Establishment and genomic characterization of the new chordoma cell line Chor-IN-1

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.

Afatinib Is a New Therapeutic Approach in Chordoma with a Unique Ability to Target EGFR and Brachyury

“…We assembled a panel of chordoma cell lines which included cells of sacral origin like the widely used U-CH1 (28) and U-CH2 (26), the recently established MUG-Chor1 (30) and JHC7 8, and the first available clival cell line UM-Chor1 (31). In addition, we tested Chor-IN-1, a new cell line derived in house from a sacral chordoma surgical sample shown to meet validation criteria for chordoma cell lines (27). All cell lines were first authenticated by STR fingerprinting.…”

“…Interestingly, in a whole kinome-targeted sequencing, evaluating in parallel the differential expression of approximately 500 kinases in U-CH1 versus the other sacral chordoma cell lines, STK33 emerged as the only kinase with undetectable expression in U-CH1 and higher expression in the other cell lines (27). We then evaluated STK33 expression in all the cell lines by RT-qPCR and found no expression in both afatinib highly responsive U-CH1 and UM-Chor1 cell lines, while confirming relevant expression in the others.…”

“…Only a few clinical trials have been conducted so far to assess the efficacy of targeted therapeutic agents in chordoma (20)(21)(22)(23)(24), certainly limited by the exiguous number of preclinical models of this indication available so far. We recently analyzed in depth at the genomic level a panel of chordoma cell lines of sacral origin that included also the novel cell line Chor-IN-1, established and characterized in our laboratories (27). With the goal of identifying new drugs that might have an immediate therapeutic application for chordoma patients, we evaluated the in vitro antiproliferative activity of inhibitors of MET, PDGFRb, and EGFR tyrosine kinases, reported to be frequently expressed in chordomas.…”

“…MUG-Chor1 and U-CH2 (ATCC) cell lines were purchased from the ATCC. Chor-IN-1 cell line was established in house from a surgical sample (27). Chordoma cell lines were cultured in collagen-coated plates with IMDM/ RPMI1640 4:1 Medium (Gibco BRL) at 37 C in a humidified atmosphere containing 5% CO 2 .…”

Molecular Targeted Therapy in the Treatment of Chordoma: A Systematic Review

“…The loss of chromosome 9 or 9p region, which contains CDKN2A, has been reported in some chordoma patients (51). The inactivation of CDKN2A universally activates the CDK4/6 and Rb pathways (70), which are highly expressed in the chordoma tissues (71). The CDK4/6 inhibitors palbociclib and LY2835219 inhibited chordoma cell growth and proliferation in vitro efficiently (72, 73).…”