A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies.
BACKGROUND
Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets.


RESULTS
In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5' CpG islands, are induced from undetectable levels by 5-aza-2'-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors.


CONCLUSIONS
By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests that we have identified a partial promoter hypermethylation signature for these common malignancies. These data suggest that while tumors in different tissues vary substantially with respect to gene expression, there may be commonalities in their promoter methylation profiles that represent targets for early detection screening or therapeutic intervention.
Shames
David S
DS
Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America.
Girard
Luc
L
Gao
Boning
B
Sato
Mitsuo
M
Lewis
Cheryl M
CM
Shivapurkar
Narayan
N
Jiang
Aixiang
A
Perou
Charles M
CM
Kim
Young H
YH
Pollack
Jonathan R
JR
Fong
Kwun M
KM
Lam
Chi-Leung
CL
Wong
Maria
M
Shyr
Yu
Y
Nanda
Rita
R
Olopade
Olufunmilayo I
OI
Gerald
William
W
Euhus
David M
DM
Shay
Jerry W
JW
Gazdar
Adi F
AF
Minna
John D
JD
D000230:Adenocarcinoma / Q000235:genetics; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D001943:Breast Neoplasms / Q000235:genetics; D018196:Carcinoma, Adenosquamous / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics; D056657:Cathepsin K; D002403:Cathepsins / Q000235:genetics; D003110:Colonic Neoplasms / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D019925:Cyclin A / Q000235:genetics; D056750:Cyclin A1; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000037:antagonists & inhibitors; D004268:DNA-Binding Proteins / Q000235:genetics; D000077209:Decitabine; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D051957:MSX1 Transcription Factor / Q000235:genetics; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011471:Prostatic Neoplasms / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014407:Tumor Cells, Cultured
C503745:CCNA1 protein, human; D019925:Cyclin A; D056750:Cyclin A1; D004268:DNA-Binding Proteins; D051957:MSX1 Transcription Factor; C484083:MSX1 protein, human; D014157:Transcription Factors; C077914:BNC1 protein, human; D000077209:Decitabine; D015254:DNA Modification Methylases; D002403:Cathepsins; C534130:CTSK protein, human; D056657:Cathepsin K; D001374:Azacitidine