Human induced pluripotent stem cellâ??derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Paul Burridge
PROVIDER: E-GEOD-79413 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Microarray data on H9 hESC-derived cardiomyocytes (d30) treated with 0, 0.1, 1, or 10 uM of doxorubicin for 24 h Establish effects of increasing doses of doxorubicin on control H9 hESC-derived cardiomyocytes
2016-03-22 | GSE79413 | GEO
Project description:In this study, we generated wildtype H9 hESC derived cardiomyocytes (CM) and neural stem cells (NSC) by in vitro differentiation. Global gene expression profiles were compared among undifferentiated H9 hESC and the derived CM and NSC. Comparison of global gene expression profiles of undifferentiated H9 hESC and the derived CM and NSC populations.
2013-08-31 | E-GEOD-48257 | biostudies-arrayexpress
Project description:The aim of this study is to analyze the change in genome wide expression levels in HAP1 cells upon loss of SMARCB1, SMARCA4 or both these genes together. The SMARCB1 and SMARCA4 genes were the hits from a genome wide screen involving genetrap mutagenesis to find new players that are involved in sensitivity to Doxorubicin (Dox). It was found that loss of SMARCB1 and SMARCA4 genes impart resistance in HAP1 cells to Dox. To validate this, the genes were knocked out in HAP1 cells with CRISPR-Cas9 technology. Gene expression levels in SMARCB1 null, SMARCA4 null and SMARCB1-SMARCA4 double null cells were compared to wildtype HAP1 cells using RNAseq. From these experiments it was found that SMARCB1 loss caused several fold increase in ABCB1 gene levels. ABCB1 is an efflux pump in cells responsible for flushing out many small-molecule drugs. Further analysis of this gene confirmed that ABCB1 was the main factor responsible for Dox resistance upon SMARCB1 loss. In total there are four different cell types with two replicates for each cell type. Therefore, 8 samples in total.
2016-08-22 | E-GEOD-75515 | biostudies-arrayexpress
Project description:Purpose: Authentic preclinical models of renal cell carcinoma (RCC) are lacking. We aimed to establish and characterize primary RCC cultures and demonstrate the feasibility of evaluating drug responses in vitro and in vivo. Materials and Methods: Previously published methodology, with minor modifications, was used to establish, cryopreserve, and serially passage RCC cells from nephrectomy and tumorgraft specimens. Cells were characterized for immuno- and molecular phenotype by immunochemistry, DNA sequencing and gene expression profiling. Tumorigenic potential was evaluated by implanting cells under the renal capsule of immunocompromised mice. The ability to monitor xenograft growth by magnetic resonance imaging (MRI) was investigated. Responses to a tyrosine kinase inhibitor (TKI) and an mTOR inhibitor were measured. Results: Primary cultures were successfully established from 11 clear cell and 1 chromophobe RCC, cryopreserved and serially passaged. Retention of immuno- and molecular phenotypes was demonstrated. Cultured cells formed xenografts in mice that could be measured by MRI. Patient-specific responses to drugs were observed in vitro and response to an TKI was confirmed in vivo. Conclusions: Our study is the first to show the derivation of primary cultures from RCC tumorgrafts, and to demonstrate the ability of primary RCC cultures to generate xenografts in mice. Our results suggest the feasibility of establishing large, well-annotated banks of RCC primary cultures for high-throughput drug screening in vitro and validation in vivo, providing a versatile platform together with xenografts and patient-derived precision-cut tissue slice tumorgrafts we developed previously for precilinical studies of RCC. Microarray analyses were performed to compare the gene expression profile of one of the primary cultures (case 7) to its parental tumor and tissue slice tumorgrafts in the study. Tissue slice grafts and parent tumors were preserved in Allprotect tissue reagent (Qiagen, Valencia, CA) at -20°C prior to RNA extraction using an AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA). The quality of RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA). Microarray hybridization was performed using Illumina Human HT-12 v4 Beadchips (Illumina Inc., San Diego, CA) according to the manufacturerâ??s directions. Expression data was rank invariant normalized using BeadStudio software (Illumina Inc.).
2016-07-03 | E-GEOD-47356 | biostudies-arrayexpress
Project description:Purpose: Discovery of curative therapies for renal cell carcinoma (RCC) is hampered by lack of authentic preclinical models. Tumorgrafts, generated by direct implantation of patient-derived tissues into mice, have demonstrated superior ability to predict therapeutic response. We evaluated âtissue slice graftsâ (TSGs) as an improved tumorgraft model of RCC. Experimental Design: Cores of fresh RCC were precision-cut at 300-μm and implanted under the renal capsule of RAG2-/-γC-/- mice. Engraftment rate, histology, biomarker expression, genetic fidelity and metastatic potential were evaluated. Magnetic resonance imaging (MRI) was tested as a non-invasive method to measure tumor volume, and response to a targeted therapy was determined. Results: All 13 cases of RCC engrafted and displayed characteristic histology and biomarkers. TSG volume quantified non-invasively by MRI highly correlated with graft weights, providing a unique tool for monitoring orthotopic growth. Moreover, in 2 cases, cancer cells from TSGs metastasized to clinically relevant sites, including bone. Microarray analysis and DNA sequencing demonstrated a high degree of correlation of global gene expression and VHL status between TSGs and parental tumors. Treatment of TSGs with sunitinib significantly decreased graft weight and mean vessel density compared to controls. Conclusions: The TSG model of RCC faithfully recapitulates tumor pathology, gene expression, genetic mutation and drug response. The high engraftment rate and metastatic potential of this authentic model, in conjunction with the ability to generate large first-generation animal cohorts and to quantitate tumor volume at the orthotopic site by MRI, proffer significant advantages compared to other preclinical platforms. Three pairs of tissue slice graftes and parent tumors were included in the study. Tissue slice grafts and parent tumors were preserved in Allprotect tissue reagent (Qiagen, Valencia, CA) at -20°C prior to RNA extraction using an AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA). The quality of RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA). Microarray hybridization was performed using Illumina Human HT-12 v4 Beadchips (Illumina Inc., San Diego, CA) according to the manufacturerâs directions. Expression data was rank invariant normalized using BeadStudio software (Illumina Inc.).
2016-07-03 | E-GEOD-44548 | biostudies-arrayexpress
Project description:Genetic mutations on leucine-rich repeat kinase 2 (LRRK2) have been associated with an increased risk of Parkinson's disease. The Gly2019Ser (G2019S) mutation on LRRK2 gene is a relatively common cause of familial Parkinson's disease in Caucasian population. In this study, we generated H9 hESC harboring LRRK2 (G2019S) mutation by gene knockin. Wildtype and LRRK2 mutant hESC were differentiated into NSC using a chemically defined protocol. LRRK2 mutant NSC were treated with or without the LRRK2 kinase specific inhibitor (LRRK2-IN-1). Global gene expression analysis was performed to assess the overall similarity of gene expression profiles among three NSC groups (wildtype; LRRK2 mutant; LRRK2 mutant with inhibitor treatment).
2012-10-17 | E-GEOD-36321 | biostudies-arrayexpress
Project description:In this study, we generated wildtype H9 hESC derived cardiomyocytes (CM) and neural stem cells (NSC) by in vitro differentiation. Global gene expression profiles were compared among undifferentiated H9 hESC and the derived CM and NSC.
2013-08-31 | GSE48257 | GEO
Project description:Macrophages rapidly engulf apoptotic cells to limit the release of noxious cellular contents and to restrict autoimmune responses against self antigens. Although factors participating in recognition and engulfment of apoptotic cells have been identified, the transcriptional basis for the sensing and silently disposing of apoptotic cells is unknown. Here we show that peroxisome proliferator activated receptor delta (PPARdelta) is induced when macrophages engulf apoptotic cells and functions as a transcriptional sensor of dying cells. Genetic deletion of PPARdelta decreases expression of opsonins, such as C1qb, resulting in impairment of apoptotic cell clearance and reduction in anti-inflammatory cytokine production. This increases autoantibody production and predisposes global and macrophage-specific PPARdelta deficient mice to autoimmune kidney disease, a phenotype resembling the human disease systemic lupus erythematosus. Thus, PPARdelta plays a pivotal role in orchestrating the timely disposal of apoptotic cells by macrophages, ensuring that tolerance to self is maintained. HoxA9 immortalized ES cell derived myeloid precursors were created and differentiated as in Odegaard et al, 2007. After expansion, macrophages were differentiated for 8 days in the presence of MCSF in 20% L929 conditioned media with 2.5% bovine serum albumin in low glucose media. Macrophages were harvested for RNA using Qiagen's RNeasy Kit. A common reference was generated using e17.5 C57Bl/6 embryos. 30ug of either reference or macrophage RNA was labeled with Cy3 and Cy5 (Amersham) and hybridized to Stanford Functional Genomics Facility mouse cDNA microarrays for 16 hours. The arrays were washed and scanned on an Agilent G2505A ChipScan v. A.6.3.1. Florescence values were extracted using GenePix Pro v. 5.0.0.51. The data were normalized using regression correlation. Subsequently, missing values were imputed and significantly differentially expressed genes were found with Significance Analysis of Microarrays. For the Nature Medicine manuscript, significantly differentially expressed genes including genes involved in the process of uptake of apoptotic cells were extracted and clustered by complete linkage using Cluster and visualized using TreeView. Key to genotypes: "J1 untreated" are WT differentiated macrophages; "18 Untreated" are PPARd-/- differentiated macrophages Genotype: Wild type (WT) or PPAR delta minus (PPARd -/-) macrophages genetic_modification_design
2010-06-21 | E-GEOD-17890 | biostudies-arrayexpress
Project description:A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a key regulator in this self-renewal/differentiation switch, and it operates in the absence of canonical Wnt signaling. We found that TCF7 is the most downregulated transcription factor when CD34+ cells switch into CD34- cells using RNA-Seq. We subsequently identified the target genes bound by TCF7 using ChIP-Seq. We show that TCF7 binds to Runx1 (Aml1) promoter region, and RUNX1 and TCF7 co-regulate. Gene Set Enrichment Analysis suggests that TCF7 primarily acts as a positive regulator of genes preferentially expressed in CD34+ cells. Consistent with this possibility, knocking-down TCF7 represses many up-regulated genes in Lin-CD34+ cells. Finally a network of up-regulated transcription factors of CD34+ cells which defines the self-renewing state was constructed. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems. The gene expression changes when TCF7 is knocked-down by shRNA in Lin-SCA+CD34+ cells were identified by microarray analysis of one control and two experimental samples.
2012-03-29 | E-GEOD-30068 | biostudies-arrayexpress
Project description:Purpose: Common genetic variation at chromosome 4q25 lead to the strongest locus associated with atrial fibrillation (AF), the most frequent arrhythmia. The mechanism of association is currently unknown. We recently have identified a novel noncoding RNA expressed in the left atria. To determine the potential functional roles of the LNCRNA adjacent to PITX2 (PANCR) via knockdown in cardiomyocytes Methods and Results: H9 differentiated cardiomyocytes were treated with siRNA targeting PANCR and PITX2c and a scrambled control in triplicate. RNA and small RNA extracted and sent for sequencing. Approximately 50 million read fragments mapped to the transcriptome using STAR aligner to hg19 and fragments counted with htseq. EdgeR was used to quantify the differences between treatment groups. There were significant changes upon knocking down PITX2c or PANCR in the RNA sequencing with high concordance of effect sizes between the two treatments (r2 = 0.85). Similar to the RNAseq analysis, this miRNAseq analysis shows that the effects of PANCR knockdown on miRNA expression may be largely mediated by through its effect on PITX2c expression. Conclusion: PANCR knockdown decreased PITX2c expression in H9 differentiated cardiomyocytes, and altered the transcriptome similar to PITX2c knockdown. H9 derived cardiomyoctyes were treated with siRNA knockdown (scrambled control, PANCR, PITX2c) in triplicate and RNA and smallRNAs extracted for sequencing.
2015-04-15 | E-GEOD-67844 | biostudies-arrayexpress