Gene expression analysis of HESC derived teratomas
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE13586 | GEO | 2008/11/14
SECONDARY ACCESSION(S): PRJNA110691
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression analysis of human embryonic stem cell derived tumors (teratomas). Experiment Overall Design: Undifferentiated HESCs were injected into the testis or under the kidney capsule of SCID-NOD mice and were let to grow for one month prior to tumor harvesting.
2008-11-21 | E-GEOD-13586 | biostudies-arrayexpress
Project description:mRNA expression profiles of teratomas derived from mouse embryonic stem cells containing Sox2 WT and Sox2 T258A mutations
2021-06-06 | GSE176212 | GEO
Project description:Canonical and non-canonical Wnt signaling play key roles during development and tumorigenesis. In this study we compared gene expression in teratomas grown from mouse embryonic stem cells that overexpress Evi/Wls and teratomas from normal embryonic stem cells cells.
2016-03-06 | E-MTAB-3995 | biostudies-arrayexpress
Project description:Teratoma formation is the gold standard assay for testing the capacity of human stem cells to differentiate into all embryonic germ layers. Although widely used, little effort has been made to transform this qualitative assay into a quantitative one. Using gene expression data from a wide variety of cells, we created a gene scorecard representing tissues from all three germ layers as well as an extraembryonic tissue. A calculated grade using this gene list successfully distinguishes pluripotent stem cell-initiated teratomas from malignant tumors, thereby translating cell potency into a quantitative measure. This new methodology, named TeratoScore, thus assesses the pluripotency of human cells, and is easily performed using an open-source code. The new teratoma database also allowed us to examine the gene expression differences between tumors with a diploid karyotype and those initiated by aneuploid cells. We found that while teratomas originating from aneuploid cells pass the TeratoScore benchmark for pluripotency, they exhibit aberrant gene expression congruent with human chromosomal syndromes (such as Down syndrome). This gene expression signature is significantly different from that of teratomas originating from diploid cells, particularly in central nervous system-specific genes, suggesting aberrant teratomas may be beneficial for in vivo disease modeling. Teratoma formation followed by TeratoScore analysis can rapidly assess cell potency and allows comparison between different pluripotent cell lines. Total RNA was extracted from hPSC (diploid or aneuploid)-derived teratomas using RNeasy mini kit (Qiagen), according to the manufacture instruction. RNA was subjected to Human Genome U133 Plus 2.0 microarray platform (Affymetrix); washing and scanning were performed according to the manufacturer’s protocol
2015-06-10 | E-GEOD-64669 | biostudies-arrayexpress
Project description:Human pluripotent stem cells (hPSCs) tend to acquire genomic aberrations in culture, the most common of which is the trisomy of chromosome 12. Interestingly, trisomy 12 is also prevalent in germ cell tumors (GCTs). Here, we aimed to dissect the cellular and molecular implications of trisomy 12 in hPSCs. A genome-wide gene expression analysis revealed that trisomy 12 profoundly affects the global gene expression profile of hPSCs, inducing a transcriptional program very similar to that of CGTs. Direct comparison of the proliferation, replication, differentiation and apoptosis between diploid and aneuploid hPSCs revealed that trisomy 12 significantly increases the proliferation rate of hPSCs. Increased replication largely accounts for the increased proliferation observed, and may explain the selection advantage that trisomy 12 confers to hPSCs. A comparison of the tumors induced by diploid and aneuploid hPSCs further demonstrated that trisomy 12 increases the tumorigenicity of hPSCs, inducing transcriptionally-distinct teratomas, from which pluripotent cells can be recovered. Lastly, a chemical screen of 89 anticancer drugs against diploid and aneuploid hPSCs discovered that trisomy 12 raises the sensitivity of hPSCs to several replication inhibitors, suggesting that the increased proliferation and tumorigenicity of these aberrant cells also makes them more vulnerable, and might potentially be used for their selective elimination from culture. Together, our findings demonstrate the extensive effect of trisomy 12 on the gene expression signature and on the cellular behavior of hPSCs, and highlight the danger posed by this trisomy for the successful use of hPSCs in basic research and in regenerative medicine. Expression data from diploid and aneuoploid human pluripotent stem cells, teratomas derived from them, and pluripotent-like cells recovered from these teratomas total RNA was isolated from undifferentiated human pluripotent stem cells grown under standard human ES conditions, or from teratomas derived from them, or from ES-like cells recovered from these teratomas.
2014-09-01 | E-GEOD-51455 | biostudies-arrayexpress
Project description:Teratoma formation is the gold standard assay for testing the capacity of human stem cells to differentiate into all embryonic germ layers. Although widely used, little effort has been made to transform this qualitative assay into a quantitative one. Using gene expression data from a wide variety of cells, we created a gene scorecard representing tissues from all three germ layers as well as an extraembryonic tissue. A calculated grade using this gene list successfully distinguishes pluripotent stem cell-initiated teratomas from malignant tumors, thereby translating cell potency into a quantitative measure. This new methodology, named TeratoScore, thus assesses the pluripotency of human cells, and is easily performed using an open-source code. The new teratoma database also allowed us to examine the gene expression differences between tumors with a diploid karyotype and those initiated by aneuploid cells. We found that while teratomas originating from aneuploid cells pass the TeratoScore benchmark for pluripotency, they exhibit aberrant gene expression congruent with human chromosomal syndromes (such as Down syndrome). This gene expression signature is significantly different from that of teratomas originating from diploid cells, particularly in central nervous system-specific genes, suggesting aberrant teratomas may be beneficial for in vivo disease modeling. Teratoma formation followed by TeratoScore analysis can rapidly assess cell potency and allows comparison between different pluripotent cell lines.
2015-06-10 | GSE64669 | GEO
Project description:Skeletal muscle stem cells are essential to muscle homeostasis and regeneration after injury. An attractive approach to obtain these cells is via differentiation of pluripotent stem cells (PSCs). We have recently reported that teratomas derived from mouse PSCs are a rich source of skeletal muscle stem cells. Here, we showed that the teratoma formation method is also capable of producing skeletal myogenic progenitors from human PSCs. Using single-cell transcriptomics, we discovered multiple lineages in human PSC-derived teratomas. Interestingly, we observed several distinct skeletal myogenic subpopulations. Trajectory analysis revealed that these subpopulations represented progressive stages of skeletal myogenic development. We further discovered that ERBB3 and CD82 are effective surface markers for prospective isolation of the skeletal myogenic lineage in human PSC-derived teratomas. Therefore, teratoma formation provides an accessible model for obtaining human skeletal myogenic progenitors from PSCs.
2022-05-18 | GSE189985 | GEO
Project description:Defining the skeletal myogenic lineage in human pluripotent stem cell-derived teratomas
| PRJNA785485 | ENA
Project description:Purpose: Pancreatic islet transplantation is an effective cell therapy for type 1 diabetes (T1D), but its clinical application is limited by the shortage of donor pancreata. Among the potential alternatives, the differentiation of human embryonic stem cells (hESc) into insulin-producing β-cells has taken an early lead. However, while the proportion of β-cells obtained through current methods is relatively high, a significant percentage of undefined non-endocrine cell types are still generated. Most importantly, there is the potential for carry-over of non-differentiated cell types that may produce teratomas upon transplantation. In order to address these issues, we sought to modify hESc so that their differentiated progeny could be selectively devoid of tumorigenic cells and enriched for cells of the desired phenotype (in this case, pancreatic β-cells). Methods: mRNA profiles of λH1-hESC derived β-like cells were developed by mRNA sequencing, in triplicate, using Illumina HiSeq PE Cluster Kit v4 and Illumina HiSeq Flow Cell v4 with 50 nt paired end reads plus dual index reads using the Illumina HiSeq SBS kit v4. Sequence reads that passed quality filters were analyzed at the transcript isoform level following alignment using TopHat v2.1.0 followed by exon and gene level counting using Bioconductor easyRNASeq v 2.4.7. Conclusions: Our study demonstrates that λH1-hESC derived β-like cells have a transcriptional expression profile similar to ESC derived β-like cells.
2018-12-14 | GSE108056 | GEO
Project description:The balance between pluripotency and differentiation is critical during development and regeneration. miR-203 is a microRNA previously involved in differentiation of different tissues as well as in tumor suppression in multiple malignancies. We have shown that miR-203 is able to promote differentiation of embryonic stem (ES) and induced pluripotent stem (iPS) cells without decreasing pluripotency. We have observed that transient expression of miR-203 significantly improves the efficiency of ES/iPS cells in the generation of quimeras and tetraploid complementation assays, in addition to inducing complex embryo-like structures when these pluripotent cells are injected in mice. In the present RNA seq, we intend to analyze the trascriptomic profile of WT IPSCs, compared to miR-203 KO IPSCs and miR-203 tKI IPSCs (in which we have induced a transient over-expression of miR-203). Moreover, we analyze the mRNA profiles of the teratomas derived from those IPSCs.
2020-07-05 | GSE81133 | GEO