High-resolution whole-genome analysis of skull base chordomas implicates FHIT loss in chordoma pathogenesis

Abstract

Chordoma is a rare tumor arising in the sacrum, clivus, or vertebrae. It is often not completely resectable and shows a high incidence of recurrence and progression with shortened patient survival and impaired quality of life. Chemotherapeutic options are limited to investigational therapies at present. Therefore, adjuvant therapy for control of tumor recurrence and progression is of great interest, especially in skull base lesions where complete tumor resection is often not possible because of the proximity of cranial nerves. To understand the extent of genetic instability and associated chromosomal and gene losses or gains in skull base chordoma, we undertook whole-genome single-nucleotide polymorphism microarray analysis of flash frozen surgical chordoma specimens, 21 from the clivus and 1 from C1 to C2 vertebrae. We confirm the presence of a deletion at 9p involving CDKN2A, CDKN2B, and MTAP but at a much lower rate (22%) than previously reported for sacral chordoma. At a similar frequency (21%), we found aneuploidy of chromosome 3. Tissue microarray immunohistochemistry demonstrated absent or reduced fragile histidine triad (FHIT) protein expression in 98% of sacral chordomas and 67%of skull base chordomas. Our data suggest that chromosome 3 aneuploidy and epigenetic regulation of FHIT contribute to loss of the FHIT tumor suppressor in chordoma. The finding that FHIT is lost in a majority of chordomas provides new insight into chordoma pathogenesis and points to a potential new therapeutic target for this challenging neoplasm.

Figure 1

Frequency of DNA copy number changes detected by SNP array analysis in 22 skull base chordomas. Losses were more frequent than gains.

Figure 2

Genomic imbalances detected in individual tumor samples. Gains (red) and losses (blue) of genomic material were detected in all tumor samples by SNP array analysis. Each row corresponds to a unique sample and each column represents a specific chromosome. Chondroid and classic chordoma samples have been grouped to facilitate comparison. Note the acquisition of chromosome 3 loss and the similarity of gains and losses in the recurrent tumor sample (CHD20) to the primary tumor sample (CHD19).

Figure 3

Map of chromothripsis found in chromosome 22 in CHD1 and chromosome 7 in CHD8. There are 43 genes affected on chromosome 22 and 32 genes affected on chromosome 7.

Figure 4

Gene network maps for the top networks formed by genes found (A, B) within focal amplifications and (C) within focal deletions. Gray nodes indicate deleted or amplified genes, whereas white nodes are interacting genes not part of focal amplifications or deletions. Solid lines indicate direct protein interaction. Solid arrows indicate direct action on and dashed arrows indicate indirect action on.

Figure 5

Histogram showing tissue microarray scoring for FHIT protein immunostaining in skull base and sacral chordomas. A score of 0 represents no staining, 0.5 equivocal staining, 1 minimal staining, 2 moderate staining, and 3 intense staining.

Figure 6

Immunostaining for FHIT protein in four different classic clival chordomas. (A) Secondary antibody-only control; scale bar, 50 µm. (B) Moderate staining in a region of physaliferous cells, 22-year-old female; scale bar, 50 µm. (C) Minimal cytoplasmic staining and moderate nucleolar staining in a tumor from a 39-year-old female; scale bar, 50 µm. (D) Intense staining of nucleoli and variable cytoplasmic staining in a tumor from a 78-year-old male; scale bar, 50 µm. (E) Regions of moderate cytoplasmic staining juxtaposed with regions of no cytoplasmic staining in a recurrent tumor from a 44-year-old male; scale bar, 0.5 mm. (F) Intense cytoplasmic and nuclear staining in tumor-associated macrophages; scale bar, 50 µm.