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T (brachyury) gene duplication confers major susceptibility to familial chordoma.

ABSTRACT: Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex families with at least three cases of chordoma, a cancer of presumed notochordal origin. The duplicated region contains only the T (brachyury) gene, which is important in notochord development and is expressed in most sporadic chordomas. Our findings highlight the value of screening for complex genomic rearrangements in searches for cancer-susceptibility genes.

SUBMITTER: Yang XR

PROVIDER: S-EPMC2901855 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature

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T (brachyury) gene duplication confers major susceptibility to familial chordoma.

Yang Xiaohong R XR Ng David D Alcorta David A DA Liebsch Norbert J NJ Sheridan Eamonn E Li Sufeng S Goldstein Alisa M AM Parry Dilys M DM Kelley Michael J MJ

Nature genetics 20091004 11

Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex families with at least three cases of chordoma, a cancer of presumed notochordal origin. The duplicated region contains only the T (brachyury) gene, which is important in notochord development and is expressed in most sporadic chordomas. Our findings highlight the value of screening for complex genomic rearrangements in searches for cancer-susceptibility genes. ...[more]

PMID: 19801981

Similar Datasets

T (Brachyury) gene duplication confers major susceptibility to familial chordoma

Project description:Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex (≥ with ≥ 3 cases) families of chordoma, a cancer of presumed notochordal origin.

2009-10-04 | GSE17668 | GEO

T (Brachyury) gene duplication confers major susceptibility to familial chordoma

2009-10-04 | E-GEOD-17668 | biostudies-arrayexpress

The embryonic transcription factor Brachyury confers chordoma chemoresistance via upregulating CA9.

Project description:Being a rare malignant bone tumor on the axial skeleton, chordoma is locally invasive and has a high rate of recurrence. Despite extensive studies, the mechanisms of chordoma recurrence after surgical intervention, as well as resistance to radiation and chemotherapy, remain elusive. In this study, primary chordoma cell lines PCH1 and PCH2 were established and characterized by chordoma specific markers. We found that the embryonic transcription factor Brachyury inhibits Paclitaxel induced apoptosis in different cells, including PCH1 and U2OS cells. T gene regulated genes were identified in PCH1 and U2OS using microarray. After comparing gene regulated by Brachyury in different cells and the chromatin immunoprecipitation assay, we identified carbonic anhydrase IX (CA9) as a common target gene of Brachyury. Besides, immunohistochemical staining of CA9 and Brachyury in chordoma tissues revealed that their expression levels were positively correlated. We further showed that CA9 is responsible for Paclitaxel resistance in PCH1 cell. Our data suggest that CA9 plays a role in Brachyury mediated Paclitaxel resistance and serves as a potential target for chordoma treatment.

| S-EPMC5883134 | biostudies-literature

Small-molecule targeting of brachyury transcription factor addiction in chordoma.

Project description:Chordoma is a primary bone cancer with no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors2,3. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors4,5. In chordoma, we find that T is associated with a 1.5-Mb region containing 'super-enhancers' and is the most highly expressed super-enhancer-associated transcription factor. Notably, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. In vivo, CDK7/12/13-inhibitor treatment substantially reduces tumor growth. Together, these data demonstrate small-molecule targeting of brachyury transcription factor addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.

| S-EPMC6633917 | biostudies-literature

From notochord formation to hereditary chordoma: the many roles of Brachyury.

Project description:Chordoma is a rare, but often malignant, bone cancer that preferentially affects the axial skeleton and the skull base. These tumors are both sporadic and hereditary and appear to occur more frequently after the fourth decade of life; however, modern technologies have increased the detection of pediatric chordomas. Chordomas originate from remnants of the notochord, the main embryonic axial structure that precedes the backbone, and share with notochord cells both histological features and the expression of characteristic genes. One such gene is Brachyury, which encodes for a sequence-specific transcription factor. Known for decades as a main regulator of notochord formation, Brachyury has recently gained interest as a biomarker and causative agent of chordoma, and therefore as a promising therapeutic target. Here, we review the main characteristics of chordoma, the molecular markers, and the clinical approaches currently available for the early detection and possible treatment of this cancer. In particular, we report on the current knowledge of the role of Brachyury and of its possible mechanisms of action in both notochord formation and chordoma etiogenesis.

| S-EPMC3626178 | biostudies-literature

Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity.

Project description:Chordomas are rare spinal tumors addicted to expression of the developmental transcription factor brachyury. In chordomas, brachyury is super-enhancer associated and preferentially downregulated by pharmacologic transcriptional CDK inhibition, leading to cell death. To understand the underlying basis of this sensitivity, we dissect the brachyury transcription regulatory network and compare the consequences of brachyury degradation with transcriptional CDK inhibition. Brachyury defines the chordoma super-enhancer landscape and autoregulates through binding its super-enhancer, and its locus forms a transcriptional condensate. Transcriptional CDK inhibition and brachyury degradation disrupt brachyury autoregulation, leading to loss of its transcriptional condensate and transcriptional program. Compared with transcriptional CDK inhibition, which globally downregulates transcription, leading to cell death, brachyury degradation is much more selective, inducing senescence and sensitizing cells to anti-apoptotic inhibition. These data suggest that brachyury downregulation is a core tenet of transcriptional CDK inhibition and motivates developing strategies to target brachyury and its autoregulatory feedback loop.

| S-EPMC7817874 | biostudies-literature

Rare Germline Variants in Chordoma-Related Genes and Chordoma Susceptibility.

Project description:Chordoma is a rare bone cancer with an unknown etiology. TBXT is the only chordoma susceptibility gene identified to date; germline single nucleotide variants and copy number variants in TBXT have been associated with chordoma susceptibility in familial and sporadic chordoma. However, the genetic susceptibility of chordoma remains largely unknown. In this study, we investigated rare germline genetic variants in genes involved in TBXT/chordoma-related signaling pathways and other biological processes in chordoma patients from North America and China. We identified variants that were very rare in general population and internal control datasets and showed evidence for pathogenicity in 265 genes in a whole exome sequencing (WES) dataset of 138 chordoma patients of European ancestry and in a whole genome sequencing (WGS) dataset of 80 Chinese patients with skull base chordoma. Rare and likely pathogenic variants were identified in 32 of 138 European ancestry patients (23%), including genes that are part of notochord development, PI3K/AKT/mTOR, Sonic Hedgehog, SWI/SNF complex and mesoderm development pathways. Rare pathogenic variants in COL2A1, EXT1, PDK1, LRP2, TBXT and TSC2, among others, were also observed in Chinese patients. We identified several rare loss-of-function and predicted deleterious missense variants in germline DNA from patients with chordoma, which may influence chordoma predisposition and reflect a complex susceptibility, warranting further investigation in large studies.

| S-EPMC8197919 | biostudies-literature

Familial Lymphoproliferative Malignancies and Tandem Duplication of NF1 Gene.

Project description:Background. Neurofibromatosis type 1 is a genetic disorder caused by loss-of-function mutations in a tumor suppressor gene (NF1) which codifies the protein neurofibromin. The frequent genetic alterations that modify neurofibromin function are deletions and insertions. Duplications are rare and phenotype in patients bearing duplication of NF1 gene is thought to be restricted to developmental abnormalities, with no reference to cancer susceptibility in these patients. We evaluated a patient who presented with few clinical signs of neurofibromatosis type 1 and a conspicuous personal and familiar history of different types of cancer, especially lymphoproliferative malignancies. The coding region of the NF-1 gene was analyzed by real-time polymerase chain reaction and direct sequencing. Multiplex ligation-dependent probe amplification was performed to detect the number of mutant copies. The NF1 gene analysis showed the following alterations: mosaic duplication of NF1, TRAF4, and MYO1D. Fluorescence in situ hybridization using probes (RP5-1002G3 and RP5-92689) flanking NF1 gene in 17q11.2 and CEP17 for 17q11.11.1 was performed. There were three signals (RP5-1002G3conRP5-92689) in the interphases analyzed and two signals (RP5-1002G3conRP5-92689) in 93% of cells. These findings show a tandem duplication of 17q11.2. Conclusion. The case suggests the possibility that NF1 gene duplication may be associated with a phenotype characterized by lymphoproliferative disorders.

| S-EPMC4279825 | biostudies-literature

Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish.

Project description:The aberrant activation of developmental processes triggers diverse cancer types. Chordoma is a rare, aggressive tumor arising from transformed notochord remnants. Several potentially oncogenic factors have been found to be deregulated in chordoma, yet causation remains uncertain. In particular, sustained expression of TBXT - encoding the notochord regulator protein brachyury - is hypothesized as a key driver of chordoma, yet experimental evidence is absent. Here, we employ a zebrafish chordoma model to identify the notochord-transforming potential of implicated genes in vivo We find that Brachyury, including a form with augmented transcriptional activity, is insufficient to initiate notochord hyperplasia. In contrast, the chordoma-implicated receptor tyrosine kinases (RTKs) EGFR and Kdr/VEGFR2 are sufficient to transform notochord cells. Aberrant activation of RTK/Ras signaling attenuates processes required for notochord differentiation, including the unfolded protein response and endoplasmic reticulum stress pathways. Our results provide the first in vivo evidence against a tumor-initiating potential of Brachyury in the notochord, and imply activated RTK signaling as a possible initiating event in chordoma. Furthermore, our work points at modulating endoplasmic reticulum and protein stress pathways as possible therapeutic avenues against chordoma.

| S-EPMC6679381 | biostudies-literature

The FGFR/MEK/ERK/brachyury pathway is critical for chordoma cell growth and survival.

Project description:Recent evidence suggests that the expression of brachyury is necessary for chordoma growth. However, the mechanism associated with brachyury-regulated cell growth is poorly understood. Fibroblast growth factor (FGF), a regulator of brachyury expression in normal tissue, may also play an important role in chordoma pathophysiology. Using a panel of chordoma cell lines, we explored the role of FGF signaling and brachyury in cell growth and survival. Western blots showed that all chordoma cell lines expressed fibroblast growth factor receptor 2 (FGFR2), FGFR3, mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK), whereas no cell lines expressed FGFR1 and FGFR4. Results of enzyme-linked immunosorbent assay indicated that chordoma cells produced FGF2. Neutralization of FGF2 inhibited MEK/ERK phosphorylation, decreased brachyury expression and induced apoptosis while reducing cell growth. Activation of the FGFR/MEK/ERK/brachyury pathway by FGF2-initiated phosphorylation of FGFR substrate 2 (FRS2)-α (Tyr196) prevented apoptosis while promoting cell growth and epithelial-mesenchymal transition (EMT). Immunofluorescence staining showed that FGF2 promoted the translocation of phosphorylated ERK to the nucleus and increased brachyury expression. The selective inhibition of FGFR, MEK and ERK phosphorylation by PD173074, PD0325901 and PD184352, respectively, decreased brachyury expression, induced apoptosis, and inhibited cell growth and EMT. Moreover, knockdown of brachyury by small hairpin RNA reduced FGF2 secretion, inhibited FGFR/MEK/ERK phosphorylation and blocked the effects of FGF2 on cell growth, apoptosis and EMT. Those findings highlight that FGFR/MEK/ERK/brachyury pathway coordinately regulates chordoma cell growth and survival and may represent a novel chemotherapeutic target for chordoma.

| S-EPMC4593008 | biostudies-literature

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