A gene‐alteration profile of human lung cancer cell lines

Aberrant proteins encoded from genes altered in tumors drive cancer development and may also be therapeutic targets. Here we derived a comprehensive gene‐alteration profile of lung cancer cell lines. We tested 17 genes in a panel of 88 lung cancer cell lines and found the rates of alteration to be higher than previously thought. Nearly all cells feature inactivation at TP53 and CDKN2A or RB1, whereas BRAF, MET, ERBB2, and NRAS alterations were infrequent. A preferential accumulation of alterations among histopathological types and a mutually exclusive occurrence of alterations of CDKN2A and RB1 as well as of KRAS, epidermal growth factor receptor (EGFR), NRAS, and ERBB2 were seen. Moreover, in non‐small‐cell lung cancer (NSCLC), concomitant activation of signal transduction pathways known to converge in mammalian target of rapamycin (mTOR) was common. Cells with single activation of ERBB2, PTEN, or MET signaling showed greater sensitivity to cell‐growth inhibition induced by erlotinib, LY294002, and PHA665752, respectively, than did cells featuring simultaneous activation of these pathways, underlining the need for combined therapeutic strategies in targeted cancer treatments. In conclusion, our gene‐alteration landscape of lung cancer cell lines provides insights into how gene alterations accumulate and biological pathways interact in cancer. Hum Mutat 30,1–8, 2009. © 2009 Wiley‐Liss, Inc.

[1]  Marc-André Elsliger,et al.  Rare cancer-specific mutations in PIK3CA show gain of function , 2007, Proceedings of the National Academy of Sciences.

[2]  Thomas LaFramboise,et al.  Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing , 2006, Nature Medicine.

[3]  Giovanni Parmigiani,et al.  Mutational Analysis of the Tyrosine Phosphatome in Colorectal Cancers , 2004, Science.

[4]  S. Gabriel,et al.  EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy , 2004, Science.

[5]  R. Sclafani,et al.  Cyclin D1 overexpression vs. retinoblastoma inactivation: implications for growth control evasion in non-small cell and small cell lung cancer. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[6]  A. Iafrate,et al.  Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling , 2007, Proceedings of the National Academy of Sciences.

[7]  Laura A. Sullivan,et al.  Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer , 2007, Cell.

[8]  J. Carretero,et al.  Novel and natural knockout lung cancer cell lines for the LKB1/STK11 tumor suppressor gene , 2004, Oncogene.

[9]  J. Minna,et al.  Abnormalities in structure and expression of the human retinoblastoma gene in SCLC. , 1988, Science.

[10]  H. Aburatani,et al.  Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer , 2007, Nature.

[11]  C. D. Edwards,et al.  Reciprocal Rb inactivation and p16INK4 expression in primary lung cancers and cell lines. , 1995, Cancer research.

[12]  A. Okamoto,et al.  Variable mutations of the RB gene in small-cell lung carcinoma. , 1990, Oncogene.

[13]  Y. Mizushima,et al.  Gene analysis of K-, H-ras, p53, and retinoblastoma susceptibility genes in human lung cancer cell lines by the polymerase chain reaction/single-strand conformation polymorphism method , 2005, Journal of Cancer Research and Clinical Oncology.

[14]  E. Buckley,et al.  Oncogenic point mutations in the human retinoblastoma gene: their application to genetic counseling. , 1989, The New England journal of medicine.

[15]  F. Kaye,et al.  A single amino acid substitution results in a retinoblastoma protein defective in phosphorylation and oncoprotein binding. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[16]  S. Steinberg,et al.  Differential inactivation of CDKN2 and Rb protein in non-small-cell and small-cell lung cancer cell lines. , 1995, Journal of the National Cancer Institute.

[17]  S. Gabriel,et al.  High-throughput oncogene mutation profiling in human cancer , 2007, Nature Genetics.

[18]  K. Guan,et al.  Upstream of the mammalian target of rapamycin: do all roads pass through mTOR? , 2006, Oncogene.

[19]  S. Steinberg,et al.  RB protein status and clinical correlation from 171 cell lines representing lung cancer, extrapulmonary small cell carcinoma, and mesothelioma. , 1994, Oncogene.

[20]  G. Parmigiani,et al.  The Consensus Coding Sequences of Human Breast and Colorectal Cancers , 2006, Science.

[21]  J. Minna,et al.  Mutations of ras genes distinguish a subset of non-small-cell lung cancer cell lines from small-cell lung cancer cell lines. , 1991, Oncogene.

[22]  S. Hirohashi,et al.  Alterations of the p53 gene are common and critical events for the maintenance of malignant phenotypes in small-cell lung carcinoma. , 1992, Oncogene.

[23]  J. Ptak,et al.  High Frequency of Mutations of the PIK3CA Gene in Human Cancers , 2004, Science.

[24]  Steven P Gygi,et al.  Signaling networks assembled by oncogenic EGFR and c-Met , 2008, Proceedings of the National Academy of Sciences.

[25]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[26]  S. Rodenhuis,et al.  K‐ras oncogene activation in lung adenocarcinomas from former smokers evidence that K‐ras mutations are an early and irreversible event in the development of adenocarcinoma of the lung , 1993 .

[27]  M. Stratton,et al.  COSMIC 2005 , 2006, British Journal of Cancer.

[28]  M. Sanchez-Cespedes.  A role for LKB1 gene in human cancer beyond the Peutz–Jeghers syndrome , 2007, Oncogene.

[29]  J. Minna,et al.  NCI‐navy medical oncology branch cell line data base , 1996, Journal of cellular biochemistry. Supplement.

[30]  J. Cigudosa,et al.  Expression signatures in lung cancer reveal a profile for EGFR‐mutant tumours and identify selective PIK3CA overexpression by gene amplification , 2008, The Journal of pathology.

[31]  J. Yokota,et al.  Comprehensive analysis of p53 gene mutation characteristics in lung carcinoma with special reference to histological subtypes. , 1999, International journal of oncology.

[32]  J. Herman,et al.  A gene hypermethylation profile of human cancer. , 2001, Cancer research.

[33]  N. Hanna,et al.  MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling , 2008 .

[34]  J. Yokota,et al.  Activation of RB tumor suppressor protein and growth suppression of small cell lung carcinoma cells by reintroduction of p16INK4A gene. , 1999, International journal of oncology.

[35]  J. Minna,et al.  Prevalence and specificity of LKB1 genetic alterations in lung cancers , 2007, Oncogene.

[36]  M. Sanchez-Cespedes.  Dissecting the genetic alterations involved in lung carcinogenesis. , 2003, Lung cancer.

[37]  Jun Yokota,et al.  Frequent BRG1/SMARCA4–inactivating mutations in human lung cancer cell lines , 2008, Human mutation.

[38]  Spyro Mousses,et al.  A transforming mutation in the pleckstrin homology domain of AKT1 in cancer , 2007, Nature.

[39]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[40]  J. Yokota,et al.  Altered expression of the retinoblastoma (RB) gene in small-cell carcinoma of the lung. , 1988, Oncogene.

[41]  Patricia L. Harris,et al.  Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. , 2004, The New England journal of medicine.

[42]  S. Hirohashi,et al.  Inactivation of the retinoblastoma gene in a human lung carcinoma cell line detected by single-strand conformation polymorphism analysis of the polymerase chain reaction product of cDNA. , 1991, Oncogene.

[43]  R. Weinberg,et al.  Frequent inactivation of the retinoblastoma anti-oncogene is restricted to a subset of human tumor cells. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[44]  A. Knudson.  Mutation and cancer: statistical study of retinoblastoma. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[45]  S. Steinberg,et al.  p53 gene mutations in non-small-cell lung cancer cell lines and their correlation with the presence of ras mutations and clinical features. , 1992, Oncogene.

[46]  F. Kaye,et al.  Absence of p16INK4 protein is restricted to the subset of lung cancer lines that retains wildtype RB. , 1994, Oncogene.