Transcriptional Profiling Supports the Notochordal Origin of Chordoma and Its Dependence on a TGFB1-TBXT Network

Abstract

Chordoma is a rare malignant tumor demonstrating notochordal differentiation. It is dependent on brachyury (TBXT), a hallmark notochordal gene and transcription factor, and shares histologic features and the same anatomic location as the notochord. This study involved a molecular comparison of chordoma and notochord to identify dysregulated cellular pathways. The lack of a molecular reference from appropriate control tissue limits our understanding of chordoma and its relationship to notochord. Therefore, an unbiased comparison of chordoma, human notochord, and an atlas of normal and cancerous tissue was conducted using gene expression profiling to clarify the chordoma/notochord relationship and potentially identify novel drug targets. The study found striking consistency in gene expression profiles between chordoma and notochord, supporting the hypothesis that chordoma develops from notochordal remnants. A 12-gene diagnostic chordoma signature was identified and the TBXT/transforming growth factor beta (TGF-β)/SOX6/SOX9 pathway was hyperactivated in the tumor, suggesting that pathways associated with chondrogenesis were a central driver of chordoma development. Experimental validation in chordoma cells confirmed these findings and emphasized the dependence of chordoma proliferation and survival on TGF-β. The computational and experimental evidence provided the first molecular connection between notochord and chordoma and identified core members of a chordoma regulatory pathway involving TBXT. This pathway provides new therapeutic targets for this unique malignant neoplasm and highlights TGF-β as a prime druggable candidate. Chordoma is a rare malignant tumor demonstrating notochordal differentiation. It is dependent on brachyury (TBXT), a hallmark notochordal gene and transcription factor, and shares histologic features and the same anatomic location as the notochord. This study involved a molecular comparison of chordoma and notochord to identify dysregulated cellular pathways. The lack of a molecular reference from appropriate control tissue limits our understanding of chordoma and its relationship to notochord. Therefore, an unbiased comparison of chordoma, human notochord, and an atlas of normal and cancerous tissue was conducted using gene expression profiling to clarify the chordoma/notochord relationship and potentially identify novel drug targets. The study found striking consistency in gene expression profiles between chordoma and notochord, supporting the hypothesis that chordoma develops from notochordal remnants. A 12-gene diagnostic chordoma signature was identified and the TBXT/transforming growth factor beta (TGF-β)/SOX6/SOX9 pathway was hyperactivated in the tumor, suggesting that pathways associated with chondrogenesis were a central driver of chordoma development. Experimental validation in chordoma cells confirmed these findings and emphasized the dependence of chordoma proliferation and survival on TGF-β. The computational and experimental evidence provided the first molecular connection between notochord and chordoma and identified core members of a chordoma regulatory pathway involving TBXT. This pathway provides new therapeutic targets for this unique malignant neoplasm and highlights TGF-β as a prime druggable candidate. Chordoma is an indolent malignant tumor of the axial skeleton. It is uncommon and accounts for <4% of all primary bone tumors.1Scott D. Pedlow F. Hecht A. Hornicek F. Chapter 11: Tumors: primary benign and malignant extradural spine tumors.in: The Adult and Pediatric Spine. ed 3. Lippincott Williams & Wilkins, Philadelphia, PA2004: 191-246Google Scholar The yearly incidence of chondroma is 0.5 cases per million in the United States.1Scott D. Pedlow F. Hecht A. Hornicek F. Chapter 11: Tumors: primary benign and malignant extradural spine tumors.in: The Adult and Pediatric Spine. ed 3. Lippincott Williams & Wilkins, Philadelphia, PA2004: 191-246Google Scholar It usually arises in adults aged >50 years, although occasional pediatric cases are observed.1Scott D. Pedlow F. Hecht A. Hornicek F. Chapter 11: Tumors: primary benign and malignant extradural spine tumors.in: The Adult and Pediatric Spine. ed 3. Lippincott Williams & Wilkins, Philadelphia, PA2004: 191-246Google Scholar Chordoma typically develops in the axial skeleton, and approximately 50% of cases arise in the sacrum.1Scott D. Pedlow F. Hecht A. Hornicek F. Chapter 11: Tumors: primary benign and malignant extradural spine tumors.in: The Adult and Pediatric Spine. ed 3. Lippincott Williams & Wilkins, Philadelphia, PA2004: 191-246Google Scholar The 5-year survival rate of patients with chordoma is 67%, and the median survival time is 6.3 years.2McMaster M.L. Goldstein A.M. Bromley C.M. Ishibe N. Parry D.M. Chordoma: incidence and survival patterns in the United States, 1973-1995.Cancer Causes Control. 2001; 12: 1-11Crossref PubMed Scopus (744) Google Scholar Surgery is the primary treatment option, with radiotherapy used as an adjuvant.3DeLaney T.F. Liebsch N.J. Pedlow F.X. Adams J. Dean S. Yeap B.Y. McManus P. Rosenberg A.E. Nielsen G.P. Harmon D.C. Spiro I.J. Raskin K.A. Suit H.D. Yoon S.S. Hornicek F.J. Phase II study of high-dose photon/proton radiotherapy in the management of spine sarcomas.Int J Radiat Oncol Biol Phys. 2009; 74: 732-739Abstract Full Text Full Text PDF PubMed Scopus (219) Google Scholar Clinical trials using cytotoxic chemotherapy have shown little benefit for the treatment of chordoma; however, initial tests of targeted therapies have shown some promising results in small cohorts of patients.4Hofheinz R.D. Kubicka S. Wollert J. Arnold D. Hochhaus A. Gefitinib in combination with 5-fluorouracil (5-FU)/folinic acid and irinotecan in patients with 5-FU/oxaliplatin-refractory colorectal cancer: a phase I/II study of the Arbeitsgemeinschaft fur Internistische Onkologie (AIO).Onkologie. 2006; 29: 563-567Crossref PubMed Scopus (16) Google Scholar, 5Stacchiotti S. Longhi A. Ferraresi V. Grignani G. Comandone A. Stupp R. Bertuzzi A. Tamborini E. Pilotti S. Messina A. Spreafico C. Gronchi A. Amore P. Vinaccia V. Casali P.G. Phase II study of imatinib in advanced chordoma.J Clin Oncol. 2012; 30: 914-920Crossref PubMed Scopus (200) Google Scholar, 6Meng T. Jin J. Jiang C. Huang R. Yin H. Song D. Cheng L. Molecular targeted therapy in the treatment of chordoma: a systematic review.Front Oncol. 2019; 9: 30Crossref PubMed Scopus (62) Google Scholar The molecular mechanisms underlying chordoma are poorly understood; therefore, clinical trials based on genetic mechanisms are limited. The current study attempted to expand our understanding of genetically driven cellular pathways to provide new therapeutic targets to explore. Current hypotheses about chordoma development rely mostly on histologic and immunohistochemical studies that show similarities between chordoma and embryonic human notochord. During higher vertebrate development, most fetal notochordal cells regress during embryogenesis; however, remnants within the adult vertebral disk and bone can occur. Benign notochordal cell tumors are relatively common lesions in the adult vertebral bodies, and their etiology is unclear.7Picci P. Vanel D. Alberghini M. Mirra J.M. Errani C. Staals E.L. Mercuri M. Giant notochordal rests misdiagnosed and treated as chordomas: a retrospective clinical, radiological and histologic study of four cases.JCO. 2008; 26: 21503Crossref Google Scholar,8Yamaguchi T. Iwata J. Sugihara S. McCarthy E.F. Karita M. Murakami H. Kawahara N. Tsuchiya H. Tomita K. Distinguishing benign notochordal cell tumors from vertebral chordoma.Skeletal Radiol. 2008; 37: 291-299Crossref PubMed Scopus (87) Google Scholar In some cases of chordoma, benign notochordal cell tumors have been found within the affected vertebral body,9Arain A. Hornicek F.J. Schwab J.H. Chebib I. Damron T.A. Chordoma arising from benign multifocal notochordal tumors.Skeletal Radiol. 2017; 46: 1745-1752Crossref PubMed Scopus (16) Google Scholar suggesting that benign notochordal cell tumors may be a precursor lesion. Limited molecular examinations support the connection between chordoma and embryonic notochord vestiges. The transcription factor brachyury (TBXT), encoded by the gene TBXT been identified as in the development of the normal A. The encoded by is a transcription J. PubMed Scopus Google Scholar and for chordoma N. A. H. N. D. R. D. S. P. A. F. K. A.M. of the transcription factor in the of chordoma: a genetic and PubMed Scopus Google Scholar The TBXT gene been found in some and have been identified in D. Liebsch N.J. E. S. Goldstein A.M. Parry D.M. gene to 2009; PubMed Scopus Google N. V. N. K. D. F. S. D. J. R. A.M. A common in is associated with 2012; PubMed Scopus Google Scholar Chordoma cell have been shown to on its expression to cell N. A. H. N. D. R. D. S. P. A. F. K. 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A. H. N. D. R. D. S. P. A. F. K. A.M. of the transcription factor in the of chordoma: a genetic and PubMed Scopus Google Scholar The tumors were all in and tumors are to and be dependent on and tumors have in pathway D. S. A. A. A. P. R. M. P. K. and are in and 2017; PubMed Scopus Google S. E. F. D. K. dependence of to chordoma to a understanding of in 11: PubMed Scopus Google Scholar The results were from and cell were used to validation the current results are to tumors of a is the anatomic location for H. Chordoma: a systematic of the and clinical and J. PubMed Scopus Google Scholar notochord the to chordoma the of and molecular support to the relationship between notochord and chordoma and In a pathway was identified that to a in chordoma development and with TGF-β as a TGF-β an therapeutic as by genetic and pathway were that have the molecular profiling and of chordoma the of from chordoma was is of the and and of the A.M. H. M. from with and for to Clin 2001; PubMed Scopus (87) Google S. S. T. H. J. M. P. of by and of the first human chordoma cell 2001; PubMed Scopus Google Scholar The in similarities and in gene expression between chordoma and notochord. A was that gene expression in with that in a atlas of normal and a to the of and C. C. 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A common in is associated with 2012; PubMed Scopus Google Scholar the of brachyury in is although some studies have that to a M. P. J. C. The transcription factor in human tumor Clin PubMed Scopus Google Scholar, M. F. A. J. R. L. M. D. Huang J. J. C. a driver of the is in human an for novel 2012; PubMed Scopus Google Scholar, R. S. H. S. J. of brachyury to tumor by in Clin PubMed Scopus Google Scholar The current that brachyury is a unique of chordoma and notochord, and is in normal its in underlying chordoma although is primary is in tumor In the current that brachyury in the TGF-β a for brachyury in chordoma that The of the molecular chordoma in the current study that the of chondrogenesis was the most and cellular this pathway is common to J.M. J.M. Scholar, S. S. Song gene is a of and 2009; PubMed Scopus Google Scholar, S. T. M. S. S. 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