Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer.
OBJECTIVE
Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality in the world. Novel diagnostic biomarkers may augment both existing NSCLC screening methods as well as molecular diagnostic tests of surgical specimens to more accurately stratify and stage candidates for adjuvant chemotherapy. Hypermethylation of CpG islands is a common and important alteration in the transition from normal tissue to cancer.


METHODS
Following previously validated methods for the discovery of cancer-specific hypermethylation changes, we treated eight NSCLC cell lines with the hypomethylating agent deoxyazacitidine or trichostatin A. We validated the findings using a large publicly available database and two independent cohorts of primary samples.


RESULTS
We identified >300 candidate genes. Using The Cancer Genome Atlas (TCGA) and extensive filtering to refine our candidate genes for the greatest ability to distinguish tumor from normal, we define a three-gene panel, CDO1, HOXA9, and TAC1, which we subsequently validate in two independent cohorts of primary NSCLC samples. This three-gene panel is 100% specific, showing no methylation in 75 TCGA normal and seven primary normal samples and is 83% to 99% sensitive for NSCLC depending on the cohort.


CONCLUSIONS
This degree of sensitivity and specificity may be of high value to diagnose the earliest stages of NSCLC. Addition of this three-gene panel to other previously validated methylation biomarkers holds great promise in both early diagnosis and molecular staging of NSCLC.
Authors' Affiliations: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland; Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; MDxHealth Inc, Irvine, California; Shinshu University School of Medicine, Asahi, Matsumoto, Nagano, Japan; and Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
John
J
Wrangle
Emi Ota
EO
Machida
Ludmila
L
Danilova
Alicia
A
Hulbert
Noreli
N
Franco
Wei
W
Zhang
Sabine C
SC
Glöckner
Mathewos
M
Tessema
Leander
L
Van Neste
Hariharan
H
Easwaran
Kornel E
KE
Schuebel
Julien
J
Licchesi
Craig M
CM
Hooker
Nita
N
Ahuja
Jun
J
Amano
Steven A
SA
Belinsky
Stephen B
SB
Baylin
James G
JG
Herman
Malcolm V
MV
Brock
D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D002289:Carcinoma, Non-Small-Cell Lung / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D018899:CpG Islands / Q000235:genetics; D050558:Cysteine Dioxygenase / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics; D005260:Female; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D016016:Proportional Hazards Models; D015320:Tachykinins / Q000235:genetics*
D014408:Biomarkers, Tumor; D018398:Homeodomain Proteins; D015320:Tachykinins; C097899:homeobox protein HOXA9; C579734:CDO1 protein, human; D050558:Cysteine Dioxygenase