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Molecular profiling of chordoma
Stefanie Scheil-Bertram1, Roland Kappler2, Alexandra von Baer3
1Institute of Pathology, University Hospitals of Ulm, Germany.
Abstract:
The molecular basis of chordoma is still poorly understood, particularly with respect to differentially expressed genes involved in the primary origin of chordoma. In this study, therefore, we compared the transcriptional expression profile of one sacral chordoma recurrence, two chordoma cell lines (U-CH1 and U-CH2) and one chondrosarcoma cell line (U-CS2) with vertebral disc using a high-density oligonucleotide array. The expression of 65 genes whose mRNA levels differed significantly (p<0.001; ≥6-fold change) between chordoma and control (vertebral disc) was identified. Genes with increased expression in chordoma compared to control and chondrosarcoma were most frequently located on chromosomes 2 (11%), 5 (8%), 1 and 7 (each 6%), whereas interphase cytogenetics of 33 chordomas demonstrated gains of chromosomal material most prevalent on 7q (42%), 12q (21%), 17q (21%), 20q (27%) and 22q (21%). The microarray data were confirmed for selected genes by quantitative polymerase chain reaction analysis. As in other studies, we showed the expression of brachyury. We demonstrate the expression of new potential candidates for chordoma tumorigenesis, such as CD24, ECRG4, RARRES2, IGFBP2, RAP1, HAI2, RAB38, osteopontin, GalNAc-T3, VAMP8 and others. Thus, we identified and validated a set of interesting candidate genes whose differential expression likely plays a role in chordoma.
Insights
Researchers identified key genes involved in chordoma development by comparing gene expression in chordoma samples and normal tissue. This study reveals new potential targets for understanding and treating this rare bone cancer.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- The molecular underpinnings of chordoma, a rare bone tumor, remain largely unknown, especially regarding gene expression in its primary origin.
- Understanding differential gene expression is crucial for elucidating chordoma tumorigenesis.
Purpose of the Study:
- To compare the transcriptional expression profiles of chordoma and chondrosarcoma cell lines with vertebral disc tissue.
- To identify differentially expressed genes associated with chordoma development.
Main Methods:
- Utilized high-density oligonucleotide arrays to analyze gene expression in chordoma samples and cell lines.
- Confirmed microarray findings for selected genes using quantitative polymerase chain reaction (qPCR).
- Performed interphase cytogenetics on 33 chordoma samples to identify chromosomal abnormalities.
Main Results:
- Identified 65 genes with significantly different mRNA levels (p<0.001; ≥6-fold change) between chordoma and control (vertebral disc) tissues.
- Found increased gene expression in chordoma on chromosomes 2, 5, 1, and 7.
- Cytogenetics revealed chromosomal gains prevalent on 7q, 12q, 17q, 20q, and 22q.
- Validated expression of known markers like brachyury and identified novel candidates including CD24, ECRG4, RARRES2, and IGFBP2.
Conclusions:
- Identified and validated a set of candidate genes (e.g., CD24, ECRG4, RARRES2, IGFBP2) with differential expression in chordoma.
- These genes are potential contributors to chordoma tumorigenesis and warrant further investigation.
- The study provides valuable insights into the molecular basis of chordoma.
