Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization

Abstract

Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology.

HPV‐negative and HPV‐positive HNSCC cell lines show similar numerical but different structural chromosomal aberrations

“…For DNA ploidy, similar data were measured by others also showing no difference between HPV‐negative and HPV‐positive cell lines. Quite similar values for the mean numbers of chromosomes were previously found for other HNSCC cell lines …”

“…Surprisingly, the overall variation in ploidy seen here was very similar (supplement Figure S6) to the data obtained from other HNSCC cell lines . Tumor CIN is regarded to arise from a defect in chromosomal segregation, mostly resulting from an abnormal amplification of centrosomes .…”

“…Quite similar values for the mean numbers of chromosomes were previously found for other HNSCC cell lines. [49][50][51][52] We also observed that for both HPV-negative as well as HPV-positive cell lines, there was an excellent and identical correlation between the DNA index and the respective mean number of chromosomes ( Figure 2D) as previously already observed by Roa et al 49 This finding demonstrates that for both entities DNA aneuploidy is primarily caused by an amplification of whole chromosomes and less due to an amplification of certain genomic regions, which is in line with the general concept of tumor aneuploidy. 53 When ploidy was determined for each specific chromosome using M-FISH, a strong variation was seen for both entities ranging from diploid, triploid to tetraploid.…”

“…15 Surprisingly, the overall variation in ploidy seen here was very similar (supplement Figure S6) to the data obtained from other HNSCC cell lines. 52,54 Tumor CIN is regarded to arise from a defect in chromosomal segregation, mostly resulting from an abnormal amplification of centrosomes. 53,55 Loss or mutational inactivation of wild-type p53 may lead to this abnormality, 56 which is considered to result from its direct physical binding to the centrosomes.…”

In vitro assays and techniques utilized in anticancer drug discovery

“…As the probes are smaller than metaphase chromosomes, the resolution of array CGH is correspondingly higher than conventional CGH (Jong, Marchiori, Meijer, Vaart, & Ylstra, ; Shinawi & Cheung, ). Singchat et al () have used CGH to study genomic alteration in head and neck squamous cell carcinoma. Array CGH has been used by Rausch et al () in a study conducted to detect genomic copy number alterations in pancreatic ductal adenocarcinoma.…”