Genotyping Cancer-Associated Genes in Chordoma Identifies Mutations in Oncogenes and Areas of Chromosomal Loss Involving CDKN2A, PTEN, and SMARCB1

Abstract

The molecular mechanisms underlying chordoma pathogenesis are unknown. We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets. Given the relatively high costs of whole genome sequencing, we performed a focused genetic analysis using matrix-assisted laser desorption/ionization-time of flight mass spectrometer (Sequenom iPLEX genotyping). We tested 865 hotspot mutations in 111 oncogenes and selected tumor suppressor genes (OncoMap v. 3.0) of 45 human chordoma tumor samples. Of the analyzed samples, seven were identified with at least one mutation. Six of these were from fresh frozen samples, and one was from a paraffin embedded sample. These observations were validated using an independent platform using homogeneous mass extend MALDI-TOF (Sequenom hME Genotyping). These genetic alterations include: ALK (A877S), CTNNB1 (T41A), NRAS (Q61R), PIK3CA (E545K), PTEN (R130), CDKN2A (R58*), and SMARCB1 (R40*). This study reports on the largest comprehensive mutational analysis of chordomas performed to date. To focus on mutations that have the greatest chance of clinical relevance, we tested only oncogenes and tumor suppressor genes that have been previously implicated in the tumorigenesis of more common malignancies. We identified rare genetic changes that may have functional significance to the underlying biology and potential therapeutics for chordomas. Mutations in CDKN2A and PTEN occurred in areas of chromosomal copy loss. When this data is paired with the studies showing 18 of 21 chordoma samples displaying copy loss at the locus for CDKN2A, 17 of 21 chordoma samples displaying copy loss at PTEN, and 3 of 4 chordoma samples displaying deletion at the SMARCB1 locus, we can infer that a loss of heterozygosity at these three loci may play a significant role in chordoma pathogenesis.

EGFR inhibitors identified as a potential treatment for chordoma in a focused compound screen

“…A common cause for EGFR activation is the presence of mutations and gene amplification, as seen in non‐small cell lung cancer and glioblastoma . However, this is not the case for the cell lines in our study, which is consistent with published EGFR genetic profiling reports and the unpublished data from ∼30 whole genomes/whole exomes from our laboratory. The absence of EGFR mutations in chordomas is shared with other cancers, such as head and neck squamous cell carcinoma and colorectal and pancreatic cancers, which are known to respond to anti‐EGFR therapy to varying degrees .…”

The driver landscape of sporadic chordoma

“…The principal treatment of chordoma is radical surgical resection, augmented by adjuvant radiotherapy 2 . Chordoma does not respond to cytotoxic chemotherapy 3 . Most patients cannot be cured 3 .…”

“…Chordoma does not respond to cytotoxic chemotherapy 3 . Most patients cannot be cured 3 . They often suffer from the debilitating consequences of tumour progression and its surgical treatment before dying from their disease 3 .…”

Preclinical Characterization of Novel Chordoma Cell Systems and Their Targeting by Pharmocological Inhibitors of the CDK4/6 Cell-Cycle Pathway

“…We found that the tumor suppressor p16 (CDKN2A) is deleted and that p16 protein is not expressed in these cell lines. This deletion has been described in the majority of chordomas (25)(26)(27). The downstream machinery of p16 can be efficiently inhibited by CDK4/6 inhibitors such as palbociclib (28).…”