Assessing the developmental and malignant potential of human pluripotent stem cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA383525 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5714380_1.fastq.gz | Fastqsanger.gz | |||
| SRR5714380_2.fastq.gz | Fastqsanger.gz | |||
| SRR5714390_1.fastq.gz | Fastqsanger.gz | |||
| SRR5714390_2.fastq.gz | Fastqsanger.gz | |||
| SRR5714400_1.fastq.gz | Fastqsanger.gz |
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Project description:The International Stem Cell Initiative compared three common approaches for assessing pluripotent stem cells (PSC). The formation of teratomas in vivo, or embryoid bodies (EB) in vitro, provide direct tests of differentiation, whereas PluriTest predicts pluripotency through bioinformatic analysis of transcriptomes of undifferentiated cells. We studied the teratomas by histology and TeratoScore, which analyzes gene expression in each tumor. For the EB assay, we assessed differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages. Comparison of each method showed that all assays predict pluripotency, but they have different endpoints that provide different insights. For example, tumors from a subset of lines also contained undifferentiated cells and yolk sac elements that indicate possible malignant potential. This characteristic was not detected by the other two methods. Our results highlight the need for multiple assays to assess both pluripotency and potential malignancy in clinical applications of PSCs.
2017-06-20 | GSE100223 | GEO
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Project description:Assessing the developmental and malignant potential of human pluripotent stem cells by RNA-seq analysis of Teratomas
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Project description:The International Stem Cell Initiative compared several commonly used approaches to assess human pluripotent stem cells (PSC). PluriTest predicts pluripotency through bioinformatic analysis of the transcriptomes of undifferentiated cells, whereas, embryoid body (EB) formation in vitro and teratoma formation in vivo provide direct tests of differentiation. Here we report that EB assays, analyzed after differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages, are sufficient to assess the differentiation potential of PSCs. However, teratoma analysis by histologic examination and by TeratoScore, which estimates differential gene expression in each tumor, not only measures differentiation but also allows insight into a PSC's malignant potential. Each of the assays can be used to predict pluripotent differentiation potential but, at this stage of assay development, only the teratoma assay provides an assessment of pluripotency and malignant potential, which are both relevant to the pre-clinical safety assessment of PSCs.
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Project description:This project aims at identifying missing proteins in naive pluripotent and trophoblastic stem cells in the framework of the human proteome project (HPP). To date, as much as 1343 missing proteins remain to be credibly identified essentially, but not entirely, by mass spectrometry. The present results also constitute a first step towards the identification of potential biological markers for assessing stem cells and early embryo development.
2023-03-11 | PXD035768 | Pride
Project description:Mouse embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) exhibit a pluripotent developmental potential, contributing to all embryonic cell types, though rarely to extra-embryonic lineages. Unexpectedly, rare, totipotent-like stem cells have been identified in cultured ESC populations, suggesting the existence of a discrete molecular pathway that regulates the transition between totipotency and pluripotency in vitro. Here, we identify a single miRNA, miR-34a, whose deficiency in mouse pluripotent stem cells expands cell fate potential, giving rise to both embryonic and extra-embryonic lineages in vitro and in vivo. The expression profiles of the totipotent-like miR-34a-knockout murine pluripotent stem cells are characterized by a strong induction of MERVL endogenous retroviruses, a key molecular hallmark shared with totipotent mouse 2-cell blastomeres and totipotent-like mouse ESCs. In all three cell types, a subset of MERVL elements promotes the expression of specific isoforms of the proximal protein-coding genes. We demonstrate that miR-34a represses MERVL expression through transcriptional regulation, at least in part, by directly targeting the transcription factor GATA-binding protein 2 (Gata2). Since MERVL activation correlated precisely with the totipotent-like state, we hypothesized that the miR-34a/Gata2 pathway that regulates MERVL expression in ESCs/iPSCs also regulates the acquisition of totipotency in culture. Consistent with this hypothesis, gata2 knock-down in miR-34a-knockout mouse pluripotent stem cells not only reduced MERVL expression, but also abolished the expanded cell fate potential of these cells both in vitro and in vivo. Taken together, our findings not only provide key insights into the functional importance of miR-34a in restricting the totipotent cell fate potential of pluripotent stem cells, but also elucidate the underlying molecular basis by which miR-34a regulates the developmental potentials of ESCs/iPSCs.
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Project description:The Homeobox (HOX) family of genes encodes transcription factors involved in basic developmental processes, most notably during embryogenesis. A possible HOX gene link between development and oncogenesis has recently been described. Dysregulation of HOX genes may be an early event in malignant transformation likely to induce antibody response and thus provide a potential marker for early diagnosis of cancer. Ovarian cancer is characterized by poor early detection and serves as an excellent model system to develop potential markers for early diagnosis. In this study we begin to characterize HOX gene expression in malignant tumors of the ovary and analyze the potential role of HOX genes as biomarkers for early detection of ovarian cancer. Microarray analysis of mRNA from human ovarian tissues was performed on 65 samples of normal, benign, borderline malignant and malignant ovarian tissue. These samples were analyzed using the Affymetrix Human Genome Focus GeneChip (HG-Focus) microarray to distinguish the differential pattern of mRNA expression between the four types of samples. Real-time reverse transcription PCR was utilized to confirm up-regulation of HOX genes as determined by microarray analysis. Our results demonstrate multiple HOX genes to be up-regulated in ovarian cancer. We have shown stepped increase in HOX expression comparing normal, benign neoplastic, and malignant human ovarian tissue samples. This suggests dysregulation of HOX genes may be an early event in malignant transformation and warrants additional studies to validate HOX gene products as potential markers for early detection of ovarian cancer. Experiment Overall Design: 67 samples were analyzed. 4 groupings based on pathology (normal, benign, borderline malignant, malignant). An average of normal samples was used as controls. Cell lines were used as ovarian cancer control samples.
2008-10-17 | E-GEOD-4122 | biostudies-arrayexpress
Project description:Rationale: Cardiac development is a complex process that results in the first integrated, multi-lineage embryonic tissue. Imperfect developmental progression leads to congenital heart disease, the most common birth defect with developmental corruption affecting more than 1% of all live births. Interrogation of individual genes has provided the backbone for cardiac developmental biology, yet a comprehensive transcriptome derived from natural cardiogenesis is required to establish an unbiased roadmap to gauge innate developmental milestones necessary for stem cell-based differentiation and in vitro disease modeling. Objective: Establish a contextual expression database of spatial-temporal cardiac structures, and validate a predictive tool to diagnose and predict cardiogenic outcomes from individual pluripotent stem cell lines. Methods and Results: Stage-specific cardiac structures were dissected from eight distinctive embryonic time points to produce a genome-wide expressome analysis across the spectrum of early to late cardiogenesis. Hierarchical clustering of the time course dataset demonstrated discrete gene expression profiles during natural embryonic development. In reference to the native cardiogenic expression roadmap, disruptive iPSC-derived cardiac expression profiles were revealed from pro-cardiogenic 3-factor (SOX2, OCT4, KLF4) compared to non-cardiogenic 4-factor (addition of c-MYC) reprogramming regimens upon stage-specific differentiation. Expression of cardiac-related genes from 3F-iPSC differentiated in vitro at day 0, 5, and 11 recapitulated expression of natural embryos at days 0, E7.5-E8.5, and E14.5-E18.5, respectively. In contrast, 4F-iPSC demonstrated variable gastrulation gene expression profiles beginning at day 5 of differentiation. Differential gene expression within the pluripotent ground state between the archetypical high cardiogenic potential of embryonic stem cells recapitulated in 3F-iPSC vs. the low cardiogenic potential of 4F-iPSC revealed 23 distinguishing candidate genes. Upon subsequent differentiation, cell line-specific gene expression differences were magnified to 399 genes at day 5 and 726 genes at day 11. A confirmed panel of 20 genes, differentially expressed between high and low cardiogenic cell lines, was transformed into a predictive score that was sufficient to correctly rank independent iPSC lines according to cardiogenic potential. Conclusions: Transcriptome analysis attuned to the embryonic developing heart provides a robust platform to probe coordinated cardiac specification and maturation from stem cell-based cardiogenesis model systems. Based on this genome-wide expressome roadmap, a panel of pre-cardiac genes was extracted that allowed differential prognosis of cardiogenic competency from individual reprogrammed cell lines at the pluripotent state. The overall experimental design includes 3 time points (Day0, Day5, Day11) and 3 different stem cell lines: R1 embryonic stem cells (ESCs), H9 induced pluripotent stem cells (H9-iPSCs) generated/reprogrammed by 3 transcription factors (called 3F-iPSCs), and 19BL induced pluripotent stem cells (19BL-iPSCs) generated/reprogrammed by 4 transcription factors (called 4F-iPSC). At each time point, each cell line has 3 biological replicates. In total, there are 27 samples. R1-embryonic stem cells (R1-ESCs): Day0 undifferentiated ESCs - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates. 3F-iPSC (H9 iPSCs): Day 0 undifferentiated - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates. 4F-iPSC (19BL-iPSCs): Day0 undifferentiated - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates.
2013-09-23 | E-GEOD-43197 | biostudies-arrayexpress