Gene expression profiling of primary cutaneous melanoma and clinical outcome.
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.
Winnepenninckx
Véronique
V
Department of Pathology, Gustave-Roussy Institute, 94805 Villejuif Cedex, France. spatz@igr.fr.
Lazar
Vladimir
V
Michiels
Stefan
S
Dessen
Philippe
P
Stas
Marguerite
M
Alonso
Soledad R
SR
Avril
Marie-Françoise
MF
Ortiz Romero
Pablo L
PL
Robert
Thomas
T
Balacescu
Ovidiu
O
Eggermont
Alexander M M
AM
Lenoir
Gilbert
G
Sarasin
Alain
A
Tursz
Thomas
T
van den Oord
Joost J
JJ
Spatz
Alain
A
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
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