Genomic analysis of head and neck squamous cell carcinoma cell lines and human tumors: a rational approach to preclinical model selection

Abstract

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common type of cancer worldwide. The increasing amount of genomic information on human tumors and cell lines provides more biologic data to design preclinical studies. We and others previously reported whole-exome sequencing data of 106 HNSCC primary tumors. In 2012, high-throughput genomic data and pharmacologic profiling of anticancer drugs of hundreds of cancer cell lines were reported. Here, we compared the genomic data of 39 HNSCC cell lines with the genomic findings in 106 HNSCC tumors. Amplification of eight genes (PIK3CA, EGFR, CCND2, KDM5A, ERBB2, PMS1, FGFR1, and WHSCIL1) and deletion of five genes (CDKN2A, SMAD4, NOTCH2, NRAS, and TRIM33) were found in both HNSCC cell lines and tumors. Seventeen genes were only mutated in HNSCC cell lines (>10%), suggesting that these mutations may arise through immortalization in tissue culture. Conversely, 11 genes were only mutated in >10% of human HNSCC tumors. Several mutant genes in the EGF receptor (EGFR) pathway are shared both in cell lines and in tumors. Pharmacologic profiling of eight anticancer agents in six HNSCC cell lines suggested that PIK3CA mutation may serve as a predictive biomarker for the drugs targeting the EGFR/PI3K pathway. These findings suggest that a correlation of gene mutations between HNSCC cell lines and human tumors may be used to guide the selection of preclinical models for translational research.

Implications: These findings suggest that a correlation of gene mutations between HNSCC cell lines and human tumors may be used to guide the selection of preclinical models for translational research.

Figure 1. Venn diagram of unique and common HNSCC cell lines with sequence information

Cell lines derived from the squamous mucosal surfaces of the head and neck (HNSCC) were identified in the Barretina et al (blue) and/or in Garnett et al (yellow) databases and identified as unique or overlapping.

Figure 2. Comparison of gene mutation frequencies and copy numbers between HNSCC cell lines and human tumors

(A) Venn diagram of overlapping mutated genes in HNSCC cell lines (purple) and human tumors (green). Non-synonymous mutations are defined as all mutations, with the exception of silent mutations and mutations occurring in the 3’ and 5’ UTRs. (B) Comparison of the incidence of mutations in genes mutated in more than 5% of HNSCC cell lines and tumors derived from Larynx, Oral Cavity and Pharynx sites (* indicates significantly higher incidence of mutation in cell lines compared with tumors with FDR ≤ 10%). (C) Comparison of the incidence of gene copy number alterations in HNSCC cell lines and tumors. Left panel shows the incidence of the eight genes amplified both in HNSCC cell lines and tumors. Amplification is defined as having a log2 value of greater than or equal to 0.58. Right panel shows the incidence of the five genes deleted both in HNSCC cell lines and tumors. Deletion is defined as having a log2 value of less than or equal to −1.

Figure 2. Comparison of gene mutation frequencies and copy numbers between HNSCC cell lines and human tumors

(A) Venn diagram of overlapping mutated genes in HNSCC cell lines (purple) and human tumors (green). Non-synonymous mutations are defined as all mutations, with the exception of silent mutations and mutations occurring in the 3’ and 5’ UTRs. (B) Comparison of the incidence of mutations in genes mutated in more than 5% of HNSCC cell lines and tumors derived from Larynx, Oral Cavity and Pharynx sites (* indicates significantly higher incidence of mutation in cell lines compared with tumors with FDR ≤ 10%). (C) Comparison of the incidence of gene copy number alterations in HNSCC cell lines and tumors. Left panel shows the incidence of the eight genes amplified both in HNSCC cell lines and tumors. Amplification is defined as having a log2 value of greater than or equal to 0.58. Right panel shows the incidence of the five genes deleted both in HNSCC cell lines and tumors. Deletion is defined as having a log2 value of less than or equal to −1.

Figure 2. Comparison of gene mutation frequencies and copy numbers between HNSCC cell lines and human tumors

(A) Venn diagram of overlapping mutated genes in HNSCC cell lines (purple) and human tumors (green). Non-synonymous mutations are defined as all mutations, with the exception of silent mutations and mutations occurring in the 3’ and 5’ UTRs. (B) Comparison of the incidence of mutations in genes mutated in more than 5% of HNSCC cell lines and tumors derived from Larynx, Oral Cavity and Pharynx sites (* indicates significantly higher incidence of mutation in cell lines compared with tumors with FDR ≤ 10%). (C) Comparison of the incidence of gene copy number alterations in HNSCC cell lines and tumors. Left panel shows the incidence of the eight genes amplified both in HNSCC cell lines and tumors. Amplification is defined as having a log2 value of greater than or equal to 0.58. Right panel shows the incidence of the five genes deleted both in HNSCC cell lines and tumors. Deletion is defined as having a log2 value of less than or equal to −1.

Figure 3. Genes mutated in EGFR signaling pathways in HNSCC cell lines and/or tumors

Unfilled circle indicates that the gene is not mutated in either HNSCC cell lines or human tumors. Red represents a gene that is mutated both in tumors and cell lines. Green indicates a gene that is mutated only in tumors and yellow denotes a gene that is only mutated in cell lines.

Figure 4. The pharmacological sensitivities of HNSCC cell lines

(A) Drug activity areas were compared between HNSCC cell lines with all cancer cell lines in CCLE. (B) Drug response of HNSCC cell lines for EGFR pathway inhibitors AZD0530, erlotinib, lapatinib, TKI 258 and ZD-6474 as measured by the activity area. The middle bar = median. Black: Cal 27; Green: Detroit 562; Blue: Fadu; Red: HSC-2; Yellow: SCC-25; Purple: SCC-9. (C) Expression of a PIK3CA mutation (H1047R) reduces sensitivity to erlotinib in Cal 27 and SCC 9 cells. PIK3CA mutant (H1047R) or WT PIK3CA were introduced into Cal27 and SCC9 cells followed by treatment with either of two concentrations of erlotinib (2.5 μM or 8.0μM) for 48h. Cell survival was measured by MTT assay. P values were calculated using an unpaired t-test with Welch's correction. The experiments were repeated three times with similar results.

Figure 4. The pharmacological sensitivities of HNSCC cell lines

(A) Drug activity areas were compared between HNSCC cell lines with all cancer cell lines in CCLE. (B) Drug response of HNSCC cell lines for EGFR pathway inhibitors AZD0530, erlotinib, lapatinib, TKI 258 and ZD-6474 as measured by the activity area. The middle bar = median. Black: Cal 27; Green: Detroit 562; Blue: Fadu; Red: HSC-2; Yellow: SCC-25; Purple: SCC-9. (C) Expression of a PIK3CA mutation (H1047R) reduces sensitivity to erlotinib in Cal 27 and SCC 9 cells. PIK3CA mutant (H1047R) or WT PIK3CA were introduced into Cal27 and SCC9 cells followed by treatment with either of two concentrations of erlotinib (2.5 μM or 8.0μM) for 48h. Cell survival was measured by MTT assay. P values were calculated using an unpaired t-test with Welch's correction. The experiments were repeated three times with similar results.

Figure 4. The pharmacological sensitivities of HNSCC cell lines

(A) Drug activity areas were compared between HNSCC cell lines with all cancer cell lines in CCLE. (B) Drug response of HNSCC cell lines for EGFR pathway inhibitors AZD0530, erlotinib, lapatinib, TKI 258 and ZD-6474 as measured by the activity area. The middle bar = median. Black: Cal 27; Green: Detroit 562; Blue: Fadu; Red: HSC-2; Yellow: SCC-25; Purple: SCC-9. (C) Expression of a PIK3CA mutation (H1047R) reduces sensitivity to erlotinib in Cal 27 and SCC 9 cells. PIK3CA mutant (H1047R) or WT PIK3CA were introduced into Cal27 and SCC9 cells followed by treatment with either of two concentrations of erlotinib (2.5 μM or 8.0μM) for 48h. Cell survival was measured by MTT assay. P values were calculated using an unpaired t-test with Welch's correction. The experiments were repeated three times with similar results.