No abstract

Chordomas are rare, slowly growing tumors with high medical need, arising in the axial skeleton from notochord remnants. The transcription factor “brachyury” represents a distinctive molecular marker and a key oncogenic driver of chordomas. Tyrosine kinase receptors are also expressed, but so far kinase inhibitors have not shown clear clinical efficacy in chordoma patients. The need for effective therapies is extremely high, but the paucity of established chordoma cell lines has limited preclinical research. Here we describe the isolation of the new Chor-IN-1 cell line from a recurrent sacral chordoma and its characterization as compared to other chordoma cell lines. Chor-IN-1 displays genomic identity to the tumor of origin and has morphological features, growth characteristics and chromosomal abnormalities typical of chordoma, with expression of brachyury and other relevant biomarkers. Chor-IN-1 gene variants, copy number alterations and kinome gene expression were analyzed in comparison to other four chordoma cell lines, generating large scale DNA and mRNA genomic data that can be exploited for the identification of novel pharmacological targets and candidate predictive biomarkers of drug sensitivity in chordoma. The establishment of this new, well characterized chordoma cell line provides a useful tool for the identification of drugs active in chordoma.

Chordomas are rare, slowly growing but locally invasive bone tumors, derived from notocord remnants and characterized by the expression of “Brachyury” transcription factor. No standard medical therapy is available for this indication that is resistant to chemotherapy. Surgery associated to radiation, is the conventional treatment, but recurrence is extremely common and disease progression is severely crippling for patients. Expression of activated tyrosine kinase receptors and downstream pathways has been observed, including PDGFRβ and EGFR. Although some clinical responses have been obtained with Imatinib, also in combination with Sirolimus, and with Erlotinib, these treatments cannot eradicate the disease, and there is a strong need for new effective therapies. Only a handful of chordoma cell lines are available today and the paucity of in vitro models has so far limited the identification of new molecular targets and the assessment of the efficacy of small molecules inhibitors on chordoma cells proliferation. Here we present the establishment and the characterization of the new Chor-IN-1 chordoma cell line from a recurrent sacral tumor of a patient previously treated with Imatinib and radiotherapy. The cell line has a very slow growth rate, as normally observed for this type of tumors, and displays the typical chordoma physaliferous morphology. The karyotype is indicative of a single population and the Short Tandem Repeat (STR) profile is unique and 100% identical to that of the original tumor sample. The cell line expresses the most relevant chordoma biomarkers, like the product of the “T” gene Brachyury, CD24 and Cytoketatin 19. The non synonymous rs2305089 polymorphism in the “T” gene, associated with chordoma predisposition, was identified in the Chor-IN-1, as well as in the UCH-1 and UCH-2 chordoma reference cell lines. To further characterize the new cell line, its genetic background and transcriptional profile, with particular focus on kinases, was analysed by a Next Generation Sequencing (NGS) approach, in parallel with UCH-1 and UCH-2, to identify common and unique cancer related features. Finally, the cell line was characterized for its sensitivity to selected kinase inhibitor drugs already approved or in clinical testing, in parallel with the control cell lines. Among the several EGFR inhibitors tested, Afatinib resulted generally the most active, suggesting that treatment with this drug may represent a valuable therapeutic approach in chordoma. In conclusion, we report the establishment and in depth characterization of a new chordoma cell line that, retaining all the typical features of chordomas, represents a useful tool for the identification of candidate new druggable targets, or active drugs for chordoma therapy. Citation Format: Paola Magnaghi, Roberta Bosotti, Nadia Amboldi, Liviana Cozzi, Alessio Somaschini, Silvia Stacchiotti, Fabio Bozzi, Elena Tamborini, Elena Conca, Silvana Pilotti, Marco A. Pierotti, Sebastiano Di Bella, Carlo Cusi, Dario Ballinari, Arturo Galvani, Barbara Salom, Antonella Isacchi. Establishment and characterization of the new sacral chordoma cell line Chor-IN-1. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 74. doi:10.1158/1538-7445.AM2015-74

No abstract

Inhibition of kinase gene fusions (KGFs) has proven successful in cancer treatment and continues to represent an attractive research area, due to kinase druggability and clinical validation. Indeed, literature and public databases report a remarkable number of KGFs as potential drug targets, often identified by in vitro characterization of tumor cell line models and confirmed also in clinical samples. However, KGF molecular and experimental information can sometimes be sparse and partially overlapping, suggesting the need for a specific annotation database of KGFs, conveniently condensing all the molecular details that can support targeted drug development pipelines and diagnostic approaches. Here, we describe KuNG FU (KiNase Gene FUsion), a manually curated database collecting detailed annotations on KGFs that were identified and experimentally validated in human cancer cell lines from multiple sources, exclusively focusing on in-frame KGF events retaining an intact kinase domain, representing potentially active driver kinase targets. To our knowledge, KuNG FU represents to date the largest freely accessible homogeneous and curated database of kinase gene fusions in cell line models.