title: NDN and CD1A are novel prognostic methylation markers in patients with head and neck squamous carcinomas.
abstract: BACKGROUND
  HPV-associated HNSCCs have a distinct etiologic mechanism and better prognosis than those with non-HPV associated HNSCCs. However, even within the each group, there is heterogeneity in survival time. Here, we test the hypothesis that specific candidate gene methylation markers (CCNA1, NDN, CD1A, DCC, p16, GADD45A) are associated with tumor recurrence and survival, in a well-characterized, prospective, cohort of 346 HNSCC patients.
  
  
  METHODS
  Kaplan-Meier curves were used to estimate survival time distributions. Multivariable Cox Proportional Hazards models were used to test associations between each methylation marker and OST/RPFT after adjusting for known or identified prognostic factors. Stratified Cox models included an interaction term between HPV and methylation marker to test for differences in the associations of the biomarker with OST or RPFT across HPV status.
  
  
  RESULTS
  Methylation markers were differentially associated with patient characteristics. DNA hypermethylation of NDN and CD1A was found to be significantly associated with overall survival time (OST) in all HNSCC patients (NDN hazard ratio (HR): 2.35, 95% CI: 1.40-3.94; CD1A HR: 1.31, 95% CI: 1.01-1.71). Stratification by HPV status revealed hypermethylation of CD1A was associated with better OST and recurrence/persistence-free time (RPFT) (OST HR: 3.34, 95% CI: 1.88-5.93; RPFT HR: 2.06, 95% CI: 1.21-3.49), while hypomethylation of CCNA1 was associated with increased RPFT in HPV (+) patients only (HR: 0.31, 95% CI: 0.13-0.74).
  
  
  CONCLUSIONS
  This study is the first to describe novel epigenetic alterations associated with survival in an unselected, prospectively collected, consecutive cohort of patients with HNSCC. DNA hypermethylation of NDN and CD1A was found to be significantly associated with increased overall survival time in all HNSCC patients. However, stratification by the important prognostic factor of HPV status revealed the immune marker, CD1A, and the cell cycle regulator, CCNA1 to be associated with prognosis in HPV (+) patients, specifically. Here, we identified novel methylation markers and specific, epigenetic molecular differences associated with HPV status, which warrant further investigation.
authors.affiliation: Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA. shamav@umich.edu.
authors.forename: Shama
authors.initials: S
authors.lastname: Virani
authors.affiliation: Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA. lighte@med.umich.edu.
authors.forename: Emily
authors.initials: E
authors.lastname: Bellile
authors.affiliation: Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. cbradfor@umich.edu.
authors.forename: Carol R
authors.initials: CR
authors.lastname: Bradford
authors.affiliation: Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. careyte@med.umich.edu.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Carey
authors.affiliation: Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. douglas.chepeha@uhn.ca.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Chepeha
authors.affiliation: Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA. colacino@umich.edu.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Colacino
authors.affiliation: Department of Oral-Maxillofacial Surgery, University of Michigan Dental School, Ann Arbor, MI, USA. jihelman@umich.edu.|Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA. jihelman@umich.edu.
authors.forename: Joseph I
authors.initials: JI
authors.lastname: Helman
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA. jonamch@med.umich.edu.
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: McHugh
authors.affiliation: Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. peterlis@med.umich.edu.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Peterson
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. sartorma@umich.edu.
authors.forename: Maureen A
authors.initials: MA
authors.lastname: Sartor
authors.affiliation: Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA. jmgt@umich.edu.
authors.forename: Jeremy Mg
authors.initials: JM
authors.lastname: Taylor
authors.affiliation: Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. hwalline@umich.edu.
authors.forename: Heather M
authors.initials: HM
authors.lastname: Walline
authors.affiliation: Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. Gregwolf@med.umich.edu.
authors.forename: Greg T
authors.initials: GT
authors.lastname: Wolf
authors.affiliation: Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA. rozekl@umich.edu.|Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, MI, USA. rozekl@umich.edu.|1415 Washington Heights, Environmental Health Sciences 6630 SPH, Ann Arbor, MI, 48109-2029, USA. rozekl@umich.edu.
authors.forename: Laura S
authors.initials: LS
authors.lastname: Rozek
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D018949:Antigens, CD1 / Q000235:genetics*; D014408:Biomarkers, Tumor; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics* / Q000401:mortality* / Q000821:virology; D015897:Comorbidity; D019175:DNA Methylation; D005260:Female; D006258:Head and Neck Neoplasms / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics* / Q000401:mortality* / Q000821:virology; D006801:Humans; D008297:Male; D008875:Middle Aged; D009364:Neoplasm Recurrence, Local; D009367:Neoplasm Staging; D009419:Nerve Tissue Proteins / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics*; D011379:Prognosis; D012307:Risk Factors; D000077195:Squamous Cell Carcinoma of Head and Neck
chemical_list: D018949:Antigens, CD1; D014408:Biomarkers, Tumor; C419393:CD1a antigen; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; C069766:necdin