Classification of neuroblastoma patients by published gene-expression markers reveals a low sensitivity for unfavorable courses of MYCN non-amplified disease.

Currently, Pubmed lists 385 marker genes for neuroblastoma outcome. Using a customized neuroblastoma-microarray, we evaluated the prognostic impact of the gene-expression pattern of 349 of these candidates (90.6%) in 127 neuroblastoma patients with divergent outcome. By significance analysis of microarrays (SAM) and both uncorrected and Bonferroni-corrected ANOVA, 166/349 (47.5%), 218/349 (62.5%) and 128/349 (36.4%) candidates showed significant differential expression between patients with contrasting outcome. By Prediction Analysis for Microarrays (PAM), a 38-gene-classifier was derived from all markers, which classified patients outcome with an overall accuracy of 78.5%. However, patients with unfavorable outcome of MYCN non-amplified disease were largely misclassified (accuracy: 35%), suggesting that these courses are not identified by current marker genes.

Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification.

PURPOSE: To develop a gene expression-based classifier for neuroblastoma patients that reliably predicts courses of the disease. PATIENTS AND METHODS: Two hundred fifty-one neuroblastoma specimens were analyzed using a customized oligonucleotide microarray comprising 10,163 probes for transcripts with differential expression in clinical subgroups of the disease. Subsequently, the prediction analysis for microarrays (PAM) was applied to a first set of patients with maximally divergent clinical courses (n = 77). The classification accuracy was estimated by a complete 10-times-repeated 10-fold cross validation, and a 144-gene predictor was constructed from this set. This classifier's predictive power was evaluated in an independent second set (n = 174) by comparing results of the gene expression-based classification with those of risk stratification systems of current trials from Germany, Japan, and the United States. RESULTS: The first set of patients was accurately predicted by PAM (cross-validated accuracy, 99%). Within the second set, the PAM classifier significantly separated cohorts with distinct courses (3-year event-free survival [EFS] 0.86 +/- 0.03 [favorable; n = 115] v 0.52 +/- 0.07 [unfavorable; n = 59] and 3-year overall survival 0.99 +/- 0.01 v 0.84 +/- 0.05; both P < .0001) and separated risk groups of current neuroblastoma trials into subgroups with divergent outcome (NB2004: low-risk 3-year EFS 0.86 +/- 0.04 v 0.25 +/- 0.15, P < .0001; intermediate-risk 1.00 v 0.57 +/- 0.19, P = .018; high-risk 0.81 +/- 0.10 v 0.56 +/- 0.08, P = .06). In a multivariate Cox regression model, the PAM predictor classified patients of the second set more accurately than risk stratification of current trials from Germany, Japan, and the United States (P < .001; hazard ratio, 4.756 [95% CI, 2.544 to 8.893]). CONCLUSION: Integration of gene expression-based class prediction of neuroblastoma patients may improve risk estimation of current neuroblastoma trials.

Localization of 131I-labelled monoclonal antibody ERIC1 in a subcutaneous xenograft model of neuroblastoma in SCID mice.

PURPOSE: To evaluate a novel strategy of immunolocalization of human neuroblastoma by targeting the neural cell adhesion molecule (NCAM), which is over-expressed on neuroblastoma. METHODS: NCAM expression on the cell surface of established neuroblastoma cells was shown by flow cytometry. A SCID mouse model using IMR5-75 neuroblastoma cells to induce subcutaneous tumour growth was established. 131I was used to label monoclonal NCAM specific ERIC1 antibodies generating the 131I-ERIC1 antibody, which showed a high affinity to NCAM also after labelling (KD=9 x 10(-8) mol . l(-1)). RESULTS: Measurement of organ-specific radioactivity showed low organ-specific uptake (5.33%ID/g (percent of injected dose per gram of tissue) after 72 h), which continuously decreased over the 96 h investigation period, demonstrating clearance of radioactivity. In contrast, tumours accumulated radioactivity continuously up to a peak of 42.07%ID/g at the 96 h time point (31.07%ID/g at 72 h). This specific uptake could be blocked by application of unlabelled ERIC1 antibodies. Measurement of blood specific radioactivity revealed a characteristic clearance over the first 72 h. With 37 Gy, tumour-specific radioactivity reached therapeutic doses after 96 h. CONCLUSIONS: These results indicate that 131I-labelled ERIC1 has the ability to probe NCAM-expressing tumour cells in vivo with high efficiency and is a promising reagent for the diagnosis and treatment of NCAM-positive human tumours, especially for neuroblastoma.

Risk estimation in localized unresectable single copy MYCN neuroblastoma by the status of chromosomes 1p and 11q.

In localized neuroblastoma, the identification of patients requiring intensive treatment is still difficult. We retrospectively analyzed data of 280 single copy MYCN stage 2 and 3 neuroblastoma patients with gross residual tumor after initial surgery. The 3-year-event free survival of the total group was 83+/-2%, and 3-year-overall survival was 92+/-2%. Patients < or=1.5 years had a better outcome than older children. Deletions/imbalances of chromosome 1p were found in 9/90 patients and were associated with a higher event rate but not with a higher death rate. Aberrations of chromosome 11q in 14/91 patients were correlated with a higher event and death rate. Multivariate analysis identified 1p aberrations as important for event free survival and 11q aberrations for overall survival.

Characterization of a complex genomic alteration on chromosome 2p that leads to four alternatively spliced fusion transcripts in the neuroblastoma cell lines IMR-5, IMR-5/75 and IMR-32.

Genetic aberrations in neuroblastoma (NB) have been extensively characterized over the last years. Alterations of the short arm of chromosome 2 (2p) have been of particular interest, since amplification of the MYCN oncogene on 2p24 is associated with an adverse outcome in NB patients. Here, we report on the characterization of a novel genomic rearrangement involving genetic material from 2p13 and 2p24 in NB cell lines that was discovered based on a serial analysis of gene expression (SAGE) profile of the MYCN-amplified NB cell line IMR-5. By analysis of a highly expressed SAGE tag not matching a Unigene cluster we identified four alternatively spliced corresponding transcripts, each of which consisted of the first 14 exons of the anthrax toxin receptor 1 gene (2p13.1) and varying combinations of exons of an unidentified gene located 1.3 Mb telomeric of MYCN (2p24.3) that was termed novel neuroblastoma gene 1. By Southern Blotting, Fluorescent In Situ Hybridization and Long Distance Inverse-PCR we disclosed that these transcripts result from a genomic alteration including material from distinct regions of chromosome 2p and four genomic breakpoints that are joined by short sequences of unknown origin. Furthermore, we show that this rearrangement lies within the homogeneous staining regions (HSR) in IMR-32 cells and is prevalent in both IMR-32 cells and their sub-clones IMR-5 and IMR-5/75, but not in a panel of 70 primary NB tumors. Our work is the first study discovering a fusion transcript based on a SAGE profile and for the first time precisely describes the DNA sequence of amplified breakpoint regions in NB.

Quantification of clonal hematopoiesis in polycythemia vera.

Polycythemia vera (PV) is believed to represent a clonal trilineage myeloaccumulative hematopoietic disorder. This study was undertaken to estimate for the first time the proportion not only of the neoplastic clone but also of clonal and residual nonneoplastic CD34(+) progenitor cells. Chromosomal abnormalities, including trisomy 8 or 9, are phenomena associated in about 20% of PV patients. Therefore, we screened peripheral blood (PB) mononuclear cells of PV patients in the chronic phase of the disease and looked for chromosomal abnormalities performing comparative genomic hybridization. Two of the ten patients revealed cytogenetic changes, including trisomy 8 or 9. To quantify the proportion of cytogenetic abnormal cells in these patients, we applied fluorescence in situ hybridization (FISH) technique on immunomagnetically enriched cell fractions. Ninety percent of the mononuclear cells and up to 79% of PB-derived CD34(+) progenitor cells presented three signals for chromosome 8 or 9. The diagnostic value of FISH to detect trisomies in trephine biopsies was then tested in all patients under study. Although the probability to detect FISH signals in a certain section plane is reduced, constantly 10-15% of the cells revealed three signals. Concerning the CD34(+) progenitor cell pool, a distinct nonclonal population exists in these patients. Our data underline the stem cell character of PV and additionally quantify the proportion of clonal CD34(+) progenitor cells for the first time. The finding of a distinct, not aberrant, CD34(+) progenitor cell population in chronic phase PV may offer perspectives in treatment of the disease. Finally, FISH analysis of bone marrow biopsies can be helpful to consolidate diagnosis of early PV.

Expression of MHC class I, MHC class II, and cancer germline antigens in neuroblastoma.

BACKGROUND: Neuroblastoma is the most common solid extracranial tumor in childhood, still with poor survival rates for metastatic disease. Neuroblastoma cells are of neuroectodermal origin and express a number of cancer germline (CG) antigens. These CG antigens may represent a potential target for immunotherapy such as peptide-based vaccination strategies. OBJECTIVE: The purpose of this study was to analyze the presence of MAGE-A1, MAGE-A3/A6, and NY-ESO-1 on an mRNA and protein level and to determine the expression of MHC class I and MHC class II antigens within the same tumor specimens. METHODS: A total of 68 tumors were available for RT-PCR, and 19/68 tumors were available for immunohistochemical (IHC) analysis of MAGE-A1, MAGE-A3/A6, and NY-ESO-1. In parallel, the same tumors were stained with a panel of antibodies for MHC class I and MHC class II molecules. RESULTS: Screening of 68 tumor specimens by RT-PCR revealed expression of MAGE-A1 in 44%, MAGE-A3/A6 in 21%, and NY-ESO-1 in 28% of cases. Immunohistochemistry for CG antigens of selected tumors showed good agreement between protein and gene expression. However, staining revealed a heterogeneous expression of CG antigens. None of the selected tumors showed MHC class I or MHC class II expression. CONCLUSIONS: mRNA expression of MAGE-A1, MAGE-A3/A6, and NY-ESO-1 is congruent with the protein expression as determined by immunohistochemistry. The heterogeneous CG-antigen expression and the lack of MHC class I and II molecules may have implications for T-cell-mediated immunotherapy in neuroblastoma.

New definition of low-risk neuroblastoma using stage, age, and 1p and MYCN status.

Data from patients with localized and stage 4S neuroblastoma were analyzed to define a new, extended low-risk group that does not require postoperative chemotherapy. Nine hundred eight patients with stage 1 to 3 and 4S disease without MYCN amplification were included. The prognostic impacts of age, stage, serum lactate dehydrogenase (LDH) activity, histology, and alterations of chromosomes 1p, 11q, and 3p were analyzed. By univariate analysis, alterations of chromosomes 1p and 11q were correlated with poor event-free survival (EFS) and overall survival (OS). Chromosome 3p alterations were prognostic only for EFS. Age, stage, and histology were found prognostic for EFS and OS. Stage 3 patients older than 2 years showed the worst outcome and were excluded from multivariate analysis. By multivariate analysis, status of 1p (P = 0.005, hazard ratio [HR] 3.6) and 11q (P = 0.024, HR 2.8) proved prognostic for EFS but only 1p status (P = 0.009, HR 3.0) for OS. The new low-risk group was defined as no MYCN amplification and either stage 1, stage 2 without 1p alterations, stage 3 two years of age or younger without 1p alteration, or stage 4S. These patients had a better outcome (3-year EFS 88.0 +/- 1.3%, 3-year OS 97.4 +/- 0.6%) than stage 2 and 3 patients with 1p alterations and stage 3 patients older than 2 years (3-year EFS 51.7 +/- 6.5%, P < 0.001; 3-year OS 83.4 +/- 4.5%; P < 0.001). The authors conclude that postoperative chemotherapy is required only in a small group of patients with localized and stage 4S disease without MYCN amplification.

The tumor-associated antigen PRAME is universally expressed in high-stage neuroblastoma and associated with poor outcome.

PURPOSE: The tumor-associated antigen PRAME, a potential candidate for immunotherapeutic targeting, is frequently expressed in a variety of cancers. However, no information about its presence in neuroblastoma is available to date. We therefore evaluated and quantified PRAME expression in a considerable number of neuroblastoma tumors and assessed its impact on the outcome of patients. EXPERIMENTAL DESIGN: Qualitative analysis of PRAME expression was assessed by reverse transcription (RT)-PCR screening of 94 patients with primary neuroblastoma. The same cohort was used for semiquantitative determination of transcript levels by Northern blotting, comparing the signal intensities of patients with those of testis total RNA. For more precise quantification of PRAME expression, real-time RT-PCR was performed in 88 patients of the above cohort and 7 additional patients, thus leaving a total of 101 patients that were analyzed with either method. Furthermore, association with tumor stage, age of patients at diagnosis, and MYCN amplification was determined as well as the prognostic impact of PRAME expression. RESULTS: RT-PCR screening detected PRAME expression in 93% of primary neuroblastoma and 100% of patients with advanced disease. Furthermore, RT-PCR and Northern blot analysis showed a highly significant association of PRAME expression with both higher tumor stage (P < 0.01) and the age of patients at diagnosis (P < 0.01). Finally, precise quantification of PRAME expression by quantitative real-time reverse transcription-PCR displayed significant impact on the outcome of patients. CONCLUSIONS: PRAME expression in neuroblastoma is extraordinarily common and was universally seen in patients with advanced-stage disease in our study. Furthermore, significant impact of PRAME expression on the outcome of patients was shown. Thus, PRAME may present a particularly attractive target for immunotherapeutic strategies in neuroblastoma.