CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer.
BACKGROUND
CDKN2A (p16) inactivation is common in lung cancer and occurs via homozygous deletions, methylation of promoter region, or point mutations. Although p16 promoter methylation has been linked to KRAS mutation and smoking, the associations between p16 inactivation mechanisms and other common genetic mutations and smoking status are still controversial or unknown.


METHODS
We determined all three p16 inactivation mechanisms with the use of multiple methodologies for genomic status, methylation, RNA, and protein expression, and correlated them with EGFR, KRAS, STK11 mutations and smoking status in 40 cell lines and 45 tumor samples of primary non-small-cell lung carcinoma. We also performed meta-analyses to investigate the impact of smoke exposure on p16 inactivation.


RESULTS
p16 inactivation was the major mechanism of RB pathway perturbation in non-small-cell lung carcinoma, with homozygous deletion being the most frequent method, followed by methylation and the rarer point mutations. Inactivating mechanisms were tightly correlated with loss of mRNA and protein expression. p16 inactivation occurred at comparable frequencies regardless of mutational status of EGFR, KRAS, and STK11, however, the major inactivation mechanism of p16 varied. p16 methylation was linked to KRAS mutation but was mutually exclusive with EGFR mutation. Cell lines and tumor samples demonstrated similar results. Our meta-analyses confirmed a modest positive association between p16 promoter methylation and smoking.


CONCLUSIONS
Our results confirm that all the inactivation mechanisms are truly associated with loss of gene product and identify specific associations between p16 inactivation mechanisms and other genetic changes and smoking status.
*Hamon Center for Therapeutic Oncology Research and †Division of Biostatistics, University of Texas Southwestern Medical Center, Dallas, Texas; ‡Department of Integrative Oncology, British Columbia Cancer Agency Research Centre, Vancouver, B.C., Canada; §Texas Scottish Rite Hospital for Children, Dallas, Texas; ‖Department of Surgery, Biochemistry, and Molecular Biology, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, Los Angeles, California; ¶Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; #Oncology Biomarker Development, Genentech Inc., South San Francisco, California; **Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Dallas, Texas; and ††Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas.
Kit W
KW
Tam
Wei
W
Zhang
Junichi
J
Soh
Victor
V
Stastny
Min
M
Chen
Han
H
Sun
Kelsie
K
Thu
Jonathan J
JJ
Rios
Chenchen
C
Yang
Crystal N
CN
Marconett
Suhaida A
SA
Selamat
Ite A
IA
Laird-Offringa
Ayumu
A
Taguchi
Samir
S
Hanash
David
D
Shames
Xiaotu
X
Ma
Michael Q
MQ
Zhang
Wan L
WL
Lam
Adi
A
Gazdar
D006801:Humans; D000230:Adenocarcinoma / Q000235:genetics / Q000473:pathology; D000091162:AMP-Activated Protein Kinase Kinases; D018196:Carcinoma, Adenosquamous / Q000235:genetics / Q000473:pathology; D018287:Carcinoma, Large Cell / Q000235:genetics / Q000473:pathology; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics / Q000473:pathology; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics; D019175:DNA Methylation; D066246:ErbB Receptors / Q000235:genetics; D008175:Lung Neoplasms / Q000235:genetics / Q000473:pathology; D009154:Mutation / Q000235:genetics; D011379:Prognosis; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins / Q000235:genetics; D012907:Smoking / Q000009:adverse effects; D014407:Tumor Cells, Cultured
D000091162:AMP-Activated Protein Kinase Kinases; D019941:Cyclin-Dependent Kinase Inhibitor p16; C512478:EGFR protein, human; D066246:ErbB Receptors; C117307:KRAS protein, human; D017346:Protein Serine-Threonine Kinases; D011518:Proto-Oncogene Proteins; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins; C109790:STK11 protein, human