title: An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
abstract: Chordoma is a rare malignant tumour of bone, the molecular marker of which is the expression of the transcription factor, brachyury. Having recently demonstrated that silencing brachyury induces growth arrest in a chordoma cell line, we now seek to identify its downstream target genes. Here we use an integrated functional genomics approach involving shRNA-mediated brachyury knockdown, gene expression microarray, ChIP-seq experiments, and bioinformatics analysis to achieve this goal. We confirm that the T-box binding motif of human brachyury is identical to that found in mouse, Xenopus, and zebrafish development, and that brachyury acts primarily as an activator of transcription. Using human chordoma samples for validation purposes, we show that brachyury binds 99 direct targets and indirectly influences the expression of 64 other genes, thereby acting as a master regulator of an elaborate oncogenic transcriptional network encompassing diverse signalling pathways including components of the cell cycle, and extracellular matrix components. Given the wide repertoire of its active binding and the relative specific localization of brachyury to the tumour cells, we propose that an RNA interference-based gene therapy approach is a plausible therapeutic avenue worthy of investigation.
authors: Randall Division of Cell and Molecular Biophysics, New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK.
authors: Andrew C
authors: AC
authors: Nelson
authors: Nischalan
authors: N
authors: Pillay
authors: Stephen
authors: S
authors: Henderson
authors: Nadège
authors: N
authors: Presneau
authors: Roberto
authors: R
authors: Tirabosco
authors: Dina
authors: D
authors: Halai
authors: Fitim
authors: F
authors: Berisha
authors: Paul
authors: P
authors: Flicek
authors: Derek L
authors: DL
authors: Stemple
authors: Claudio D
authors: CD
authors: Stern
authors: Fiona C
authors: FC
authors: Wardle
authors: Adrienne M
authors: AM
authors: Flanagan
mesh_terms: D000818:Animals; D001859:Bone Neoplasms / Q000235:genetics* / Q000473:pathology / Q000503:physiopathology*; D002453:Cell Cycle / Q000502:physiology; D002454:Cell Differentiation / Q000502:physiology; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D002817:Chordoma / Q000235:genetics* / Q000473:pathology / Q000503:physiopathology*; D005326:Fetal Proteins / Q000235:genetics* / Q000502:physiology*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000502:physiology; D055785:Gene Knockdown Techniques; D015316:Genetic Therapy; D023281:Genomics; D006801:Humans; D051379:Mice; D009672:Notochord / Q000473:pathology; D034622:RNA Interference; D020825:T-Box Domain Proteins / Q000235:genetics* / Q000502:physiology*; D014158:Transcription, Genetic / Q000502:physiology; D014981:Xenopus; D015027:Zebrafish; D000098908:Brachyury Protein
chemical_list: D005326:Fetal Proteins; D020825:T-Box Domain Proteins; D000098908:Brachyury Protein