Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer

John Wrangle, Emi Ota Machida, Ludmila Danilova, Alicia Hulbert, Noreli Franco, Wei Zhang, Sabine C Glöckner, Mathewos Tessema, Leander Van Neste, Hariharan Easwaran, Kornel E Schuebel, Julien Licchesi, Craig M Hooker, Nita Ahuja, Jun Amano, Steven A Belinsky, Stephen B Baylin, James G Herman, Malcolm V Brock

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

PURPOSE: 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.

EXPERIMENTAL DESIGN: 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.

CONCLUSION: 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.

Original languageEnglish
Pages (from-to)1856-1864
Number of pages9
JournalClinical Cancer Research
Volume20
Issue number7
Early online date31 Jan 2014
DOIs
Publication statusPublished - 1 Apr 2014

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Non-Small Cell Lung Carcinoma
Methylation
Lung Neoplasms
Neoplasms
Atlases
Genes
trichostatin A
Biomarkers
Genome
CpG Islands
Molecular Pathology
Adjuvant Chemotherapy
Early Detection of Cancer
Routine Diagnostic Tests
Early Diagnosis
Databases
Sensitivity and Specificity
Cell Line
Mortality

Keywords

  • Aged
  • Carcinoma, Non-Small-Cell Lung
  • CpG Islands
  • Cysteine Dioxygenase
  • DNA Methylation
  • Female
  • Homeodomain Proteins
  • Humans
  • Kaplan-Meier Estimate
  • Male
  • Middle Aged
  • Neoplasm Staging
  • Proportional Hazards Models
  • Tachykinins
  • Tumor Markers, Biological

Cite this

Wrangle, J., Machida, E. O., Danilova, L., Hulbert, A., Franco, N., Zhang, W., ... Brock, M. V. (2014). Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer. Clinical Cancer Research, 20(7), 1856-1864. https://doi.org/10.1158/1078-0432.CCR-13-2109

Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer. / Wrangle, John; Machida, Emi Ota; Danilova, Ludmila; Hulbert, Alicia; Franco, Noreli; Zhang, Wei; Glöckner, Sabine C; Tessema, Mathewos; Van Neste, Leander; Easwaran, Hariharan; Schuebel, Kornel E; Licchesi, Julien; Hooker, Craig M; Ahuja, Nita; Amano, Jun; Belinsky, Steven A; Baylin, Stephen B; Herman, James G; Brock, Malcolm V.

In: Clinical Cancer Research, Vol. 20, No. 7, 01.04.2014, p. 1856-1864.

Research output: Contribution to journalArticle

Wrangle, J, Machida, EO, Danilova, L, Hulbert, A, Franco, N, Zhang, W, Glöckner, SC, Tessema, M, Van Neste, L, Easwaran, H, Schuebel, KE, Licchesi, J, Hooker, CM, Ahuja, N, Amano, J, Belinsky, SA, Baylin, SB, Herman, JG & Brock, MV 2014, 'Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer', Clinical Cancer Research, vol. 20, no. 7, pp. 1856-1864. https://doi.org/10.1158/1078-0432.CCR-13-2109
Wrangle, John ; Machida, Emi Ota ; Danilova, Ludmila ; Hulbert, Alicia ; Franco, Noreli ; Zhang, Wei ; Glöckner, Sabine C ; Tessema, Mathewos ; Van Neste, Leander ; Easwaran, Hariharan ; Schuebel, Kornel E ; Licchesi, Julien ; Hooker, Craig M ; Ahuja, Nita ; Amano, Jun ; Belinsky, Steven A ; Baylin, Stephen B ; Herman, James G ; Brock, Malcolm V. / Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer. In: Clinical Cancer Research. 2014 ; Vol. 20, No. 7. pp. 1856-1864.
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T1 - Functional identification of cancer-specific methylation of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer

AU - Wrangle, John

AU - Machida, Emi Ota

AU - Danilova, Ludmila

AU - Hulbert, Alicia

AU - Franco, Noreli

AU - Zhang, Wei

AU - Glöckner, Sabine C

AU - Tessema, Mathewos

AU - Van Neste, Leander

AU - Easwaran, Hariharan

AU - Schuebel, Kornel E

AU - Licchesi, Julien

AU - Hooker, Craig M

AU - Ahuja, Nita

AU - Amano, Jun

AU - Belinsky, Steven A

AU - Baylin, Stephen B

AU - Herman, James G

AU - Brock, Malcolm V

PY - 2014/4/1

Y1 - 2014/4/1

N2 - PURPOSE: 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.EXPERIMENTAL DESIGN: 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.CONCLUSION: 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.

AB - PURPOSE: 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.EXPERIMENTAL DESIGN: 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.CONCLUSION: 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.

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KW - CpG Islands

KW - Cysteine Dioxygenase

KW - DNA Methylation

KW - Female

KW - Homeodomain Proteins

KW - Humans

KW - Kaplan-Meier Estimate

KW - Male

KW - Middle Aged

KW - Neoplasm Staging

KW - Proportional Hazards Models

KW - Tachykinins

KW - Tumor Markers, Biological

UR - http://dx.doi.org/10.1158/1078-0432.CCR-13-2109

U2 - 10.1158/1078-0432.CCR-13-2109

DO - 10.1158/1078-0432.CCR-13-2109

M3 - Article

VL - 20

SP - 1856

EP - 1864

JO - Clinical Cancer Research

JF - Clinical Cancer Research

SN - 1078-0432

IS - 7

ER -