{"begin":2679,"end":2685},"obj":"GeneProtein"},{"id":"T231","span":{"begin":44,"end":50},"obj":"CellLine"},{"id":"T232","span":{"begin":55,"end":67},"obj":"CellLine"},{"id":"T233","span":{"begin":109,"end":111},"obj":"CellType"},{"id":"T234","span":{"begin":2913,"end":2918},"obj":"CellLine"},{"id":"T235","span":{"begin":3669,"end":3674},"obj":"CellLine"},{"id":"T236","span":{"begin":1839,"end":1844},"obj":"GeneProtein"},{"id":"T237","span":{"begin":1822,"end":1827},"obj":"GeneProtein"},{"id":"T238","span":{"begin":1737,"end":1742},"obj":"Anatomy"},{"id":"T239","span":{"begin":1565,"end":1570},"obj":"CellType"},{"id":"T240","span":{"begin":1870,"end":1876},"obj":"CellLine"},{"id":"T388","span":{"begin":870,"end":876},"obj":"CellLine"},{"id":"T389","span":{"begin":828,"end":833},"obj":"CellType"},{"id":"T390","span":{"begin":1157,"end":1161},"obj":"CellLine"},{"id":"T391","span":{"begin":744,"end":750},"obj":"CellLine"},{"id":"T392","span":{"begin":789,"end":794},"obj":"CellLine"},{"id":"T393","span":{"begin":1003,"end":1009},"obj":"CellLine"},{"id":"T394","span":{"begin":1020,"end":1025},"obj":"CellType"},{"id":"T395","span":{"begin":1220,"end":1224},"obj":"GeneProtein"},{"id":"T396","span":{"begin":1089,"end":1093},"obj":"CellLine"},{"id":"T397","span":{"begin":1132,"end":1137},"obj":"CellLine"}],"text":"Comparison of diploid pluripotent cells with NTera2 and BG01 variant\nOur previous results have suggested that EC lines share many of the properties of hESCs and can be used as a useful model for initial testing of biological questions [21]. More recently we have identified BG01V as a karyotypically abnormal variant that behaves much like its normal counterpart BG01, but is not subject to the same constraints of use as karyotypically normal hESCs [13]. Given the sensitivity of the bead array analysis, we tested its ability to detect the overall similarities and differences between NTera2 and a pooled ESC sample or between the karyotypically abnormal BG01V and its normal parent line (Figure 6).\nFigure 6 Diploid pluripotent EC cell line NTera2 and karyotypically abnormal hESC line BG01V can be distinguished from normal hESCs using Illumina array. Comparison of NTera2 and pooled hESC sample resulted a correlation coefficient of 0.8997. Two lists of genes, which were specifically expressed in NTera2 (C) or in hESCs (E) were identified. Likewise, while sharing similarities with BG01 (B, correlation coefficient= 0.9043), BG01V was different from BG01 in expression for many genes, particularly genes from the TGFβ pathway (D, F). Black dots represent genes that were detected at \u003e0 expression level, blue dots represent genes that were detected both at \u003e 0 expression level and at \u003e0.99 confidence. Genes plotted outside the two thin red lines were detected at \u003e2.5- fold difference. Our results showed that, while NTera2 shared a high similarity with hESCs [21], it did have important differences with hESC lines. Examining these differences (summarized in Figure 6C and 6E), we noted that some reflected the origin of the tumor cells from which this line was derived [14]. Several germ cell markers such as GAGE2, GAGE7 and GAGE8 were highly expressed in NTera2 but were absent (or present at low levels) in any of the hESC lines examined (See Figure 6C and Additional file 1. Note that the GAGE genes are highly similar in sequence, making it difficult to distinguish one family member from another through hybridization; thus, while all of these GAGE gene probes gave positive signal, it is difficult to say if the signal came from the specific gene itself or from cross-hybridization from one of the other family members). None of these were present in BG01V, indicating that the karyotypically abnormal variant is not the equivalent of a teratocarcinoma line such as NTera2. In addition to the expression of germ cell markers, we noticed a significant difference in the expression of genes in the TGFβ pathway, such as GDF3 (Figure 6C), TGFBI, CDKN1A, IGFBP7, IGFBP3, NODAL, CER1 and BMP2 (Figure 6E). This is consistent with the postulated role of this pathway in germ cell differentiation [22,23] and suggests that TGFβ pathway cannot be reliably tested using NTera2 as a model for hESC.\nThe BG01V showed clear differences from its normal counterpart and some major changes are summarized in Figure 6D and 6F. Early markers of differentiation appeared to be present at higher levels in BG01V as compared to any of the hESC lines examined, although hESC specific genes continued to be expressed at high levels (see Additional file 4). In particular, the Wnt pathway and the TGFβ signaling pathway (Figure 6D), both of which involved in the early process of differentiation [24,25], appeared to be activated (Additional file 4), suggesting that the role of growth factors and signaling in these early events cannot be readily studied in this cell line.\nIn summary, the analysis highlighted the utility of the potential reference standards NTera2 and BG01V, demonstrated their general similarity and provided detail on potential caveats to their application."}