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Cytogenetic characterization of the malignant primitive neuroectodermal SK-PN-DW tumor cell line
Na Du1,2, Wanguo Bao1, Kaiyu Zhang1
1Department of Infectious Diseases, the First Hospital of Jilin University, 71 Xinmin Street, Changchun, Jilin, 130021, People's Republic of China.
Background:
The SK-PN-DW cell line was established in 1979 and is commercially available. Despite the use of this cell line as an in vitro model for functional and therapeutic studies of malignant primitive neuroectodermal tumor (PNET), there is a lack of complete information about the genetic alterations that are present at the cytogenetic level. Thus, the current study aimed to characterize the cytogenetic profile of this cell line.
Methods:
Routine G-banded chromosome analysis, fluorescence in situ hybridization, and oligonucleotide array comparative genomic hybridization assays were performed to characterize the chromosomal changes in this cell line.
Results:
The G-banded karyotype analysis showed that the number of chromosomes in this cell line ranged between 36 and 41. Importantly, all cells displayed a loss of chromosomes Y, 11, 13, and 18. However, some cells showed an additional loss of chromosome 10. Additionally, the observed structural changes indicated: a) unbalanced translocation between chromosomes 1 and 7; b) translocation between chromosomes 11 and 22 at breakpoints 11q24 and 22q12, which is a classical translocation that is associated with Ewing sarcoma; c) a derivative chromosome due to a whole arm translocation between chromosomes 16 and 17 at likely breakpoints 16p10 and 17q10; and d) possible rearrangement in the short arm of chromosome 18. Moreover, a variable number of double minutes were also observed in each metaphase cell. Furthermore, the microarray assay results not only demonstrated genomic-wide chromosomal imbalance in this cell line and precisely placed chromosomal breakpoints on unbalanced, rearranged chromosomes, but also revealed information about subtle chromosomal changes and the chromosomal origin of double minutes. Finally, the fluorescence in situ hybridization assay confirmed the findings of the routine cytogenetic analysis and microarrays.
Conclusion:
The accurate determination of the cytogenetic profile of the SK-PN-DW cell line is helpful in enabling the research community to utilize this cell line for future identity and comparability studies, in addition to demonstrating the utility of the complete cytogenetic profile, as a public resource.
Insights
This study characterized the SK-PN-DW cell line, revealing significant chromosomal alterations including losses and translocations. These findings provide a crucial cytogenetic profile for future research on primitive neuroectodermal tumors.
Area of Science:
- Cytogenetics
- Cancer Cell Line Characterization
- Genomic Instability
Background:
- The SK-PN-DW cell line, established in 1979, is a widely used in vitro model for malignant primitive neuroectodermal tumor (PNET) research.
- However, a comprehensive understanding of its cytogenetic profile has been lacking, hindering precise interpretation of experimental results.
Purpose of the Study:
- To perform a detailed cytogenetic characterization of the SK-PN-DW cell line.
- To identify and document all numerical and structural chromosomal abnormalities present in this cell line.
Main Methods:
- Routine G-banded karyotype analysis to assess numerical and gross structural changes.
- Oligonucleotide array comparative genomic hybridization (aCGH) for high-resolution detection of copy number variations and precise breakpoint mapping.
- Fluorescence in situ hybridization (FISH) to confirm specific chromosomal rearrangements.
Main Results:
- Karyotype analysis revealed aneuploidy (36–41 chromosomes) with consistent loss of chromosomes Y, 11, 13, and 18, and variable loss of chromosome 10.
- Identified structural abnormalities include unbalanced translocations (chr1/7, chr11/22), whole arm translocations (chr16/17), and potential rearrangements on chr18.
- aCGH elucidated genomic-wide imbalances and the origin of double minutes, while FISH confirmed key findings.
Conclusions:
- This study provides a comprehensive cytogenetic profile of the SK-PN-DW cell line, essential for its accurate use in PNET research.
- The detailed characterization serves as a valuable public resource, enhancing the reliability and comparability of future studies utilizing this cell line.
- Highlights the utility of integrated cytogenetic techniques for thorough cell line characterization.
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