Frequent mutations in TP53 and CDKN2A found by next-generation sequencing of head and neck cancer cell lines.
OBJECTIVE
To conduct high-throughput mutational analysis in 6 commonly used head and neck cancer cell lines. Comprehensive mutation analysis of primary head and neck squamous cell carcinoma (HNSCC) tumors has recently been reported, and mutations in the NOTCH receptors, TP53 and CDKN2A, were key findings. Established cell lines are valuable tools to study cancer in vitro. Similar high-throughput mutational analysis of head and neck cancer cell lines is necessary to confirm their mutational profile.


METHODS
DNA was extracted from American Type Culture Collection (ATCC) cell lines Cal27, Detroit562, FaDu, SCC4, SCC15, and SCC25. Cell line identity was confirmed by short tandem repeat (STR) analysis, and human papillomavirus (HPV) infection status was assessed by real-time polymerase chain reaction. A total of 535 cancer-associated genes were sequenced through a limited exome capture on the Illumina HiSeq system.


METHODS
London Regional Cancer Program.


RESULTS
The identity of the 6 cell lines was confirmed by STR analysis, and all lines tested negative for HPV infection. We achieved an average of 129-fold coverage with paired-end 100 base-pair reads. Sequencing revealed an average of 38 damaging mutations in each cell line (range, 30-45). The TP53 mutations, predicted to confer loss of function, were noted in all cell lines, and damaging CDKN2A mutations were found in all lines except SCC15.


CONCLUSIONS
High-throughput sequencing of head and neck cancer cell lines revealed similar mutations to those observed in primary tumors. Thus, these lines reflect the tumor biology of HNSCC and can serve as valuable models to study HNSCC in vitro.
Departmentof Otolaryngology–Head and Neck Surgery, VictoriaHospital, London Health Science Centre, Room B3-431A, 800 Commissioners Rd E, London,ONN6A 5W9,Canada (Anthony.Nichols@lhsc.on.ca).
Anthony C
AC
Nichols
John
J
Yoo
David A
DA
Palma
Kevin
K
Fung
Jason H
JH
Franklin
James
J
Koropatnick
Joe S
JS
Mymryk
Nizar N
NN
Batada
John W
JW
Barrett
D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000821:virology; D045744:Cell Line, Tumor; D004252:DNA Mutational Analysis; D019942:Genes, p16; D005838:Genotype; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000821:virology; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics; D027383:Papillomaviridae / Q000302:isolation & purification; D030361:Papillomavirus Infections / Q000821:virology; D060888:Real-Time Polymerase Chain Reaction; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*
C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53