ORIGINAL PAPER Journal of Pathology J Pathol 2011; 223: 327–335 Published online 24 November 2010 in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/path.2816 Role of the transcription factor T (brachyury) in the pathogenesis of sporadic chordoma: a genetic and functional-based study Nad` ege Presneau, 1# Asem Shalaby, 1,2# Hongtao Ye, 3 Nischalan Pillay, 1,3 Dina Halai, 1,3 Bernadine Idowu, 1,3 Roberto Tirabosco, 2,3 Duncan Whitwell, 4 Thomas S Jacques, 5 Lars-Gunnar Kindblom, 6 Silke Br¨ uderlein, 7 Peter M¨ oller, 7 Andreas Leithner, 8 Bernadette Liegl, 9 Fernanda M Amary, 3 Nicholas N Athanasou, 4 Pancras CW Hogendoorn, 10 Fredrik Mertens, 11 Karoly Szuhai 12 and Adrienne M Flanagan* 1,2,3 1 UCL Cancer Institute, 72 Huntley Street, London WC1 6BT, UK 2 Institute of Orthopaedics and Musculoskeletal Science, University College London, Stanmore, Middlesex HA7 4LP, UK 3 Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, Middlesex HA7 4LP, UK 4 Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK 5 Neural Development Unit, UCL Institute of Child Health and Department of Histopathology, Great Ormond Street Hospital, London, UK 6 Department of Pathology, Royal Orthopaedic Hospital, Birmingham B31 2AP, UK 7 Institut of Pathology, University Hospitals of Ulm, Ulm, Germany 8 Department of Orthopaedics and Orthopaedic Surgery, Medical University of Graz, Auenbruggerplatz 25, 8036 Graz, Austria 9 Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, 8036 Graz, Austria 10 Department of Pathology, Leiden University Medical Centre, Leiden 2300 RC, The Netherlands 11 Department of Clinical Genetics, Lund University Hospital, Lund, Sweden 12 Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands *Correspondence to: Adrienne M Flanagan, UCL, Institute of Orthopaedics and Musculoskeletal Science, Royal National Orthopaedic Hospital, Stanmore, Middlesex HA7 4LP, UK e-mail: a.flanagan@ucl.ac.uk # These authors contributed equally to this study. Abstract A variety of analyses, including fluorescence in situ hybridization (FISH), quantitative PCR (qPCR) and array CGH (aCGH), have been performed on a series of chordomas from 181 patients. Twelve of 181 (7%) tumours displayed amplification of the T locus and an additional two cases showed focal amplification; 70/181 (39%) tumours were polysomic for chromosome 6, and 8/181 (4.5%) primary tumours showed a minor allelic gain of T as assessed by FISH. No germline alteration of the T locus was identified in non-neoplastic tissue from 40 patients. Copy number gain of T was seen in a similar percentage of sacrococcygeal, mobile spine and base of skull tumours. Knockdown of T in the cell line, U-CH1, which showed polysomy of chromosome 6 involving 6q27, resulted in a marked decrease in cell proliferation and morphological features consistent with a senescence-like phenotype. The U-CH1 cell line was validated as representing chordoma by the generation of xenografts, which showed typical chordoma morphology and immunohistochemistry in the NOD/SCID/interleukin 2 receptor [IL2r]γ null mouse model. In conclusion, chromosomal aberrations resulting in gain of the T locus are common in sporadic chordomas and expression of this gene is critical for proliferation of chordoma cells in vitro. Copyright  2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Keywords: chordoma; T ; amplification; copy number gain; oncogene Received 9 September 2010; Revised 5 October 2010; Accepted 15 October 2010 No conflicts of interest were declared. Introduction Chordoma is a rare malignant locally destructive tumour with a characteristic morphology and immuno- histochemical profile [cytokeratin 19 and T (brachyury)-positive] that occurs, in the majority of cases, in the clivus and vertebral bones [1–4]. T is a specific and sensitive marker for chordomas, and is rarely expressed in other neoplastic or non-neoplastic adult tissue apart from haemangioblastomas and normal spermatogenic tissue [2,3,5]. More recently, the rare occurrence of familial chordoma [6–13] has recently been linked to T duplication [14], as demonstrated by the presence of this genetic germ-line alteration in members of four of seven families in which there was a history of familial chordoma. This was the first report of T copy number gain (CNG) in any disease type [14]. It is therefore of interest that two other Copyright  2010 Pathological Society of Great Britain and Ireland. J Pathol 2011; 223: 327–335 Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk www.thejournalofpathology.com