Array-based comparative genomic hybridization study of human embryonic stem cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Afroditi Mertzanidou
PROVIDER: E-GEOD-13422 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Recurrent chromosomal abnormalities in human embryonic stem cells.
Spits Claudia C Mateizel Ileana I Geens Mieke M Mertzanidou Afroditi A Staessen Catherine C Vandeskelde Yves Y Van der Elst Josiane J Liebaers Inge I Sermon Karen K
Nature biotechnology 20081123 12
Cultured human embryonic stem (hES) cells have a known predisposition to aneuploidy of chromosomes 12, 17 and X. We studied 17 hES cell lines by array-based comparative genomic hybridization (aCGH) and found that the cells accumulate other recurrent chromosomal abnormalities, including amplification at 20q11.21 and a derivative chromosome 18. These genomic changes have a variable impact at the transcriptional level. ...[more]
Similar Datasets
Project description:G-banding of human embryonic stem cells (hESC) has proved their predisposition to aneuploidy of chromosomes 12, 17 and X. Now, using array-based comparative genomic hybridization, we find that hESC also accumulate other recurrent chromosomal abnormalities, such as duplications of stemness genes, submicroscopic instability of 20q11.21 and the appearance of a derivative chromosome 18. Keywords: comparative genomic hybridization, genomic integrity of human embryonic stem cells
2008-11-04 | GSE13422 | GEO
Project description:Cultured human embryonic stem (hES) cells can acquire genetic and epigenetic changes that make them vulnerable to transformation. As hES cells with cancer-cell characteristics share properties with normal hES cells, such as self-renewal, teratoma formation and the expression of pluripotency markers, they may be misconstrued as superior hES cells with enhanced âstemnessâ. We characterize two variant hES cell lines (v-hESC-1 and v-hESC-2) that express pluripotency markers at high levels and do not harbor chromosomal abnormalities by standard cytogenetic measures. We show that the two lines possess some features of neoplastic progression, including a high proliferative capacity, growth-factor independence, a 9- to 20-fold increase in frequency of tumor initiating cells, niche independence and aberrant lineage specification, although they are not malignant. Array comparative genomic hybridization revealed an amplification at 20q11.1-11.2 in v-hESC-1 and a deletion at 5q34a-5q34b;5q3 and a mosaic gain of chromosome 12 in v-hESC-2. These results emphasize the need for functional characterization to distinguish partially transformed and normal hES cells. Custom oligonucleotide array gene expression analysis was performed on total RNA from low passage normal and variant human embryonic stem cell (hESC) lines, all cultured in our laboratory under the same conditions. Furthermore, array-based comparative genomic hybridization was also performed on the normal and variant hESC lines. v-hESC-1 and v-hESC-2 represent two independent lines that display neoplastic characteristics with distinctive copy number alterations. v-hESC-1_A2B5 represents neural precursor cultures differentiated from variant hES cells. GSM349016-GSM349022: Gene expression analysis GSM351500-GSM351511: aCGH analysis
2010-06-24 | E-GEOD-13995 | biostudies-arrayexpress
Project description:Although it is known that cultured human cells acquire copy number variations over time, little is known about the mutation frequency in individual cells. Here we describe that human somatic and embryonic stem cell cultures show significant fractions of cells carrying unique chromosomal abnormalities, forming a non-clonal genetic mosaic. We studied 85 human single cells by array-based comparative genomic hybridisation and found that 14-31% of hESC and 8-26% of somatic cells are chromosomally abnormal. Remarkably, only 2 cells showed full-chromosome aneuploidy, while 93% of detected abnormalities were segmental, most of them telomere-spanning. Furthermore, fluorescent in situ hybridisation confirmed this finding and revealed an increased instability of the subtelomeric regions in hESC as compared to somatic cells.
2014-06-24 | GSE51126 | GEO
Project description:The self-renewal and differentiation potential of human embryonic stem cells (hESCs) suggests that hESCs could be used for regenerative medicine, especially for restoring neuronal functions in brain diseases. However, the functional properties of neurons derived from hESC are largely unknown. Moreover, since hESCs were derived under diverse conditions, the possibility arises that neurons derived from different hESC lines exhibit distinct properties, but this possibility remains unexplored. To address these issues, we developed a protocol that allows step-wise generation from hESCs of ~70-80% pure human neurons that form spontaneously active synaptic networks in culture. Comparison of neurons derived from the well-characterized HSF1 and HSF6 hESC lines revealed that HSF1- but not HSF6-derived neurons exhibit forebrain properties. Accordingly, HSF1-derived neurons initially form primarily GABAergic synaptic networks, whereas HSF6-derived neurons initially form glutamatergic networks. microRNA profiling revealed significant expression differences between the two hESC lines, suggesting that microRNAs may influence their distinct differentiation properties. These observations indicate that although both HSF1 and HSF6 hESCs differentiate into functional neurons, the two hESC lines exhibit distinct differentiation potentials, suggesting that they are pre-programmed. Information on hESC line-specific differentiation biases is crucial for neural stem cell therapy and establishment of novel disease models using hESCs. Experiment Overall Design: We directly compared the transcriptome of hNPCs derived from HSF-1 and HSF-6 hESC lines under two different neural induction conditions (embryonic body formation in presence of caudalizing factors (retinoic acid and bFGF) and monolayer conversion in presence of BMP signaling inhibitor (Noggin)). Since HSF6 hESC cannot undergo efficient neural differentiation without caudalizing factors, we cannot obtain RNA samples for HSF6 (Noggin). Experiment Overall Design: In summary, consistent with our immunostaining results, HSF1 hNPCs display more forebrain properties as compared to HSF6 hNPCs, indicated by expression of multiple forebrain specific markers. Conversely, HSF6 hNPCs show regional identity towards posterior central nervous system.
2008-06-16 | E-GEOD-8347 | biostudies-arrayexpress
Project description:Polycomb group (PcG) proteins are essential for accurate axial body patterning during embryonic development. PcG-mediated repression is conserved in metazoans and is targeted in Drosophila by Polycomb response elements (PREs). Targeting sequences in humans have not been described. While analyzing chromatin architecture in the context of human embryonic stem cell (hESC) differentiation, we discovered a 1.8kb region between HOXD11 and HOXD12 (D11.12) that is associated with PcG proteins, is nuclease hypersensitive, and shows alteration as hESCs differentiate. D11.12 repressed luciferase expression from a reporter construct both before and after differentiation of mesenchymal stem cells into adipocytes. Full repression by D11.12 required a highly conserved region and YY1 binding sites. Repression relied upon PcG proteins Bmi1 and Eed and a YY1-interacting partner, RYBP. We conclude that D11.12 is a Polycomb-dependent regulatory region with similarities to Drosophila PREs, indicating conservation in the mechanisms that target PcG function in mammals and flies. Data contains microarray measurements of the MNase-digested mononucleosomal fragments in hES cells, derived MSCs, osteoblasts and adipocytes. The ChIP-chip data includes Suz12, Bmi1 and H3K27me3 measurements in MSCs and adipocytes.
2010-06-19 | E-GEOD-19046 | biostudies-arrayexpress
Project description:Background Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration. Results We present Supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method that does take difference in genomic content into account. The performance of S-Lowess was assessed on aCGH experiments in which differentially labeled genomic DNA fragments of Lactococcus lactis IL1403 and L. lactis MG1363 strains were hybridized to IL1403 microarrays. Since both genome sequences are known (they have only on average 85 % sequence identity), the success rate in detecting deletions in the MG1363 genome of different aCGH normalization methods can be compared. S-Lowess detects 97% of the deletions, whereas other aCGH normalization methods detect up to only 60% of the deletions. Conclusions S-Lowess removes systematic errors from dual-dye aCGH data in two steps: (i) determination of likely homologous genes (LHG); and (ii) estimation of correction factors for systematic errors from spots of LHG and subset Lowess normalization of the remaining spots using these correction factors. It is implemented in a user-friendly web-tool accessible from http://bioinformatics.biol.rug.nl/websoftware/s-lowess. We demonstrate that it outperforms existing normalization methods and maximizes the number of detectable genomic deletions or duplications from microbial aCGH data. Keywords: comparative genome hybridisation In this study, 4 aCGH comparisons (slides) between L. lactis MG1363 and L. lactis IL1403 were performed (including dye swap with biological replicates; see also supplementary materials). The resulting aCGH slide signals were normalized using the different 'likely homologous gene' (LHG) sets (see above) yielding ratios of signals of labelled DNA of MG1363 over those of IL1403. A maximum of 8 ratios per amplicon (gene) were obtained for the 4 hybridized slides (each with 2 replicate spots per amplicon). Only genes with at least 5 measurements were used in this study. The normalization methods evaluated in this study are: a) no normalization, b) total signal normalization, c) grid-based Lowess (implemented in PreP; f = 0.7) [GarcM-CM--a de la Nava, J et al. 2003. Bioinformatics 19:2328-2329], and d) S-Lowess using different subsets of conserved lactococcal genes (for details see above). Results with the MANOR R package (spatial normalization; standard parameters) [Neuvial P, et al. 2006. BMC Bioinformatics 7:264; Liva S, et al. 2006. Nucleic Acids Res 34:W477-W481] are shown in our supplementary materials.
2008-07-19 | E-GEOD-9039 | biostudies-arrayexpress
Project description:Cultured human embryonic stem (hES) cells can acquire genetic and epigenetic changes that make them vulnerable to transformation. As hES cells with cancer-cell characteristics share properties with normal hES cells, such as self-renewal, teratoma formation and the expression of pluripotency markers, they may be misconstrued as superior hES cells with enhanced ‘stemness’. We characterize two variant hES cell lines (v-hESC-1 and v-hESC-2) that express pluripotency markers at high levels and do not harbor chromosomal abnormalities by standard cytogenetic measures. We show that the two lines possess some features of neoplastic progression, including a high proliferative capacity, growth-factor independence, a 9- to 20-fold increase in frequency of tumor initiating cells, niche independence and aberrant lineage specification, although they are not malignant. Array comparative genomic hybridization revealed an amplification at 20q11.1-11.2 in v-hESC-1 and a deletion at 5q34a-5q34b;5q3 and a mosaic gain of chromosome 12 in v-hESC-2. These results emphasize the need for functional characterization to distinguish partially transformed and normal hES cells.
2008-12-25 | GSE13995 | GEO
Project description:Although it is known that cultured human cells acquire copy number variations over time, little is known about the mutation frequency in individual cells. Here we describe that human somatic and embryonic stem cell cultures show significant fractions of cells carrying unique chromosomal abnormalities, forming a non-clonal genetic mosaic. We studied 85 human single cells by array-based comparative genomic hybridisation and found that 14-31% of hESC and 8-26% of somatic cells are chromosomally abnormal. Remarkably, only 2 cells showed full-chromosome aneuploidy, while 93% of detected abnormalities were segmental, most of them telomere-spanning. Furthermore, fluorescent in situ hybridisation confirmed this finding and revealed an increased instability of the subtelomeric regions in hESC as compared to somatic cells. We first validated the aCGH method by studying single cells with known genetic imbalances of different sizes. We analysed 2 amniocytes (Amniocyte C 01 - Amniocyte C 02) with a trisomy 18, eight amniocytes carrying a deletion of 5p33.3p15.55 and a duplication of 9q33q34.3 (Amniocyte A 01 - Amniocyte A 08), two amniocytes carrying a deletion of 5p15.33p15.1 (Amniocyte B 01 - Amniocyte B 02) and three hESC carrying a duplication of 3q26.33q27.3 (VUB07 P165BBB7 01 - VUB07 P165BBB7 03). From this, we found that we can reliably detect at the single-cell level CNVs that span seven consecutive BAC clones on the microarray.
2014-06-24 | E-GEOD-51126 | biostudies-arrayexpress
Project description:Although the evidence for a genetic predisposition to human essential hypertension is compelling, the genetic control of blood pressure (BP) is poorly understood. The Dahl salt-sensitive (S) rat is a model for studying the genetic component of BP. Using this model we previously reported the identification of 16 different genomic regions that contain one or more BP quantitative trait loci (QTLs). The proximal region of rat chromosome 1 contains multiple BP QTLs. Of these, we have localized the BP QTL1b region to a 13.5cM (20Mb) region. Interestingly, five additional independent studies in rats and four independent studies in humans have reported genetic linkage for BP control by regions homologous to QTL1b. To view the overall renal transcriptional topography of the positional candidate genes for this QTL, we sought a comparative gene expression profiling between a congenic strain containing QTL1b and control S rats by employing: (1) a saturated QTL1b interval specific oligonucleotide array, and (2) a whole genome cDNA microarray representing 20,465 unique genes that are positioned outside the QTL. Results indicated that 19 out of the 231 positional candidate genes for this QTL are differentially expressed between the two strains tested. Surprisingly, over 1,500 genes outside of QTL1b were differentially expressed between the two rat strains. Integrating the results from the two approaches revealed at least one complex network of transcriptional control initiated by the positional candidate Nr2f2. This network appears to account for the majority of gene expression differences occurring outside of the QTL interval. Further substitution mapping is currently underway to test the validity of each of these differentially expressed positional candidate genes. These results demonstrate the importance of using a saturated oligonucleotide array for identifying and prioritizing differentially expressed positional candidate genes of a BP QTL. Pairs of Cy5 and Cy3 labeled targets were co-hybridized onto either the oligonucleotide microarray or a custom TIGR rat cDNA array consisting of 26,401 probe elements representing 20,465 unique non-QTL1b genes. A âflip-dyeâ design was used as the experimental method of choice to account for potential dye-bias labeling effects. Seven âflip dyeâ normalized files are submitted for the oligonucleotide array and twelve individual hybridizations are submitted for the cDNA array.
2010-06-30 | E-GEOD-1622 | biostudies-arrayexpress
Project description:There is increasing evidence for tissue stem cells as potential source for cancers. However, the cellular and molecular mechanisms at the origin of this transformation remain elusive. Here we show that Delta-like1 (Dll1) mutation induces the oncogenic transformation of neural stem cell–derived neurospheres into oncogenic spheres capable of generating histological and molecular human glioblastoma (GBM)-like tumors upon subcutaneous and intracranial transplantations into nude mice. Serial transplantation assays suggest that Dll1 spheres tumorigenicity results from the oncogenic transformation of normal neural stem cell into GBM-producing stem cell. Compared differentiation of Dll1 vs. WT spheres shows the presence in Dll1 spheres of a subpopulation of cells which although fated to a glial lineage fail to differentiate terminally, in keeping with the astrocytic promoting function of Delta-Notch. This population of astrocyte progenitors proliferates actively and fails to down-regulate EGFR phosphorylation. These studies suggest that Dll1-induced tumorigenesis is restricted to the astrocytic lineage thereby providing a model for human GBM as well as an explanation for the duality of Notch signaling acting either as an oncogene or a tumor suppressor in stem/progenitor cells derived tumors, depending on the lineage commitment. Comparison between control (WT) and mutants (Dll1-3 and Dll1-5) cells was performed. Two biological replicates (n=3 each replicate) were used, and each replicate (n=3, total RNA pooled) was dye-swaped.
2011-09-23 | E-GEOD-32293 | biostudies-arrayexpress