Methylation of osteosarcoma patients
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE161407 | GEO | 2022/01/31
REPOSITORIES: GEO
Similar Datasets
Project description:Osteosarcoma (OS) is the most common primary malignant tumor of bone; it occurs most commonly in the metaphyseal regions of long bones in adolescents and young adults. Conventional osteosarcoma is characterized by complex karyotypes with a high degree of aneuploidy and numerous structural aberrations such as copy number alterations (CNAs) and genomic rearrangements. The data comprise of array copy number data (N=113) from pre-therapeutic osteosarcoma. These have been derived from Affymetrix CytoscanHD. The study searches for driver genes and examines cancer evolution. Note (added 8th June 2016): This experiment is extended in an experiment described under accession E-MTAB-4815. It contains data for 97 samples from this experiment are also included in E-MTAB-4815.
2015-11-09 | E-MTAB-3998 | biostudies-arrayexpress
Project description:Osteosarcoma (OS) is the most common primary malignant tumor of bone; it occurs most commonly in the metaphyseal regions of long bones in adolescents and young adults. Conventional osteosarcoma is characterized by complex karyotypes with a high degree of aneuploidy and numerous structural aberrations such as copy number alterations (CNAs) and genomic rearrangements. We characterized the landscape of somatic copy number alterations (SCNAs) in a large cohort (n=160) of osteosarcoma (OS) samples using the whole-genome CytoScan High Density arrays. This experiment is an extension of E-MTAB-3998. It contains data for 97 samples that is also included in E-MTAB-3998. The samples derived from E-MTAB-3998 identified using the 'Description' field in the sample attributes.
2017-06-02 | E-MTAB-4815 | biostudies-arrayexpress
Project description:Osteosarcoma is the most common primary bone cancer in children, adolescents and young adults. It is a rare cancer type. To comprehensively reveal the transcriptomic characteristics of osteosarcoma, we performed Oxford Nanopore Technologies (ONT) long-read RNA-Seq of tumor and adjacent normal tissues from 23 patients with osteosarcoma.
2023-07-19 | GSE218035 | GEO
Project description:Osteosarcoma is a rare, highly malignant tumor of the bone that presents with a highly complex and abnormal karyotype. Only a few of the genes, which are targets of genetic alteration are known. An integrated genome-wide genomic and gene expression profiling analysis was performed on human osteosarcoma tissues and osteosarcoma cell lines in order to identify and map, in a high-resolution fashion, the most drastic chromosomal changes and point out genes which could contribute to tumorigenesis by having altered expression levels of critical oncogenes and tumor suppressors. Combined gene expression and aCGH analysis on the same samples enables direct comparison between DNA and mRNA level and offers a general strategy to identify and prioritize potential targets while the parallel analysis on cell lines offers a reliable models for further functional studies.
2016-01-01 | GSE12512 | GEO
Project description:Osteosarcoma is the most common bone tumor in children, adolescents, and young adults. In contrast to other childhood malignancies, no biomarkers have been consistently identified as predictors of outcome. This study was conducted to assess the microRNAs (miRs) expression signatures in pre-treatment osteosarcoma specimens and correlate with outcome to identify biomarkers for disease relapse
2016-03-22 | GSE79181 | GEO
Project description:Background: Osteosarcomas are the most common primary malignant tumors of bone and show multiple and complex genomic aberrations. miRNAs are non-coding RNAs capable of regulating gene expression at the post transcriptional level, and miRNAs and their target genes may represent novel therapeutic targets or biomarkers for osteosarcoma. In order to investigate the involvement of miRNAs in osteosarcoma development, global microarray analyses of a panel of 19 human osteosarcoma cell lines was performed. Principal findings: We identified 177 miRNAs that were differentially expressed in osteosarcoma cell lines relative to normal bone. Among these, miR-126/miR-126*, miR-142-3p, miR-150, miR-223, miR-486-5p and members of the miR-1/miR-133a, miR-144/miR-451, miR-195/miR-497, and miR-206/miR-133b clusters were found to be downregulated in osteosarcoma cell lines. All miRNAs in the paralogous clusters miR-17-92, miR-106b-25 and miR-106a-92 were overexpressed. Furthermore, the upregulated miRNAs included miR-9/miR-9*, miR-21*, miR-31/miR-31*, miR-196a/miR-196b, miR-374a and members of the miR-29, miR-130/301 families. The most interesting inversely correlated miRNA/mRNA pairs in osteosarcoma cell lines included miR-9/TGFBR2 and miR-29/the p85M-NM-1 regulatory subunit of PI3K. PTEN mRNA correlated inversely with miR-92a and members of the miR-17 and miR-130/301 families. Expression profiles of selected miRNAs were confirmed in clinical samples. A set of miRNAs, miR-1, miR-18a, miR-18b, miR-19b, miR-31, miR-126, miR-142-3p, miR-133b, miR-144, miR-195, miR-223, miR-451 and miR-497 was identified with an intermediate expression level in osteosarcoma clinical samples compared to osteoblasts and bone, which may reflect the differentiation level of osteosarcoma relative to the undifferentiated osteoblast and fully differentiated normal bone. Significance: This study provides an integrated analysis of miRNA and mRNA in osteosarcoma, and gives new insight into the complex genetic mechanisms of osteosarcoma development and progression. 19 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones.
2012-10-16 | E-GEOD-28424 | biostudies-arrayexpress
Project description:Background: Osteosarcomas are the most common primary malignant tumors of bone and show multiple and complex genomic aberrations. miRNAs are non-coding RNAs capable of regulating gene expression at the post transcriptional level, and miRNAs and their target genes may represent novel therapeutic targets or biomarkers for osteosarcoma. In order to investigate the involvement of miRNAs in osteosarcoma development, global microarray analyses of a panel of 19 human osteosarcoma cell lines was performed. Principal findings: We identified 177 miRNAs that were differentially expressed in osteosarcoma cell lines relative to normal bone. Among these, miR-126/miR-126*, miR-142-3p, miR-150, miR-223, miR-486-5p and members of the miR-1/miR-133a, miR-144/miR-451, miR-195/miR-497, and miR-206/miR-133b clusters were found to be downregulated in osteosarcoma cell lines. All miRNAs in the paralogous clusters miR-17-92, miR-106b-25 and miR-106a-92 were overexpressed. Furthermore, the upregulated miRNAs included miR-9/miR-9*, miR-21*, miR-31/miR-31*, miR-196a/miR-196b, miR-374a and members of the miR-29, miR-130/301 families. The most interesting inversely correlated miRNA/mRNA pairs in osteosarcoma cell lines included miR-9/TGFBR2 and miR-29/the p85α regulatory subunit of PI3K. PTEN mRNA correlated inversely with miR-92a and members of the miR-17 and miR-130/301 families. Expression profiles of selected miRNAs were confirmed in clinical samples. A set of miRNAs, miR-1, miR-18a, miR-18b, miR-19b, miR-31, miR-126, miR-142-3p, miR-133b, miR-144, miR-195, miR-223, miR-451 and miR-497 was identified with an intermediate expression level in osteosarcoma clinical samples compared to osteoblasts and bone, which may reflect the differentiation level of osteosarcoma relative to the undifferentiated osteoblast and fully differentiated normal bone. Significance: This study provides an integrated analysis of miRNA and mRNA in osteosarcoma, and gives new insight into the complex genetic mechanisms of osteosarcoma development and progression. 19 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones.
2012-10-16 | E-GEOD-28423 | biostudies-arrayexpress
Project description:Osteosarcoma is a rare, highly malignant tumor of the bone that presents with a highly complex and abnormal karyotype. Only a few of the genes, which are targets of genetic alteration are known. An integrated genome-wide genomic and gene expression profiling analysis was performed on human osteosarcoma tissues and osteosarcoma cell lines in order to identify and map, in a high-resolution fashion, the most drastic chromosomal changes and point out genes which could contribute to tumorigenesis by having altered expression levels of critical oncogenes and tumor suppressors. Combined gene expression and aCGH analysis on the same samples enables direct comparison between DNA and mRNA level and offers a general strategy to identify and prioritize potential targets while the parallel analysis on cell lines offers a reliable models for further functional studies.
2016-01-01 | GSE12789 | GEO
Project description:Osteosarcoma is an aggressive tumor of the bone that primarily affects young adults and adolescents. Osteosarcoma is characterized by genomic chaos and heterogeneity. While inactivation of tumor suppressor p53 TP53 is nearly universal other high frequency mutations or structural variations have not been identified. Despite this genomic heterogeneity, key conserved transcriptional programs associated with survival have been identified across human, canine and induced murine osteosarcoma. The epigenomic landscape, including DNA methylation, plays a key role in establishing transcriptional programs in all cell types. The role of epigenetic dysregulation has been studied in a variety of cancers but has yet to be explored at scale in osteosarcoma. Here we examined genome-wide DNA methylation patterns in 24 human and 44 canine osteosarcoma samples identifying groups of highly correlated DNA methylation marks in human and canine osteosarcoma samples. We also link specific DNA methylation patterns to key transcriptional programs in both human and canine osteosarcoma. Building on previous work, we built a DNA methylation-based measure for the presence and abundance of various immune cell types in osteosarcoma. Finally, we determined that the underlying state of the tumor, and not changes in cell composition, were the main driver of differences in DNA methylation across the human and canine samples. Significance: This is the first large scale study of DNA methylation in osteosarcoma and lays the ground work for the exploration of DNA methylation programs that help establish conserved transcriptional programs in the context of different genomic landscapes.
2020-05-01 | GSE149679 | GEO
Project description:Osteosarcoma (OS)is a rare primary malignant bone tumor in adolescents and children with a poor prognosis. Identification of prognostic genes lags far behind the advance of the treatments. We identified differential genes by microarray analysis from paired OS tissues. Hub genes, gene set enrichment analysis, and pathway analysis were performed to gain an insight into the pathway alterations of OS. These results showed CPE could be served as a prognostic factor in osteoblastic OS and should be further investigated as potential therapeutic target. The present study evaluated the whole transcriptome expression of osteosarcoma progression and provided novel therapeutic targets for advanced osteosarcoma.
2023-03-01 | GSE225588 | GEO