title: Gene expression profiling of primary cutaneous melanoma and clinical outcome.
abstract: BACKGROUND
  Gene expression profiling data for human primary cutaneous melanomas are scarce because of the lack of retrospective collections of frozen tumors. To identify differentially expressed genes that may be involved in melanoma progression and prognosis, we investigated the relationship between gene expression profiles and clinical outcome in a cohort of patients with primary melanoma.
  
  
  METHODS
  Labeled complementary RNA (cRNA) from each tissue sample was hybridized to a pangenomic 44K 60-mer oligonucleotide microarray. Class comparison and class prediction analyses were performed to identify genes whose expression in primary melanomas was associated with 4-year distant metastasis-free survival among 58 patients with at least 4 years of follow-up, distant metastasis, or death. Results were validated immunohistochemically at the protein level in 176 independent primary melanomas from patients with a median clinical follow-up of 8.5 years. Survival was analyzed with a Cox multivariable model and stratified log-rank test. All statistical tests were two-sided.
  
  
  RESULTS
  We identified 254 genes that were associated with distant metastasis-free survival of patients with primary melanoma. These 254 genes include genes involved in activating DNA replication origins, such as minichromosome maintenance genes and geminin. Twenty-three of these genes were studied at the protein level; expression of five (MCM4, P = .002; MCM3, P = .030; MCM6, P = .004; KPNA2, P = .021; and geminin, P = .004) was statistically significantly associated with overall survival in the validation set. In a multivariable Cox model adjusted for tumor thickness, ulceration, age, and sex, expression of MCM4 (hazard ratio [HR] of death = 4.04, 95% confidence interval [CI] = 1.39 to 11.76; P = .010) and MCM6 (HR of death = 7.42, 95% CI = 1.99 to 27.64; P = .003) proteins was still statistically significantly associated with overall survival.
  
  
  CONCLUSIONS
  We identified 254 genes whose expression was associated with metastatic dissemination of cutaneous melanomas. These genes may shed light on the molecular mechanisms underlying poor prognosis in melanoma patients.
authors.affiliation: Department of Pathology, Gustave-Roussy Institute, 94805 Villejuif Cedex, France. spatz@igr.fr.
authors.forename: Véronique
authors.initials: V
authors.lastname: Winnepenninckx
authors.forename: Vladimir
authors.initials: V
authors.lastname: Lazar
authors.forename: Stefan
authors.initials: S
authors.lastname: Michiels
authors.forename: Philippe
authors.initials: P
authors.lastname: Dessen
authors.forename: Marguerite
authors.initials: M
authors.lastname: Stas
authors.forename: Soledad R
authors.initials: SR
authors.lastname: Alonso
authors.forename: Marie-Françoise
authors.initials: MF
authors.lastname: Avril
authors.forename: Pablo L
authors.initials: PL
authors.lastname: Ortiz Romero
authors.forename: Thomas
authors.initials: T
authors.lastname: Robert
authors.forename: Ovidiu
authors.initials: O
authors.lastname: Balacescu
authors.forename: Alexander M M
authors.initials: AM
authors.lastname: Eggermont
authors.forename: Gilbert
authors.initials: G
authors.lastname: Lenoir
authors.forename: Alain
authors.initials: A
authors.lastname: Sarasin
authors.forename: Thomas
authors.initials: T
authors.lastname: Tursz
authors.forename: Joost J
authors.initials: JJ
authors.lastname: van den Oord
authors.forename: Alain
authors.initials: A
authors.lastname: Spatz
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000235:genetics; D018797:Cell Cycle Proteins / Q000032:analysis* / Q000235:genetics; D002455:Cell Division; D002648:Child; D002675:Child, Preschool; D015331:Cohort Studies; D004268:DNA-Binding Proteins / Q000032:analysis; D018572:Disease-Free Survival; D005260:Female; D005500:Follow-Up Studies; D064248:Geminin; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007150:Immunohistochemistry; D007223:Infant; D008297:Male; D008545:Melanoma / Q000737:chemistry* / Q000235:genetics / Q000401:mortality / Q000473:pathology*; D008875:Middle Aged; D064126:Minichromosome Maintenance Complex Component 3; D064148:Minichromosome Maintenance Complex Component 4; D064151:Minichromosome Maintenance Complex Component 6; D015999:Multivariate Analysis; D009687:Nuclear Proteins / Q000032:analysis; D020411:Oligonucleotide Array Sequence Analysis; D011237:Predictive Value of Tests; D011379:Prognosis; D016016:Proportional Hazards Models; D018075:RNA, Complementary / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012878:Skin Neoplasms / Q000737:chemistry* / Q000235:genetics / Q000401:mortality / Q000473:pathology*; D016019:Survival Analysis; D015854:Up-Regulation; D028901:alpha Karyopherins / Q000032:analysis
chemical_list: D014408:Biomarkers, Tumor; D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; C577995:GMNN protein, human; D064248:Geminin; C066470:MCM3 protein, human; D009687:Nuclear Proteins; D018075:RNA, Complementary; D028901:alpha Karyopherins; C087978:karyopherin alpha 2; C099243:MCM4 protein, human; C103258:MCM6 protein, human; D064126:Minichromosome Maintenance Complex Component 3; D064148:Minichromosome Maintenance Complex Component 4; D064151:Minichromosome Maintenance Complex Component 6