Gene expression profiling of breast fibroadenomas
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE55594 | GEO | 2014/06/13
SECONDARY ACCESSION(S): PRJNA240194
REPOSITORIES: GEO
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Project description:Fibroadenomas are the most common benign breast tumors in women under 30. Unlike their malignant counterparts, relatively molecular profiling has been done on fibroadenomas. Here we performed gene expression profiling on ten fibroadenomas in order to better characterize these tumors. Through targeted amplicon sequencing, we have found that six of these tumors have MED12 mutations. Here, we show that the MED12 mutations, among others, are associated with activated estrogen signaling, as well as increased invasiveness through upregulation of ECM remodelling genes. Microarray gene expression profiling was performed on 10 breast fibroadenomas and a combination of unsupervised and supervised clustering was performed to determine any differentially activated pathways between samples with mutated and non-mutated MED12.
2014-06-13 | E-GEOD-55594 | biostudies-arrayexpress
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2016-03-03 | GSE70653 | GEO
Project description:Uterine fibroids (UFs) are benign tumours affecting up to 80% of women of reproductive age. Although mutations in MED12 or HMGA2 account for the majority of UF occurrence, the processes by which these lead to UFs remain poorly understood. Here we present a comprehensive systems biology study, merging clinical, genetic, transcriptomic and proteomic information to better understand the patho-mechanisms underlying UF.
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2017-01-12 | GSE93519 | GEO
Project description:Meningiomas are mostly benign brain tumors, with a potential for becoming atypical or malignant. Based on comprehensive genomic, transcriptomic and epigenomic analyses of meningiomas, we compared benign tumors to atypical ones. We show that the vast majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent mutations in SMARCB1. These tumors harbor increased H3K27me3 repressive signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells (hESCs), thereby phenocopying a more primitive cellular state. Consistent with this observation, and based on differential gene expression analysis as well as correlation of mRNA:miRNA regulatory networks, atypical meningiomas exhibit up-regulation of EZH2, the catalytic subunit of the PRC2 complex, well as the E2F2 and FOXM1 transcriptional networks that promote proliferation through activation of the cell cycle pathways. In addition, based on H3K27ac ChIP-seq analysis, we show atypical tumors to display an activated super-enhancer near the meningeal identity transcription factor ZIC1, leading to its transcriptional upregulation. Importantly, these primary atypical meningiomas do not harbor activating TERT promoter mutations, which have been reported in atypical tumors that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas, differentiating their profile from benign and progressed tumors and establishing novel therapeutic targets.
2016-12-20 | GSE92558 | GEO
Project description:Meningiomas are mostly benign brain tumors, with a potential for becoming atypical or malignant. Based on comprehensive genomic, transcriptomic and epigenomic analyses of meningiomas, we compared benign tumors to atypical ones. We show that the vast majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent mutations in SMARCB1. These tumors harbor increased H3K27me3 repressive signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells (hESCs), thereby phenocopying a more primitive cellular state. Consistent with this observation, and based on differential gene expression analysis as well as correlation of mRNA:miRNA regulatory networks, atypical meningiomas exhibit up-regulation of EZH2, the catalytic subunit of the PRC2 complex, well as the E2F2 and FOXM1 transcriptional networks that promote proliferation through activation of the cell cycle pathways. In addition, based on H3K27ac ChIP-seq analysis, we show atypical tumors to display an activated super-enhancer near the meningeal identity transcription factor ZIC1, leading to its transcriptional upregulation. Importantly, these primary atypical meningiomas do not harbor activating TERT promoter mutations, which have been reported in atypical tumors that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas, differentiating their profile from benign and progressed tumors and establishing novel therapeutic targets.
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Project description:MED12 is an X-chromosome member of the Mediator complex that is a key regulator of tissue specific gene expression and moderates intracellular signaling via multiple developmental pathways. Sequence variations in the carboxy-terminus of MED12, which contains a PQL and Opa domain, are associated with X-linked mental retardation behavioral syndromes and schizophrenia. Unfortunately, the mechanism(s) through which MED12 sequence variation in the carboxy-terminus could alter vulnerability to neurodevelomental and neuropsychiatric illnesses is yet unclear. In order to elucidate a better understanding of this process, we examined the role of the MED12 carboxy-terminus in cell cycle and gene expression with full-length and domain deleted overexpression constructs and RNA interference in HEK293 cells. Our microarray data show a set of genes differentially expressed in the experimental conditions versus the GFP control. The top 50 most differentially expressed genes in the experimental conditions versus the GFP control also show that MED12 expression level differentially affects stress response and transcriptional regulation pathways. These results are consistent with prior studies showing that MED12 has a key role in determining neuronal cell fate and our theoretical understanding of the biological basis of psychosis. They also lend further insight upon the pathways through which MED12 exerts its effects upon differentiation and disease pathogenesis, which may one day lead to new approaches to the treatment of MED12-related disorders. 12 samples were analyzed, being comprised of four conditions with three biological replicates. Comparisons were made between the GFP control to experimental condition (i.e. GFP vs MED12 FL; GFP vs MED12 PQL/Opa; and GFP vs MED12 shRNA 5)
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