A robust method for estimating gene expression states using Affymetrix microarray probe level data.

BACKGROUND: Microarray technology is a high-throughput method for measuring the expression levels of thousand of genes simultaneously. The observed intensities combine a non-specific binding, which is a major disadvantage with microarray data. The Affymetrix GeneChip assigned a mismatch (MM) probe with the intention of measuring non-specific binding, but various opinions exist regarding usefulness of MM measures. It should be noted that not all observed intensities are associated with expressed genes and many of those are associated with unexpressed genes, of which measured values express mere noise due to non-specific binding, cross-hybridization, or stray signals. The implicit assumption that all genes are expressed leads to poor performance of microarray data analyses. We assume two functional states of a gene - expressed or unexpressed - and propose a robust method to estimate gene expression states using an order relationship between PM and MM measures. RESULTS: An indicator 'probability of a gene being expressed' was obtained using the number of probe pairs within a probe set where the PM measure exceeds the MM measure. We examined the validity of the proposed indicator using Human Genome U95 data sets provided by Affymetrix. The usefulness of 'probability of a gene being expressed' is illustrated through an exploration of candidate genes involved in neuroblastoma prognosis. We identified the candidate genes for which expression states differed (un-expressed or expressed) when compared between two outcomes. The validity of this result was subsequently confirmed by quantitative RT-PCR. CONCLUSION: The proposed qualitative evaluation, 'probability of a gene being expressed', is a useful indicator for improving microarray data analysis. It is useful to reduce the number of false discoveries. Expression states - expressed or unexpressed - correspond to the most fundamental gene function 'On' and 'Off', which can lead to biologically meaningful results.

Surgical intervention for patent ductus venosus.

Patent ductus venosus (PDV) is a rare condition, which usually presents secondary to hepatic atrophy and hepatic failure. We have treated eight cases of PDV, all with hypergalactosemia and hyperbilirubinemia. Ultrasonography and three-dimensional computed tomography demonstrated communication between the portal vein and the inferior vena cava. Of the eight PDV cases, three from the older age group (ages 9, 11, and 14 years) had high-density lesions in their brain nucleus, and one case (age 19 years) had undergone prior Kasai portoenterostomy for biliary atresia. Six PDV patients underwent ligation of PDV and the remaining two cases underwent partial banding of PDV with intraoperative monitoring to maintain portal vein pressure (PVP) under 30 cm H(2)O. Improvement of the intrahepatic portal vein flow was achieved by ligation or banding of PDV. Postoperatively, serum galactose and bilirubin fell to normal ranges, but portal thrombus occurred postoperatively in the first case. We subsequently administered postoperative anticoagulation in the remaining cases and experienced no major complications. These results suggest that PDV ligation and banding are effective surgical approaches for patients with PDV. Close postoperative monitoring to avoid portal thrombus is imperative in these cases.

Detection of CpG island hypermethylation of caspase-8 in neuroblastoma using an oligonucleotide array.

BACKGROUND: The caspase-8 gene (CASP8) is frequently inactivated in unfavorable neuroblastomas through DNA methylation. The present study utilized oligoarrays to evaluate the methylation status of a CpG island located between exons 2 and 3 of caspase 8 in neuroblastomas. PROCEDURE: DNA derived from 70 neuroblastomas was amplified by PCR after bisulfate modification and subjected to analysis on a self-made oligoarray that utilized a polycarbodiimide-coated slide to detect methylation of six intragenic CpG islands of caspase 8. In 30 cases, the methylation status was also analyzed by sequencing. In six cases, the PCR product was cloned into a vector and analyzed. RESULTS: Among the 70 tumor-derived DNAs, methylation was not detected in 18 cases, one methylated CpG was found in 12 cases, two in 18 cases, three in 3 cases, four in 8 cases, five in 1 case and six in 10 cases. All methylated CpG loci detected by sequencing were detected by oligoarray, but some methylated CpGs in three loci were detected by oligoarray alone. In these discrepant loci, methylation was detected in some clones after subcloning, indicating that the oligoarray might be more sensitive than sequencing. The CASP8 expression level was depressed in the tumors having two distinct CpG doublets. These results were significantly correlated with MYCN amplification and with clinical outcomes. CONCLUSIONS: A significant difference in the methylation status within the CpG island of CASP8 was shown between favorable and unfavorable subtypes, and CASP8 methylation detected by oligoarray may be useful in the clinical evaluation of neuroblastomas.

Evaluation of genes identified by microarray analysis in favorable neuroblastoma.

PURPOSE: The biological heterogeneity of neuroblastoma results in a varied outcome ranging from spontaneous regression to fatal tumor progression. Microarray expression profiling and genetic polymorphism arrays may help identify key genes that differ in aggressive neuroblastomas from those observed in tumors associated with a favorable outcome. METHODS: Total RNA was extracted from 16 neuroblastomas obtained from patients who subsequently died of the disease and from 16 favorable neuroblastomas and analyzed using a human whole genome oligomicroarray (55K CodeLink). Genes overexpressed in favorable tumors were subsequently analyzed in 121 neuroblastoma tumors obtained before chemotherapy using real-time RT-PCR. And among these cases, expression levels of these genes were also analyzed in 20 tumors obtained after chemotherapy. RESULTS: Oligomicroarray analysis revealed the overexpression of 283 genes in favorable tumors that were associated with either regressing or maturing tumors. Three candidate genes, including DHRS3, NROB1, and CYP26A1, were selected that were significantly overexpressed in favorable tumors by quantitative real-time RT-PCR (P < 0.01). No cases with overexpression of all three genes showed poor outcomes. In 20 post-chemotherapeutic tumors, the expression levels of these genes increased in the cases where patients survived but decreased in the fatal cases. CONCLUSIONS: Using microarray expression profiling, we identified genes that exhibit altered gene expression in neuroblastoma tumors associated with a favorable outcome. These candidates warrant further study for use in risk assessment and/or as therapeutic targets in neuroblastoma.

Clinical feature of anaplastic lymphoma kinase-mutated neuroblastoma.

PURPOSE: Anaplastic lymphoma kinase (ALK) has recently been identified as a gene conferring a predisposition for neuroblastoma. We have analyzed tyrosine kinase domain mutations and amplification/expression of the ALK gene and focused on clinical features of neuroblastoma cases with ALK aberrations. METHODS: The frequency of ALK mutations, copy number gain, and expression were analyzed in 538 neuroblastoma tumors derived from 361 cases, including 161 cases detected by mass screening. These cases were analyzed according to clinicopathologic features including the International Neuroblastoma Staging System and patient outcomes. RESULTS: Three cases (0.8%) had ALK amplification, and 16 cases (5.2%) had missense mutations at positions F1174, F1245, D1249, and R1275. Among them, 7 cases were diagnosed at more than 14 months of age, and 11 cases were infants, including 9 cases detected by mass screening and 1 multiple neuroblastoma with a germline mutation. Of the 11 infants, 3 cases relapsed, and 1 case died of disease. Among cases detected by screening, activated ALK cases showed significantly worse prognosis (P = .002). Of 7 older cases, 5 had MYC amplifications, and 5 died of disease. The expression levels of ALK were up-regulated in cases with unfavorable outcomes. In cases with activated ALK neuroblastoma, survival rates of patients detected by screening were significantly better than those in the clinically detected group (P = .025). CONCLUSIONS: The results of the present study support the hypothesis that activated ALK tumors represent a specific subset of neuroblastomas. These tumors usually develop in infants and may have a high capacity for recurrence.

Wnt signaling and telomerase activation of hepatoblastoma: correlation with chemosensitivity and surgical resectability.

PURPOSE: Recently, it became apparent that telomerase directly modulated Wnt signaling as a cofactor in a ß-catenin transcriptional complex. In this study, we investigated Wnt/ß-catenin signaling and telomerase activation in hepatoblastoma (HBL). METHODS: Tumors derived from 56 HBL cases treated with the Japanese Study Group for Pediatric Liver Tumors (JPLT) Protocol-2 were analyzed for oncogenic mutations (missense mutations and interstitial deletions in the third exon) of the CTNNB1 gene-encoding ß-catenin and for the expression levels of telomerase reverse transcriptase (TERT). RESULTS: Oncogenic mutations of CTNNB1 were detected in 42 cases (75%). The expression levels of TERT were significantly higher in 14 cases without mutation (P < .05) and in 8 cases with metastasis (P < .01). Interestingly, Wnt/ß-catenin target genes were significantly activated in the tumors without mutations (P = .013). In cases with mutations, preoperative chemotherapy was more effective (P = .008), and complete resection rate was higher (P = .034). Consequently, 2 patients with mutations and 4 patients without mutations died of disease (P = .013). High expression of TERT was detected in all tumors of these dead patients. CONCLUSIONS: Wnt/ß-catenin signaling in the HBLs without CTNNB1 mutations was activated by high expression of TERT. The clinical courses in HBLs without CTNNB1 mutations seemed to be unfavorable because of chemoresistance and low rates of resectability.

Telomere biology in neuroblastoma: telomere binding proteins and alternative strengthening of telomeres.

PURPOSE: Neuroblastoma (NBL) shows remarkable biologic heterogeneity, resulting in favorable or unfavorable prognoses. Previously, we reported that most unfavorable NBLs express high telomerase activity to maintain telomere length. Recently, telomere binding proteins (TBPs) and alternative lengthening of telomeres (ALTs) have been identified as key factors of telomere maintenance. METHODS: To evaluate the correlation between telomerase activity, telomere length, and the expression levels of TBPs in NBL, we analyzed and quantified these factors in 121 untreated NBLs. RESULTS: Shortened and elongated telomeres were detected in 21 (17.3%) and 11 cases (9.0%), respectively, and there was a significant correlation between telomere length and the length of the 3'-overhang. The tumors with shortened or elongated telomeres showed significant lower expression of TBPs, except for RAP1. Although telomerase activity did not correlate with telomere length, 16 of 22 cases with high telomerase activity and 5 of 9 cases (ALT tumors) that showed long telomeres without high telomerase activity resulted in death. High-dose chemotherapy did not have much effect on these deceased ALT cases, but their survival periods were more than 2 years and relatively long compared with the deceased cases with nonelongated telomeres, suggesting that chemoresistance in ALT tumors may be related to slow growth rates. CONCLUSIONS: High telomerase activity is a poor prognostic factor in NBL. In the cases without high telomerase activity, those with elongated telomere also showed poor outcomes because of chemoresistance. Therefore, ALT and TBPs may be biomarkers for chemosensitivity in NBL. Thus, a better understanding of telomere biology may help define the characteristics of individual NBLs.