Differential expression profiling analyses identifies downregulation of 1p, 6q, and 14q genes and overexpression of 6p histone cluster 1 genes as markers of recurrence in meningiomas

Abstract

The majority of meningiomas are probably benign but a number of tumors display considerable histological and/or clinical aggressivity, sometimes with unexpectedly high recurrence rates after radical removal. Understanding the potential behavior of these tumors in individual patients is critical for rational therapeutic decision-making. This study aimed to identify gene expression profiles and candidate markers associated with original and recurrent meningiomas. Unsupervised hierarchical clustering of the samples confirmed 2 main groups of meningiomas with distinct clinical behaviors. The gene expression profiling study identified genes and pathways potentially associated with meningioma recurrence, revealing an overall lower level of gene expression. The differential gene expression profiling analyses of original and recurrent meningiomas identified 425 known genes and expressed sequence tags related to meningioma recurrence, with SFRP1 (8p12), TMEM30B (14q23), and CTGF (6q23) showing the most disparate expression. Most of the differentially expressed genes were located at 1p, 6q, and 14q and were underexpressed in recurrences. Loss of such chromosomal regions has previously been associated with a higher risk of meningioma recurrence or malignant progression. Thus, at these locations, we propose the existence of novel candidate genes that could be involved in meningioma recurrence. In addition, the overexpression of genes of histone cluster 1 (6p) in recurrent meningiomas is reported here for the first time. Finally, the altered genes related to meningioma recurrence are involved in pathways such as Notch, TGFβ, and Wnt, as described previously, and in other pathways such as cell cycle, oxidative phosphorylation, PPAR, and PDGF, not related before to meningioma recurrence.

Fig. 1.

Unsupervised hierarchical cluster analysis of 44 meningiomas corresponding to all WHO grades and including 8 recurrences. Meningiomas of WHO grade I, II, and III are shown in green, orange and dark red, respectively. Recurrences are indicated with striped bars. Asterisks denote samples collected at diagnosis from original tumors that relapsed.

Fig. 2.

Validation of selected genes differentially expressed in original and recurrent meningioma by qRT–PCR analysis. (A) TMEM30B, (B) SFRP1, (C) CTGF, and (D) TGFBR3. Mean expression values related to the internal control glyceraldehyde 3-phosphate dehydrogenase (GAPDH) or TATA box binding protein (TBP) and to the mean of nontumoral meningothelial tissue pools are plotted. Box plots indicate the expression values of the 25th and 75th percentiles, and the extremes of the vertical lines represent the maximum and the minimum log₂ expression. P < .05 for all genes except for TGFBR3.

Fig. 3.

Immunohistochemistry results of 2 genes differentially expressed in original and recurrent tumors. Photomicrograph of meningioma samples with (A) positive and (B) negative expression of LMO4 (original magnification, ×400). (C) Percentage of cases with LMO4-positive expression. Photomicrograph of tumor tissue with (D) negative and (E) positive expression of HIST1H1C (original magnification, ×400). (F) Percentage of cases with HIST1H1C-positive expression.

Fig. 4.

Molecularly altered pathways related to meningioma recurrence ordered by the normalized enrichment score. This value is obtained by normalizing the enrichment score that reflects the degree to which a set of genes, S, is over-represented at the extremes (top or bottom) of an entire ranked list, L. Molecular pathways under- or overexpressed in green or red, respectively, in recurrences.

Fig. 5.

(A) Diagram of the frequency of locations of genes differentially expressed in original (O) and recurrent (R) meningiomas. (B) The locations of the genes differentially expressed (O vs R) relative to the locations of the genes in the microarray. Black bars indicate the significant and most frequent locations.

Fig. 6.

The location of the genes differentially expressed in original and recurrent meningiomas on chromosomes 1, 6, and 14, plotted according to their map position. Genes with lower (green) and higher (red) levels of expression in recurrences than in original tumors are shown on the left and the right, respectively, of the chromosome ideogram.

Fig. 7.

(A) Frequency of 1p loss in original meningioma that relapsed, nonrecurrent meningioma, and recurrences. The total numbers of evaluated tumors are shown. (B) Frequency of 1p loss in WHO grades I, II, and III. The total numbers of evaluated tumors are shown. (C) The Kaplan–Meier curves of recurrence-free survival. Curves are shown for the absence and the presence of 1p loss (n = 40 and 19, respectively; P = .020). Six recurrent events are shown.