Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.
Cervical cancer is a major health concern among women in Latin America due to its high incidence and mortality. Therefore, the discovery of molecular markers for cervical cancer screening and triage is imperative. The aim of this study was to use a genome wide DNA methylation approach to identify novel methylation biomarkers in cervical cancer. DNA from normal cervical mucosa and cervical cancer tissue samples from Chile was enriched with Methylated DNA Immunoprecipitation (MeDIP), hybridized to oligonucleotide methylation microarrays and analyzed with a stringent bioinformatics pipeline to identify differentially methylated regions (DMRs) as candidate biomarkers. Quantitative Methylation Specific PCR (qMSP) was used to study promoter methylation of candidate DMRs in clinical samples from two independent cohorts. HPV detection and genotyping were performed by Reverse Line Blot analysis. Bioinformatics analysis revealed GGTLA4, FKBP6, ZNF516, SAP130, and INTS1 to be differentially methylated in cancer and normal tissues in the Discovery cohort. In the Validation cohort FKBP6 promoter methylation had 73% sensitivity and 80% specificity (AUC = 0.80). ZNF516 promoter methylation was the best biomarker, with both sensitivity and specificity of 90% (AUC = 0.92), results subsequently corroborated in a Prevalence cohort. Together, ZNF516 and FKBP6 exhibited a sensitivity of 84% and specificity of 81%, when considering both cohorts. Our genome wide DNA methylation assessment approach (MeDIP-chip) successfully identified novel biomarkers that differentiate between cervical cancer and normal samples, after adjusting for age and HPV status. These biomarkers need to be further explored in case-control and prospective cohorts to validate them as cervical cancer biomarkers.
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile.
Priscilla
P
Brebi
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA.
Leonel
L
Maldonado
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Gynecologic Oncology; University Medical Center Groningen; Groningen, the Netherlands.
Maartje G
MG
Noordhuis
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile.
Carmen
C
Ili
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile.
Pamela
P
Leal
School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile.
Patricia
P
Garcia
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Clinical Research Coordination; Instituto Nacional de Câncer; Rio de Janeiro, Brazil.
Mariana
M
Brait
Pharmacology Unit; Department of Experimental Medicine; University of Lleida; Lleida, Spain.
Judit
J
Ribas
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA.
Christina
C
Michailidi
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA.
Jimena
J
Perez
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA.
Ethan
E
Soudry
School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile.
Oscar
O
Tapia
School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile.
Pablo
P
Guzman
School of Medicine; Department of Public Health; Universidad de La Frontera; Temuco, Chile.
Sergio
S
Muñoz
MDxHealth PharmacoDx; Ghent, Belgium.
Leander
L
Van Neste
MDxHealth PharmacoDx; Ghent, Belgium; BIOBIX; Department of Bioscience Engineering; Ghent University; Ghent Belgium.
Wim
W
Van Criekinge
Bloomberg School of Public Health; Biostatistics Department; The Johns Hopkins University; Baltimore, MD USA.
Rafael
R
Irizarry
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA.
David
D
Sidransky
School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile; School of Medicine; Department of Pathology; Pontificia Universidad Católica de Chile; Santiago, Chile.
Juan C
JC
Roa
Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA.
Rafael
R
Guerrero-Preston
D000328:Adult; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D002677:Chile; D019175:DNA Methylation; D005260:Female; D015894:Genome, Human; D052161:Human papillomavirus 18; D006801:Humans; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D022021:Tacrolimus Binding Proteins / Q000235:genetics* / Q000378:metabolism; D002583:Uterine Cervical Neoplasms / Q000208:ethnology / Q000235:genetics* / Q000821:virology; D016335:Zinc Fingers
D014408:Biomarkers, Tumor; C115725:FKBP6 protein, human; D022021:Tacrolimus Binding Proteins
MeDIP; biomarkers; cervical cancer; companion diagnostics; promoter methylation