Portrait of ependymoma recurrence in children: biomarkers of tumor progression identified by dual-color microarray-based gene expression analysis.
BACKGROUND
Children with ependymoma may experience a relapse in up to 50% of cases depending on the extent of resection. Key biological events associated with recurrence are unknown.


RESULTS
To discover the biology behind the recurrence of ependymomas, we performed CGHarray and a dual-color gene expression microarray analysis of 17 tumors at diagnosis co-hybridized with the corresponding 27 first or subsequent relapses from the same patient. As treatment and location had only limited influence on specific gene expression changes at relapse, we established a common signature for relapse. Eighty-seven genes showed an absolute fold change ≥2 in at least 50% of relapses and were defined as the gene expression signature of ependymoma recurrence. The most frequently upregulated genes are involved in the kinetochore (ASPM, KIF11) or in neural development (CD133, Wnt and Notch pathways). Metallothionein (MT) genes were downregulated in up to 80% of the recurrences. Quantitative PCR for ASPM, KIF11 and MT3 plus immunohistochemistry for ASPM and MT3 confirmed the microarray results. Immunohistochemistry on an independent series of 24 tumor pairs at diagnosis and at relapse confirmed the decrease of MT3 expression at recurrence in 17/24 tumor pairs (p = 0.002). Conversely, ASPM expression was more frequently positive at relapse (87.5% vs 37.5%, p = 0.03). Loss or deletion of the MT genes cluster was never observed at relapse. Promoter sequencing after bisulfite treatment of DNA from primary tumors and recurrences as well as treatment of short-term ependymoma cells cultures with a demethylating agent showed that methylation was not involved in MT3 downregulation. However, in vitro treatment with a histone deacetylase inhibitor or zinc restored MT3 expression.


CONCLUSIONS
The most frequent molecular events associated with ependymoma recurrence were over-expression of kinetochore proteins and down-regulation of metallothioneins. Metallothionein-3 expression is epigenetically controlled and can be restored in vitro by histone deacetylase inhibitors.
Peyre
Matthieu
M
Université Paris-Sud, CNRS UMR 8203 Vectorology and Anticancer Treatments, Gustave Roussy Institute, Villejuif, France.
Commo
Frédéric
F
Dantas-Barbosa
Carmela
C
Andreiuolo
Felipe
F
Puget
Stéphanie
S
Lacroix
Ludovic
L
Drusch
Françoise
F
Scott
Véronique
V
Varlet
Pascale
P
Mauguen
Audrey
A
Dessen
Philippe
P
Lazar
Vladimir
V
Vassal
Gilles
G
Grill
Jacques
J
D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D002648:Child; D002675:Child, Preschool; D018450:Disease Progression; D004806:Ependymoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007223:Infant; D008297:Male; D008668:Metallothionein / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation; D012008:Recurrence
D014408:Biomarkers, Tumor; D008668:Metallothionein