Article Figures & Data
Figures
- Fig. 1.
A, clustering of 15 WTs and clinical information; B, three-dimensional clustering of these cases. The clustering of patients (using Pearson’s correlation) is based on global gene expression profiles consisting of median polished data of 5,594 well-measured spots. The tumors clustered into approximately two main groups with one group consisting of mostly tumors with high stage (stage III, IV) and the other consisting of mostly tumors with low stage (stage I, II). Among high-stage tumors, two patients who died of cancer (Wilms 6, 15) and one patient who had recurrence (Wilms 11) were closely clustered together. One patient (Wilms 14 in A and represented by orange circle in B), who had stage II disease but developed recurrence and died of cancer, was clustered with high-stage tumors. Abbreviations in A: D, died from disease; A, alive; R, recurrence; N/A, not available; NE, no evidence of recurrence.
- Fig. 2.
The 30 cDNAs that are significantly differentially expressed between high stage (stage III, IV) and low stage (stage I, II), with the clustering of the 30 cDNA expression levels. Rows, individual cDNA; columns, individual tumor samples. The color of each square, the median-polished, normalized ratio of gene expression in a tumor relative to noncancerous kidney tissue: red, expression levels greater than the median; green, expression levels below the median; black, expression levels equal to the median; gray, inadequate or missing data. The color saturation indicates the degree of divergence from the median. The estimated FDR for this set of genes (α ≤ 0.05) is 9.0%.
- Fig. 3.
Real-time relative quantitative PCR analysis of Topo IIα (A), IGF II (IB), stathmin 1 (C), Integrin α-8 (D), CRABP2 (E), DBCCR1 (F). The left side bar in black of each sample, the expression ratio of tumor to noncancerous kidney by real-time PCR; the right side bar in white, the expression ratio of tumor to noncancerous kidney by microarray experiments. Data grouped based on clinical parameters are given as the mean and the SE. They are evaluated statistically using the Mann-Whitney U test. Real-time PCR was performed in triplicate and each expression data were normalized against the endogenous control, 18S rRNA. The data were averaged and compared with microarray data. Topo IIα and IGF II express much higher in WT compared with noncancerous kidney through all of the samples by microarray and real-time PCR. Real-time PCR showed a higher expression ratio of Topo IIα(P = 0.0771) in high-stage tumors, and IGF II was significantly more highly expressed in high-stage tumors (P = 0.0251; A and B). Stathmin 1 and integrin α-8 were overexpressed in most WTs and were significantly more highly expressed in high-stage tumors (P = 0.0451 and 0.0133, respectively; C and D). CRABP2 and DBCCR1 were also overexpressed in most WTs. DBCCR1 was significantly more highly expressed in WT with poor outcome compared with reference (P = 0.0335; F) and CRABP2 tended to be more highly expressed in WT with poor outcome (P = 0.079; E). All of the real-time PCR data were consistent with microarray data.
Tables
- Table 1
Significantly overexpressed genes in WTs
Top 40 cDNAs that are significantly overexpressed in Wilms tumors (n = 15). A sign test for a one-sample mean was used to identify genes whose expression changed at least 2-fold in a significant number of samples (α ≤ 0.001).
Accession IDa Gene name Average foldb (T/N) AA026682 Topo (DNA) ii α (Mr 170,000) 80.8 H98218 high-mobility group (nonhistone chromosomal) protein 36.2 AA504348 Topo (DNA) ii α (Mr 170,000) 32.1 AA419229 G protein-coupled receptor 39 (GPR39) 25.2 AA701455 centromere protein F (Mr 350,000/400,000, mitosin) (CENPF) 25.1 AA071486 serine/threonine kinase 12 (STK12) 23.5 N67487 microfibrillar-associated protein 2 (MFAP2) 22.1 N74623 IGF II (somatomedin A) 21.9 W68220 ESTs 18.5 AA460685 baculoviral IAP repeat-containing 5 (survivin) 16.2 H73968 chromosome 20 open reading frame 1 C20orf1 15.3 N40940 transmembrane protein with EGF-like 15.3 AA598674 ESTs 14.5 AA430744 enhancer of zeste (Drosophila) homolog 2 (EZH2) 12.7 AA598945 metallocarboxypeptidase CPX-1 (CPX-1) 12.4 AA598974 not found 12.0 AA873060 stathmin 1/oncoprotein 18 (STMN1) 11.4 AA598508 CRABP2 11.2 W58368 eukaryotic translation initiation factor 2B, subunit 3 11.2 T67524 zinc finger protein 205 (ZNF205) 11.1 AA629262 ESTs 11.0 AA485665 ephrin-B3 (EFNB3), mRNA, EPHRIN B1,2,3 11.0 AA449336 ESTs 10.9 H80685 p311 10.4 AA430032 ESTs 10.4 N91887 thymosin β identified in neuroblastoma cells 10.1 N94616 laminin α 4 (LAMA4) 9.8 AA454572 minichromosome maintenance deficient (Saccharomyces cerevisiae) 2 9.5 AA700832 retinol-binding protein 1, cellular (RBP1) 9.5 T87341 ESTs 9.5 H92234 ESTs 9.3 AA102130 ectodermal-neural cortex (with BTB-like domain) 9.2 AA598610 mesoderm-specific transcript (mouse) homolog (MEST) 8.9 AA460849 mitochondrial ribosomal protein L9 8.8 R62603 collagen type VI α3 (COL6A3) 8.7 AA101875 chondroitin sulfate proteoglycan 2 (versican) (CSPG2) 8.6 R85090 ectodermal-neural cortex (with BTB-like domain) 8.4 R45941 protein tyrosine phosphatase receptor type, N 8.1 R41787 cadherin 13, H-cadherin (heart) (CDH13) 8.0 AA453170 hypothetical protein FLJ14299 7.9 -
a ID, identification.
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b Average fold shows the interquartile mean of the tumor versus non-cancerous tissue (T/N) gene expression values.
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c EST, expressed sequence tag.
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- Table 2
Differentially expressed genes between different outcome groups at 5 yearsa
A total of 80 cDNAs were found to be differentially expressed between the different outcome groups at 5 years.
Accession IDb Gene name Fold changec P FDRd (%) AA131240 EST 6.4 0.0001 0.1 AA598508 CRABP2 5.6 0.0130 3.9 AA621201 solute carrier family 30 (zinc transporter) member 3 5.2 0.0110 4.1 H10959 deleted in bladder cancer chromosome region candidate 5.1 0.0170 4.7 AA448394 Homo sapiens mRNA for KIAA1783 protein, partial cds −4.4 0.0001 0.1 AA436401 TU3A protein (TU3A) 4.2 0.0180 4.6 R98074 betaine-homocysteine methyltransferase 2 (BHMT2) −4.2 0.0001 0.1 AA454572 minichromosome maintenance deficient (Saccharomyces cerevisiae) 2 3.9 0.0093 3.1 AA252470 Homo sapiens cDNA FLJ11606 fis −3.7 0.0001 0.1 AA600214 putative integral membrane transporter (LC27) 3.7 0.0290 6.4 H93086 EST −3.5 0.0047 2.1 AA456088 EPHB3 3.4 0.0290 6.4 AA446005 DKFZP434N061 protein −3.3 0.0001 0.1 AA449463 PI-3-kinase-related kinase SMG-1 −3.3 0.0040 1.9 T94293 ESTs, highly similar to PA2X −3.3 0.0040 1.9 H21943 thymopoietin 3.2 0.0300 7.1 N91887 thymosin β identified in neuroblastoma cells 3.1 0.0360 7.1 R73672 Homo sapiens, clone IMAGE:3881549 3.1 0.0140 4.1 T67045 DKFZP434N061 protein −3.1 0.0001 0.1 N52394 hypothetical protein FLJ20008 −3 0.0300 7 N53581 phosphodiesterase 4C, cAMP-specific −3 0.0001 0.1 N21550 EST −2.9 0.0001 0.1 T86714 EST −2.9 0.0350 7 AA487590 novel human gene mapping to chromosome 13 −2.8 0.0460 8.7 H19105 ESTs, weakly similar to TNP1 2.8 0.0001 0.1 H84154 cyclin D2 (CCND2) 2.8 0.0450 8.7 W15574 EST −2.8 0.0056 2.1 AA062802 KIAA0354 KELCH-related 2.7 0.0001 0.1 AA481758 heat shock Mr 40,000 protein 1 (HSPF1) 2.7 0.0001 0.1 AA490144 EST 2.7 0.0001 0.1 H10045 vav3 oncogene (VAV3) −2.7 0.0160 4.3 R31673 EST −2.7 0.0050 2 R97226 PI-3-kinase-related kinase SMG-1 −2.7 0.0140 4 T91807 FLJ10154 −2.7 0.0001 0.1 T99793 meningioma-expressed antigen 6 −2.7 0.0040 1.9 AA429657 KIAA0080 protein 2.6 0.0240 5.6 AA478950 nuclear factor of activated T-cells 5 −2.6 0.0001 0.1 AA844831 carboxypeptidase A2 (pancreatic) (CPA2) 2.6 0.0190 4.8 N69661 TPA-regulated locus −2.6 0.0001 0.1 R55334 ESTs, weakly similar to B34087 hypothetical protein −2.6 0.0001 0.1 -
a The 40 most differential expressed cDNAs between the two groups.
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b ID, identification.
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c A positive fold change indicates the poor outcome group had relatively higher expression; a negative value indicates the good outcome group had relatively higher expression.
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d An estimate of the FDR shown for each gene.
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Volume 62, Issue 22
