Gene expression changes between sensitive and YK-4-279-resistant Ewing's Sarcoma cell lines
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE61042 | GEO | 2014/09/04
SECONDARY ACCESSION(S): PRJNA260133
REPOSITORIES: GEO
Similar Datasets
Project description:Microarray gene expression analysis conducted from cell lines in each of three cohorts: (1) Resistant ES cell lines, (2) Sensitive parental ES cell lines treated with YK-4-279 for 72 hours, and (3) untreated sensitive parental ES cell lines (Three replicates from TC32 & TC71 original parental cell lines) We used microarrays to detail the global programme of gene expression underlying mechanism of resistance to YK-4-279 within parental sensitive and resistant selected Ewing's Sarcoma cell lines. We identified distinct classes of up-regulated genes during this process. Total RNA was extracted from the cell lines using the Qiagen miRNeasy Mini kit. RNA quality was assessed to have an RNA integrity number before amplification and labeling using AffymetrixM-bM-^@M-^Ys GeneChip GeneChipM-BM-.3M-bM-^@M-^Y IVT Express Kit following manufacturerM-bM-^@M-^Ys instructions. Amplified and biotinylated cRNAs were hybridized onto Affymetrix GeneChip Human Genome U133A 2.0 cartridge arrays, Washed, and Stained with kit following manufacturerM-bM-^@M-^Ys instructions. Arrays were scanned using Affymetrix GeneChip Scanner 3000 and the initial raw data were extracted using Affymetrix GeneChip Command Console-Expression software. The statistical analyses of scanned data were performed using default setting on GeneSpring GX 12.1 software (Agilent).
2014-09-04 | E-GEOD-61042 | biostudies-arrayexpress
Project description:Ewing sarcoma (ES) is the second most common pediatric malignancy of the bones and soft tissue, but few advances in therapeutic options have been made over the past several decades. A characteristic feature of ES that and an attractive therapeutic targets is the EWS-FLI1 fusion protein. A small molecule inhibitor of EWS-FLI1, YK-4-279 was as a targeted therapy option for Ewing sarcoma patients. A YK-4-279 analog, TK216, is currently in clinical trial. With any targeted therapy, there is always the risk that tumors will become resistant and stop responding to treatment. Here, we investigated resistance mechanisms to YK-4-279 (YK) by developing ES cell lines specifically resistant to YK. We found that expression of the cell surface protein CD99 was elevated in YK-resistant cells. Increased CD99 expression occurs within five days of YK treatment in vivo. When CD99 expression is reduced by shRNA, resistant cells regain sensitivity to YK but reducing CD99 expression in non-resistant cells does not affect sensitivity. Little is known about CD99 function in the context of Ewing sarcoma, but the data presented here indicates the function of CD99 is altered upon acquisition of YK resistance, and that CD99 serves a critical function in developed resistance to YK-4-279. RNA sequencing analysis yielded candidate genes that may also be involved in the YK resistance mechanism. We identified a potential modulator of CD99 function, ANO1, a member of the ANO family and a participant in membrane-bound ion channel activity. CD99 has previously been linked with membrane-associated ion channels. A functional association between the two proteins remains to be investigated.
2020-03-21 | GSE132762 | GEO
Project description:Hotspot mutations in the core promoter region of the telomerase reverse transcriptase (TERT) gene have been well established to associate with aggressive clinical characteristics, radioiodine refractory, tumor recurrence and mortality in thyroid cancer. Several E-twenty-six (ETS) transcription factors were reported to selectively bound to the mutant TERT promoter and activated TERT expression. In this study we aimed to investigate whether TERT promoter mutations confer sensitivity to ETS inhibitor YK-4-279 in thyroid cancer cells and whether this inhibitor could be served as a potential therapeutic agent for thyroid cancer. In vitro assays showed that YK-4-279 treatment sharply suppressed cell viability, colony formation, migration and invasion, as well as induced cell cycle arrest and apoptosis in a panel of thyroid cancer cells. The cell viability after YK-4-279 treatment were similar between cell lines harboring mutant and wild-type TERT promoter. Furthermore, YK-4-279 treatment reduced both luciferase activity and mRNA expression of TERT independent of TERT promoter mutation status. Data from RNA-seq further revealed that YK-4-279 significantly affected biological processes including DNA replication and cell cycle. Reduced DNA helicase activity and decreased expression of several helicase genes were observed after YK-4-279 treatment. Moreover, YK-4-279 significantly inhibited tumor growth and induced apoptosis in a xenograft mice model. Thus, ETS inhibitor YK-4-279 suppressed TERT expression and conferred anti-tumor activity in a TERT promoter mutation-independent manner, and it could be a potential agent for the treatment of advanced thyroid cancers.
2021-04-06 | GSE171473 | GEO
Project description:A chimeric fusion between the RNA binding protein EWS and the ETS family transcription factor FLI1 (EWS-FLI1), created from a chromosomal translocation, is implicated in driving the majority of Ewing sarcomas (ES) by modulation of transcription and alternative splicing. The small molecule YK-4-279 inhibits EWS-FLI1 function and induces apoptosis. We tested 69 anti-cancer drugs in combination with YK-4-279 and found that vinca alkaloids exhibited synergy with YK-4-279 in five ES cell lines. The combination of YK-4-279 and vincristine reduced tumor burden and increased survival in mice bearing ES xenografts. We determined that independent drug-induced events converged to cause this synergistic therapeutic effect. YK-4-279 rapidly induced G2/M arrest, increased the abundance of cyclin B1, and decreased EWS-FLI1–mediated expression of microtubule-associated proteins, which rendered cells more susceptible to microtubule depolymerization by vincristine. YK-4-279 reduced the expression of the EWS-FLI1 target gene encoding ubiquitin ligase UBE2C, and this in part contributed to the increase in cyclin B1. Biochemical assays revealed that YK-4-279 also increased the abundance of proapoptotic isoforms of MCL1 and BCL2, presumably through inhibition of alternative splicing by EWS-FLI1, thus promoting cell death in response to vincristine. Thus a combination of vincristine and YK-4-279 might be therapeutically effective in ES patients.
2017-09-14 | GSE103837 | GEO
Project description:TMD8 and U2932 were treated with YK-4-279 for 4 and 8 hours.
2021-05-01 | GSE114022 | GEO
Project description:ERG activity was blocked using YK-4-279 in three subcutaneously implanted ERG+ (LuCaP 23.1, 86.2, and 35) and one ERG- (LuCaP 96) PDX. Tumor volume (TV), body weight (BW), serum prostate specific antigen (PSA), and overall survival (OS) were compared to vehicle treated controls. Changes in gene expression were assessed by RNASeq and tissue microarrays were constructed to assess necrosis, proliferation, apoptosis, microvessel density, and ERG expression.
2017-11-16 | GSE86387 | GEO
Project description:Characterization of Ewing sarcoma resistance to the EWS-FLI1 inhibitor YK-4-279
| PRJNA548934 | ENA
Project description:Gene expression changes between sensitive and YK-4-279-resistant Ewing's Sarcoma cell lines
| PRJNA260133 | ENA
Project description:The synthesis and processing of mRNA, from transcription to translation initiation, often requires splicing of intragenic material. The final mRNA composition varies based upon proteins that modulate splice site selection. EWS-FLI1 is an Ewing sarcoma (ES) oncogene with an interactome that we demonstrate to have multiple partners in spliceosomal complexes. We evaluate EWS-FLI1 upon post-transcriptional gene regulation using both exon array and RNA-seq. Genes that potentially regulate oncogenesis including CLK1, CASP3, PPFIBP1, and TERT validate as alternatively spliced by EWS-FLI1. EWS-FLI1 also alters splicing by directly binding to known splicing factors including DDX5, hnRNPK, and PRPF6. Reduction of EWS-FLI1 produces an isoform of g-TERT that has increased telomerase activity compared to WT TERT. The small molecule YK-4-279 is an inhibitor of EWS-FLI1 oncogenic function that disrupts specific protein interactions including DDX5 and RNA helicase A (RHA) that alters RNA splicing ratios. As such, YK-4-279 validates the splicing mechanism of EWS-FLI1 showing alternatively spliced gene patterns that significantly overlap with EWS-FLI1 reduction and WT human mesenchymal stem cells. Exon array analysis of 75 ES patient samples show similar isoform expression patterns to cell line models expressing EWS-FLI1, supporting the clinical relevance of our findings. These experiments establish systemic alternative splicing as an oncogenic process modulated by EWS-FLI1. EWS-FLI1 modulation of mRNA splicing may provide insight into the contribution of splicing towards oncogenesis, and reciprocally, EWS-FLI1 interactions with splicing proteins may inform the splicing code. Alternative splicing of RNA allows a limited number of coding regions in the human genome to produce proteins with diverse functionality. Alternative splicing has also been implicated as an oncogenic process. Identifying aspects of cancer cells that differentiate them from non-cancer cells remains an ongoing challenge and our research suggests that alternatively spliced mRNA and subsequent protein isoforms will provide new anti-cancer targets. We determined that the key oncogene of Ewing sarcoma (ES), EWS-FLI1, regulates alternative splicing in multiple cell line models. These experiments establish oncogenic aspects of splicing which are specific to cancer cells and thereby illuminate potentially oncogenic splicing shifts as well as provide a useful stratification mechanism for ES patients. We analyzed three models of EWS-FLI1 using Affymetrix GeneChip Human Exon 1.0 ST microarray: (i) Ewing's sarcoma TC32 wild-type cells expressing EWS-FLI1, and TC32 cells where EWS-FLI1 was reduced with a lentiviral shRNA; (ii) A673i, which has a doxycycline-inducible shRNA to reduce EWS-FLI1 expression, and wild-type EWS-FLI1 to screen for alternative splicing as measured by exon-specific expression changes; and (iii) human mesenchymal stem cells (hMSC), a putative cell of origin of Ewing's sarcoma, exogenously expressing EWS-FLI1, and hMSC wild-type cells without EWS-FLI1. Three biological replicates were included for each condition. The Bioconductor package "oligo" in the R programming language was used for normalization and background correction. Analysis was carried out using only core probesets, as defined by the manufacturer.
2015-03-31 | E-GEOD-65941 | biostudies-arrayexpress
Project description:The ETS inhibitor YK-4-279 suppresses thyroid cancer progression independent of TERT promoter mutations
| PRJNA719780 | ENA