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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)

Chordoma: Gene Expression

  • Expression of AR (alias HUMARA; a polymorphic x-linked gene) gene alleles from each of the two X chromosomes was present in chordoma tumors, indicating a polyclonal pattern of proliferation in seven informative cases of chordoma. [1]
  • Of 65 SBCs and 29 NSBCs, mitosis was observed in 26 SBCs and 22 NSBCs, and apoptosis in 19 SBCs and 13 NSBCs. [2]
  • Up-regulation of extracellular matrix genes was found in both chordomas and chondrosarcomas [3]
  • Out of 8 chordomas, EPHA2, DVL1, and CASP9 transcripts wereabsent in 1, 4, and 5 tumors, respectively. A 350 bp DVL1 gene transcript was detected in 3 tumors which showed out of frame exon 9, 10 and 11 skipping. [4]
  • PAX7- and DAN-specific transcripts were observed in 8 or 8 chordoma samples. CASP9 was present in 3 of 8 tumors and EPHA2 was present in 7 of 8 tumors. [4]
  • RT-PCR of DVL1 showed a 350 bp fragment in 4 chordomas, which was absent from placenta and brain but present in the nucleus pulposus together with the normal 524 bp fragment. Sequencing revealed the skipping of 3 exons in the smallest DVL1 fragment, thus leading to a frameshift and predicting a truncated DVL1 gene product. [4]
  • Several genes were found to be overexpressed in chordoma relative to both soft tissue sarcomas and nucleus pulposus including: Keratin 19, T Brachury, and CD24, Keratin 8, Keratin 13, Keratin 15, Keratin 17 and Keratin 18, MMP 9 and MMP 19, SOX 9, Matrilin 3, TGF-alpha, S100 P, EXT1, integrin ß like 1, integrin alpha-3, IL18 and discoidin domain receptor family. [3]
  • Most of the genes found to be overexpressed in both chordoma and chondrosarcoma, relative to soft tissue sarcomas, are involved in the synthesis or regulation of extracellular matrix, matrix metabolism and degradation, and cell-matrix interactions(type II collagen, aggrecan, type X collagen, matrillin 3, MMP 9 and MMP 19, fibronectin, integrins, HMW-MAA and ADAM28). [3]
  • RT-PCR on tumor samples from patients with classic, sporadic chordoma found the same level of S6 transcript in samples with S6 protein expression as in those without its expression. [5]
  • In situ hybridization detected Histone H3 mRNA in 0 of 17 (0%) intracranial chordoma samples from 10 patients. [6]
Brachyury (T)
Receptor Tyrosine Kinase
  • FOSB was one of the top ranked genes showing overexpression in chordoma compared to nucleus pulposus, along with c-Fos and c-jun, the epidermal growth factor receptor (EGFR) and the EGF ligand. [3]
  • RT-PCR found expression of EGF and TGF-alpha in 22 of 22 (100%) and expression of PDGFB in 21 of 21 (100%) tumor samples from patients with classic, sporadic chordoma. [5]
  • RT-PCR analysis revealed expression of the PDGFA gene in 8 of 14 (57.1%) samples of skull base chordoma. [11]
  • RT-PCR analysis revealed expression of the PDGFB gene in 9 of 14 (64.3%) samples of skull base chordoma. [11]
  • 38 of 98 (38.8%) non-skull-based and 24 of 49 (49.0%) skull-based chordoma samples were positive by FISH for EGFR. These samples also demonstrated high-level polysomy for EGFR. Among the FISH-negative samples, 27 (18.4%) were low-level polysomic and 58 (39.5%) were disomic for chromosome 7 (EGFR). [12]
  • Amplification of the HER2 gene was absent in 95 of 95 (100%) chordoma samples, as assessed by FISH. Among these, however, 34 (35.8%) showed high-level polysomy of chromosome 17. Within this subset, 17 of 34 (50.0%) also had high-level polysomy of chromosome 7. [12]
  • 33 of 77 (42.9%) chordoma samples immunoreactive for EGFR were also positive for EGFR by FISH. Similarly, 23 of 35 (65.7%) samples immuno-negative for EGFR were also negative for it by FISH. [12]
Cytokine Receptor
  • RT-PCR analysis revealed expression of the SCF gene in 1 of 14 (7.1%) samples of skull base chordoma. [11]
  • One sacrococcygeal chordoma with a germ-line TSC2 mutation demonstrated LOH of TSC2, which was consistent with the focal loss of tuberin staining in the chordoma on IHC. Another sacrococcygeal chordoma with a germ-line TSC1 mutation did not unequivocally demonstrate LOH of TSC1 but showed absence of hamartin, suggesting that a more subtle intragenic mutation or hypermethylation caused loss of function of the second allele in this tumor. [13]
  • Tumor necrosis factor receptor superfamily genes TNFRSF8, TNFRSF9, and TNFRSF14 were differently expressed in chordoma compared with nucleus pulposus in 40%–53% cases, suggesting that the deregulation of these three genes might have a role in chordoma tumorigenesis. [14]


  1. Clonality studies in sacral chordoma. Klingler, L., Trammell, R., Allan, D.G., Butler, M.G., Schwartz, H.S. Cancer. Genet. Cytogenet. (2006) [Pubmed]
  2. Skull base and nonskull base chordomas: clinicopathologic and immunohistochemical study with special reference to nuclear pleomorphism and proliferative ability. Naka, T., Boltze, C., Samii, A., Herold, C., Ostertag, H., Iwamoto, Y., Oda, Y., Tsuneyoshi, M., Kuester, D., Roessner, A. Cancer. (2003) [Pubmed]
  3. Chordoma and chondrosarcoma gene profile: implications for immunotherapy. Schwab, J.H., Boland, P.J., Agaram, N.P., Socci, N.D., Guo, T., O'Toole, G.C., Wang, X., Ostroumov, E., Hunter, C.J., Block, J.A., Doty, S., Ferrone, S., Healey, J.H., Antonescu, C.R. Cancer. Immunol. Immunother. (2009) [Pubmed]
  4. Mapping of candidate region for chordoma development to 1p36.13 by LOH analysis. Riva, P., Crosti, F., Orzan, F., Dalprà, L., Mortini, P., Parafioriti, A., Pollo, B., Fuhrman Conti, A.M., Miozzo, M., Larizza, L. Int. J. Cancer. (2003) [Pubmed]
  5. Analysis of receptor tyrosine kinases (RTKs) and downstream pathways in chordomas. Tamborini, E., Virdis, E., Negri, T., Orsenigo, M., Brich, S., Conca, E., Gronchi, A., Stacchiotti, S., Manenti, G., Casali, P.G., Pierotti, M.A., Pilotti, S. Neuro. Oncol. (2010) [Pubmed]
  6. Immunohistochemical examination of proliferative potentials and the expression of cell cycle-related proteins of intracranial chordomas. Matsuno, A., Sasaki, T., Nagashima, T., Matsuura, R., Tanaka, H., Hirakawa, M., Murakami, M., Kirino, T. Hum. Pathol. (1997) [Pubmed]
  7. Brachyury and chordoma: the chondroid-chordoid dilemma resolved? Romeo, S., Hogendoorn, P.C. J. Pathol. (2006) [Pubmed]
  8. Brachyury, a crucial regulator of notochordal development, is a novel biomarker for chordomas. Vujovic, S., Henderson, S., Presneau, N., Odell, E., Jacques, T.S., Tirabosco, R., Boshoff, C., Flanagan, A.M. J. Pathol. (2006) [Pubmed]
  9. Molecular analysis of chordomas and identification of therapeutic targets. Shalaby, AAE. Diss. University College London, London. Print. (2010) WikiGenes. Article
  10. Role of the transcription factor T (brachyury) in the pathogenesis of sporadic chordoma: a genetic and functional-based study. Presneau, N., Shalaby, A., Ye, H., Pillay, N., Halai, D., Idowu, B., Tirabosco, R., Whitwell, D., Jacques, T.S., Kindblom, L.G., Brüderlein, S., Möller, P., Leithner, A., Liegl, B., Amary, F.M., Athanasou, N.N., Hogendoorn, P.C., Mertens, F., Szuhai, K., Flanagan, A.M. J. Pathol. (2011) [Pubmed]
  11. Expression study of the target receptor tyrosine kinase of Imatinib mesylate in skull base chordomas. Orzan, F., Terreni, M.R., Longoni, M., Boari, N., Mortini, P., Doglioni, C., Riva, P. Oncol. Rep. (2007) [Pubmed]
  12. The role of epidermal growth factor receptor in chordoma pathogenesis: a potential therapeutic target. Shalaby, A., Presneau, N., Ye, H., Halai, D., Berisha, F., Idowu, B., Leithner, A., Liegl, B., Briggs, T.R., Bacsi, K., Kindblom, L.G., Athanasou, N., Amary, M.F., Hogendoorn, P.C., Tirabosco, R., Flanagan, A.M. J. Pathol. (2011) [Pubmed]
  13. Sacrococcygeal chordomas in patients with tuberous sclerosis complex show somatic loss of TSC1 or TSC2. Lee-Jones, L., Aligianis, I., Davies, P.A., Puga, A., Farndon, P.A., Stemmer-Rachamimov, A., Ramesh, V., Sampson, J.R. Genes. Chromosomes. Cancer. (2004) [Pubmed]
  14. Evaluation of 1p36 markers and clinical outcome in a skull base chordoma study. Longoni, M., Orzan, F., Stroppi, M., Boari, N., Mortini, P., Riva, P. Neuro. Oncol. (2008) [Pubmed]
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