FISH analyses for alterations in chromosomes 1, 2, 3, and 11 define high-risk groups in neuroblastoma

More Abundant Superoxide Dismutase2 Protein Levels in Blood May Act as a Prognostic Marker for High-Risk Neuroblastoma Patients

Purpose: Determination of proteomic differences plays an important role in biomarker investigations. Due to its heterogenic molecular background, identification of certain biomarkers is still a demand both for diagnosis and for prognosis of neuroblastoma. In this study, it is aimed to identify some marker proteins/mechanisms that may play role in neuroblastoma prognosis. Methods: A proteomic approach was performed for different risk groups of the disease by using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF/TOF) approach. Mononuclear cell pools from blood samples of patients for risk groups were constructed and protein expression changes for different groups were identified. Real-time PCR analysis were performed for N-MYC, 11q, 1p and 17q status of these patients and risk groups were determined from tumor samples. Results: Manganese-superoxide dismutase (SOD2) protein was significantly increased in high-risk group of neuroblastoma patients. Conclusion: SOD2 may play an important role in neuroblastoma progression and be a candidate prognostic peripheral blood marker for neuroblastoma patients.

Mutations of 1p genes do not consistently abrogate tumor suppressor functions in 1p-intact neuroblastoma

Background

Deletion of 1p is associated with poor prognosis in neuroblastoma, however selected 1p-intact patients still experience poor outcomes. Since mutations of 1p genes may mimic the deleterious effects of chromosomal loss, we studied the incidence, spectrum and effects of mutational variants in 1p-intact neuroblastoma.

Methods

We characterized the 1p status of 325 neuroblastoma patients, and correlated the mutational status of 1p tumor suppressors and neuroblastoma candidate genes with survival outcomes among 100 1p-intact cases, then performed functional validation of selected novel variants of 1p36 genes identified from our patient cohort.

Results

Among patients with adverse disease characteristics, those who additionally had 1p deletion had significantly worse overall survival. Among 100 tumor-normal pairs sequenced, somatic mutations of 1p tumor suppressors KIF1Bβ and CHD5 were most frequent (2%) after ALK and ATRX (8%), and BARD1 (3%). Mutations of neuroblastoma candidate genes were associated with other synchronous mutations and concurrent 11q deletion (P = 0.045). In total, 24 of 38 variants identified were novel and predicted to be deleterious or pathogenic. Functional validation identified novel KIF1Bβ I1355M variant as a gain-of-function mutation with increased expression and tumor suppressive activity, correlating with indolent clinical behavior; another novel variant CHD5 E43Q was a loss-of-function mutation with decreased expression and increased long-term cell viability, corresponding with aggressive disease characteristics.

Conclusions

Our study showed that chromosome 1 gene mutations occurred frequently in 1p-intact neuroblastoma, but may not consistently abrogate the function of bonafide 1p tumor suppressors. These findings may augment the evolving model of compounding contributions of 1p gene aberrations toward tumor suppressor inactivation in neuroblastoma.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09800-0.

MYCN in Neuroblastoma: "Old Wine into New Wineskins"

MYCN Proto-Oncogene, BHLH Transcription Factor (MYCN) has been one of the most studied genes in neuroblastoma. It is known for its oncogenetic mechanisms, as well as its role in the prognosis of the disease and it is considered one of the prominent targets for neuroblastoma therapy. In the present work, we attempted to review the literature, on the relation between MYCN and neuroblastoma from all possible mechanistic sites. We have searched the literature for the role of MYCN in neuroblastoma based on the following topics: the references of MYCN in the literature, the gene's anatomy, along with its transcripts, the protein's anatomy, the epigenetic mechanisms regulating MYCN expression and function, as well as MYCN amplification. MYCN plays a significant role in neuroblastoma biology. Its functions and properties range from the forming of G-quadraplexes, to the interaction with miRNAs, as well as the regulation of gene methylation and histone acetylation and deacetylation. Although MYCN is one of the most primary genes studied in neuroblastoma, there is still a lot to be learned. Our knowledge on the exact mechanisms of MYCN amplification, etiology and potential interventions is still limited. The knowledge on the molecular mechanisms of MYCN in neuroblastoma, could have potential prognostic and therapeutic advantages.

11q Deletion or ALK Activity Curbs DLG2 Expression to Maintain an Undifferentiated State in Neuroblastoma

High-risk neuroblastomas typically display an undifferentiated or poorly differentiated morphology. It is therefore vital to understand molecular mechanisms that block the differentiation process. We identify an important role for oncogenic ALK-ERK1/2-SP1 signaling in the maintenance of undifferentiated neural crest-derived progenitors through the repression of DLG2, a candidate tumor suppressor gene in neuroblastoma. DLG2 is expressed in the murine "bridge signature" that represents the transcriptional transition state when neural crest cells or Schwann cell precursors differentiate to chromaffin cells of the adrenal gland. We show that the restoration of DLG2 expression spontaneously drives neuroblastoma cell differentiation, highlighting the importance of DLG2 in this process. These findings are supported by genetic analyses of high-risk 11q deletion neuroblastomas, which identified genetic lesions in the DLG2 gene. Our data also suggest that further exploration of other bridge genes may help elucidate the mechanisms underlying the differentiation of NC-derived progenitors and their contribution to neuroblastomas.

Intratumoral immunosuppression profiles in 11q-deleted neuroblastomas provide new potential therapeutic targets

High‐risk neuroblastoma (NB) patients with 11q deletion frequently undergo late but consecutive relapse cycles with fatal outcome. To date, no actionable targets to improve current multimodal treatment have been identified. We analyzed immune microenvironment and genetic profiles of high‐risk NB correlating with 11q immune status. We show in two independent cohorts that 11q‐deleted NB exhibits various immune inhibitory mechanisms, including increased CD4+ resting T cells and M2 macrophages, higher expression of programmed death‐ligand 1, interleukin‐10, transforming growth factor‐beta‐1, and indoleamine 2,3‐dioxygenase 1 (P < 0.05), and also higher chromosomal breakages (P ≤ 0.02) and hemizygosity of immunosuppressive miRNAs than MYCN‐amplified and other 11q‐nondeleted high‐risk NB. We also analyzed benefits of maintenance treatment in 83 high‐risk stage M NB patients focusing on 11q status, either with standard anti‐GD2 immunotherapy (n = 50) or previous retinoic acid‐based therapy alone (n = 33). Immunotherapy associated with higher EFS (50 vs. 30, P = 0.028) and OS (72 vs. 52, P = 0.047) at 3 years in the overall population. Despite benefits from standard anti‐GD2 immunotherapy in high‐risk NB patients, those with 11q deletion still face poor outcome. This NB subgroup displays intratumoral immune suppression profiles, revealing a potential therapeutic strategy with combination immunotherapy to circumvent this immune checkpoint blockade.

Gene Expression Signature of Acquired Chemoresistance in Neuroblastoma Cells

Drug resistance of childhood cancer neuroblastoma is a serious clinical problem. Patients with relapsed disease have a poor prognosis despite intense treatment. In the present study, we aimed to identify chemoresistance gene expression signatures in vincristine resistant neuroblastoma cells. We found that vincristine-resistant neuroblastoma cells formed larger clones and survived under reduced serum conditions as compared with non-resistant parental cells. To identify the possible mechanisms underlying vincristine resistance in neuroblastoma cells, we investigated the expression profiles of genes known to be involved in cancer drug resistance. This specific gene expression patterns could predict the behavior of a tumor in response to chemotherapy and for predicting the prognosis of high-risk neuroblastoma patients. Our signature could help chemoresistant neuroblastoma patients in avoiding useless and harmful chemotherapy cycles.

Deletion of 11q in Neuroblastomas Drives Sensitivity to PARP Inhibition

Purpose: Despite advances in multimodal therapy, neuroblastomas with hemizygous deletion in chromosome 11q (20%-30%) undergo consecutive recurrences with poor outcome. We hypothesized that patients with 11q-loss may share a druggable molecular target(s) that can be exploited for a precision medicine strategy to improve treatment outcome.Experimental Design: SNP arrays were combined with next-generation sequencing (NGS) to precisely define the deleted region in 17 primary 11q-loss neuroblastomas and identify allelic variants in genes relevant for neuroblastoma etiology. We assessed PARP inhibitor olaparib in combination with other chemotherapy medications using both in vitro and in vivo models.Results: We detected that ATM haploinsufficiency and ATM allelic variants are common genetic hallmarks of 11q-loss neuroblastomas. On the basis of the distinct DNA repair pathways triggered by ATM and PARP, we postulated that 11q-loss may define a subgroup of neuroblastomas with higher sensitivity to PARP inhibitors. Noteworthy, concomitant treatment with olaparib and DNA alkylating agent temozolomide potently inhibited growth of cell lines harboring 11q-loss. This drug synergism was less potent when temozolomide was exchanged for cisplatin or irinotecan. Intact 11q cells concomitantly treated with ATM inhibitor displayed growth arrest and enhanced apoptosis, revealing a role for ATM in the mechanism that mediates sensitivity to temozolomide-olaparib. Interestingly, functional TP53 is required for efficacy of this treatment. In an in vivo model, coadministration of temozolomide-olaparib resulted in sustained xenograft regression.Conclusions: Our findings reveal a potent synergism between temozolomide and olaparib in treatment of neuroblastomas with 11q-loss and provide a rationale for further clinical investigation. Clin Cancer Res; 23(22); 6875-87. ©2017 AACR.

Incidence, Survival, and Treatment of Localized and Metastatic Neuroblastoma in Germany 1979-2015

BACKGROUND

A comprehensive clinical long-term survey over the complete spectrum of neuroblatoma disease is lacking in the literature.

OBJECTIVE

Our objective was to describe the incidence, risk profiles, therapies, and outcomes for the total cohort of German patients with neuroblastoma including all clinical stages and risk groups.

METHODS

Epidemiological, clinical, and outcome data of neuroblastoma patients who participated in one of the six consecutive national trials between 1979 and 2015 were analyzed retrospectively.

RESULTS

Of all German neuroblastoma patients known to the national childhood cancer registry, ninety seven percent enrolled in one of the trials. The absolute neuroblastoma rate has increased slightly, whereas the median age at diagnosis has decreased. Except for the screening period (1995-2000), the risk factors lactate dehydrogenase (LDH), ferritin, chromosome 1p, and the MYCN oncogene have remained largely constant, with the exception of an increase in MYCN amplification at stage 4 for those aged ≥18 months between trials NB97 (27%) and NB2004 (35%). The 10-year overall survival increased in patients with stage 1-3 neuroblastoma from 83 to 91%, for stage 4S from 80 to 85%, and for stage 4 aged ≥18 months from 2 to 38%. The fraction of patients in stages 1-3 who never received chemotherapy (neither for frontline nor at recurrence) increased from 35 to 60%. The proportion of macroscopically complete surgical resections of the primary tumor decreased for the total population as well as for patients with stage 4 aged ≥18 months. The impact of chemotherapy response on the outcome was trial dependent. The overall proportion of toxic death during the time of the protocol therapy was 6% for stage 4 patients aged ≥18 months and 2% for low-/intermediate-risk patients. The most frequently reported late sequelae in stage 4 patients aged ≥18 months were renal dysfunctions, hypothyroidism, major hearing impairment, and second malignancies.

CONCLUSION

The body of data for incidences, risk profiles, and survival rates from this survey of more than 37 years provides a useful perspective for future studies on neuroblastoma sub-cohorts.

Treatment and outcome of Ganglioneuroma and Ganglioneuroblastoma intermixed

Background

Ganglioneuroma (GN) and ganglioneuroblastoma intermixed (GNBI) are mature variants of neuroblastic tumors (NT). It is still discussed whether incomplete resection of GN/GNBI impairs the outcome of patients.

Methods

Clinical characteristics and outcome of localized GN/GNBI were retrospectively compared to localized neuroblastoma (NB) and ganglioneuroblastoma-nodular (GNBN) registered in the German neuroblastoma trials between 2000 and 2010.

Results

Of 808 consecutive localized NT, 162 (20 %) were classified as GN and 55 (7 %) as GNBI. GN/GNBI patients presented more often with stage 1 disease (68 % vs. 37 %, p < 0.001), less frequently with adrenal tumors (31 % vs. 43 %, p = 0.001) and positive mIBG-uptake (34 % vs. 90 %, p < 0.001), and had less often elevated urine catecholamine metabolites (homovanillic acid 39 % vs. 62 %, p < 0.001, vanillylmandelic acid 27 % vs. 64 %, p < 0.001). Median age at diagnosis increased with grade of differentiation (NB/GNBN: 9; GNBI: 61; GN-maturing: 71; GN-mature: 125 months, p < 0.001). Complete tumor resection was achieved at diagnosis in 70 % of 162 GN and 67 % of 55 GNBI, and after 4 to 32 months of observation in 4 GN (2 %) and 5 GNBI (9 %). Eleven patients received chemotherapy without substantial effect. Fifty-five residual tumors (42 GN, 13 GNBI) are currently under observation (median: 44 months). Five patients (3 GN, 2 GNBI) showed local progression; all had tumor residuals > 2 cm. No progression occurred after subtotal resection. Two patients died of treatment, none of tumor progression.

Conclusions

GN/GNBI account for one quarter of localized NT and differ from immature tumors in their clinical features. Chemotherapy is not effective. Subtotal resection appears to be a sufficient treatment.

Trial registration

ClinicalTrials.gov identifiers - NB97 (NCT00017225; registered June 6, 2001); NB2004 (NCT00410631; registered December 11, 2006)

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-016-2513-9) contains supplementary material, which is available to authorized users.

Significance of clinical and biologic features in Stage 3 neuroblastoma: a report from the International Neuroblastoma Risk Group project

BACKGROUND

International Neuroblastoma Staging System (INSS) Stage 3 neuroblastoma is a heterogeneous disease. Data from the International Neuroblastoma Risk Group (INRG) database were analyzed to define patient and tumor characteristics predictive of outcome.

PROCEDURE

Of 8,800 patients in the INRG database, 1,483 with INSS Stage 3 neuroblastoma and complete follow-up data were analyzed. Secondary analysis was performed in 1,013 patients (68%) with MYCN-non-amplified (NA) tumors. Significant prognostic factors were identified via log-rank test comparisons of survival curves. Multivariable Cox proportional hazards regression model was used to identify factors independently predictive of event-free survival (EFS).

RESULTS

Age at diagnosis (P < 0.0001), tumor MYCN status (P < 0.0001), and poorly differentiating/undifferentiated histology (P = 0.03) were independent predictors of EFS. Compared to other Stage 3 subgroups, outcome was inferior for patients ≥ 547 days with MYCN-NA neuroblastoma (P < 0.0001), and within this cohort, serum ferritin ≥ 96 ng/ml was associated with inferior EFS (P = 0.02). For patients <547 days of age with MYCN-NA tumors, serum ferritin levels were prognostic of overall survival (OS) (P = 0.04) and chromosome 11q aberration was prognostic of EFS (P = 0.03).

CONCLUSIONS

Among patients with INSS Stage 3 neuroblastoma patients, age at diagnosis, MYCN status and histology predict outcome. Patients <547 days of age with MYCN-NA tumors that lack chromosome 11q aberrations or those with serum ferritin <96 ng/ml have excellent prognosis and should be considered for therapy reduction. Prospective clinical trials are needed to identify optimal therapy for those patients ≥ 547 days of age with undifferentiated histology or elevated serum ferritin.

Sensitive detection of viral transcripts in human tumor transcriptomes

In excess of % of human cancer incidents have a viral cofactor. Epidemiological studies of idiopathic human cancers indicate that additional tumor viruses remain to be discovered. Recent advances in sequencing technology have enabled systematic screenings of human tumor transcriptomes for viral transcripts. However, technical problems such as low abundances of viral transcripts in large volumes of sequencing data, viral sequence divergence, and homology between viral and human factors significantly confound identification of tumor viruses. We have developed a novel computational approach for detecting viral transcripts in human cancers that takes the aforementioned confounding factors into account and is applicable to a wide variety of viruses and tumors. We apply the approach to conducting the first systematic search for viruses in neuroblastoma, the most common cancer in infancy. The diverse clinical progression of this disease as well as related epidemiological and virological findings are highly suggestive of a pathogenic cofactor. However, a viral etiology of neuroblastoma is currently contested. We mapped transcriptomes of neuroblastoma as well as positive and negative controls to the human and all known viral genomes in order to detect both known and unknown viruses. Analysis of controls, comparisons with related methods, and statistical estimates demonstrate the high sensitivity of our approach. Detailed investigation of putative viral transcripts within neuroblastoma samples did not provide evidence for the existence of any known human viruses. Likewise, de-novo assembly and analysis of chimeric transcripts did not result in expression signatures associated with novel human pathogens. While confounding factors such as sample dilution or viral clearance in progressed tumors may mask viral cofactors in the data, in principle, this is rendered less likely by the high sensitivity of our approach and the number of biological replicates analyzed. Therefore, our results suggest that frequent viral cofactors of metastatic neuroblastoma are unlikely.

Many human cancers are caused by infections with tumor viruses and identification of these pathogens is considered a critical contribution to cancer prevention. Deep sequencing enables us to systematically investigate viral nucleotide signatures in order to either verify or exclude the existence of viruses in idiopathic human cancers. We have developed Virana, a novel computational approach for identifying tumor viruses in human cancers that is applicable to a wide variety of tumors and viruses. Virana firstly addresses several important biological confounding factors that may hinder successful detection of these pathogens. We applied our approach in the first systematic search for cancer-causing viruses in metastatic neuroblastoma, the most common form of cancer in infancy. Although the heterogeneous clinical progression of this disease as well as epidemiological and virological findings are suggestive of a pathogenic cofactor, the viral etiology of neuroblastoma is currently contested. We conducted an analysis of experimental controls, comparisons with related approaches, as well as statistical analyses in order to validate our method. In spite of the high sensitivity of our approach, analyses of neuroblastoma transcriptomes did not provide evidence for the existence of any known or unknown human viruses. Our results therefore suggest that frequent viral cofactors of metastatic neuroblastoma are unlikely.

Acute lymphoblastic leukemia in a patient with constitutional chromosome 1pter-p36.31 duplication and 1q43-qter deletion

Chromosome 1 is the largest of all human chromosomes, containing 3141 genes. It is linked to 890 known genetic diseases including congenital hypothyroidism, hemochromatosis, and prostate cancer. Recognized deletion and duplication syndromes have been described. Deletions in the short arm (p) of the chromosome have been identified in tumors of the brain and kidneys. Duplications in the long (q) arm of the chromosome are reported in myelodysplastic syndromes. Solitary 1p36 deletion or 1q42 duplication are rarely reported entities and their associations with malignancy have not been characterized. We report a case of a child with constitutional 1pter-p36.31 duplication and 1q43-qter deletion who developed acute lymphoblastic leukemia (ALL). The patient's oncologic presentation and subsequent clinical course raise the question of the association of the underlying genetic abnormality and its malignant potential, specifically in relation to ALL. Acquired chromosome 1 deletions and duplications have been well described in other malignant diseases. Constitutional chromosome 1p duplication and 1q deletions have not been described with ALL.

Progress in treatment and risk stratification of neuroblastoma: impact on future clinical and basic research

Close international collaboration between pediatric oncologists has led to marked improvements in the cure of patients, seen as a long-term overall survival rate of about 80%. Despite this progress, neuroblastoma remains a challenging disease for both clinicians and researchers. Major clinical problems include lack of acceptable cure rates in high-risk neuroblastoma and potential overtreatment of subsets of patients at low and intermediate risk of the disease. Many years of intensive international cooperation have recently led to a promising joint effort to further improve risk classification for treatment stratification, the new International Neuroblastoma Risk Group Classification System. This approach will facilitate comparison of the results of clinical trials performed by different international collaborative groups. This, in turn, should accelerate refinement of risk stratification and thereby aid selection of appropriate therapies for individual patients. To be able to identify new therapeutic modalities, it will be necessary to elucidate the pathogenesis of the different subtypes of neuroblastoma. Basic and translational research have provided new tools for molecular characterization of blood and tumor samples including high-throughput technologies for analysis of DNA, mRNAs, microRNAs and other non-coding RNAs, as well as proteins and epigenetic markers. Most of these studies are array-based in design. In neuroblastoma research they aim to refine risk group stratification through incorporation of molecular tumor fingerprints and also to enable personalized treatment modalities by describing the underlying pathogenesis and aberrant signaling pathways in individual tumors. To make optimal use of these new technologies for the benefit of the patient, it is crucial to have a systematic and detailed documentation of both clinical and molecular data from diagnosis through treatment to follow-up. Close collaboration between clinicians and basic scientists will provide access to combined clinical and molecular data sets and will create more efficient steps in response to the remaining treatment challenges. This review describes the current efforts and trends in neuroblastoma research from a clinical perspective in order to highlight the urgent clinical problems we must address together with basic researchers.

Prognostic value of partial genetic instability in neuroblastoma with ≤50% neuroblastic cell content

AIMS

Better understanding of neuroblastoma genetics will improve with genome-wide techniques. However, performing these analyses in samples with <60% neuroblast cells is not adequate. We evaluated the utility of fluorescence in situ hybridization (FISH) on tissue microarrays (TMA) in detecting partial genetic instability (PGI), focusing on samples with ≤50% neuroblast cells.

METHODS AND RESULTS

Alterations of 11q and 17q were detected by FISH on 369 neuroblastoma samples in TMA. Status of the MYCN gene and 1p36 region has been established previously by FISH diagnosis. Partial genetic instability (PGI) was defined as the ratio between segmental genetic alterations detected and number of genetic markers diagnosed in each tumour. Of primary tumours, 14.6% harboured 11q deletions, whereas 42.6% showed 17q gain. PGI was established in 260 primary tumours, 67 of which contained ≤50% neuroblasts. Outcomes were statistically worse for patients whose tumours presented high PGI (P < 0.0001). Multivariate analysis revealed moderate and high PGI as prognostic factors.

CONCLUSIONS

In the cohort examined in this study, univariate and multivariate analysis confirmed the effect of PGI in patient outcome. PGI established by FISH on TMA is a useful method to identify high-risk patients even if tumours have a cell content of ≤50% neuroblast cells.

Regulation of BIRC5 and its isoform BIRC5-2B in neuroblastoma

We analysed the expression of BIRC5 and BIRC5-2B in primary neuroblastoma (NB) tumors and NB model systems. In tumors, overexpression of BIRC5 correlated closely with its isoform BIRC5-2B. Expression of both transcripts was stage-dependent, associated with poor prognosis and with the expression of the transcription factor E2F1. In cell culture, we identified BIRC5 as a direct transcriptional target of activating E2Fs, primarily when p21(Cip1) and p27(Kip1), two other E2F1 targets, are strongly suppressed. Deregulated MYCN indirectly induces BIRC5 through suppression of CDKN1A/p21(Cip1) and induction of Skp2, which in turn favors the degradation of p27(Kip1). In addition, increased BIRC5 protein stability via phosphorylation is mediated by expression of E2F targets such as CDC2. In line with this, selective knock down of CDC2 inhibited BIRC5 abundance and suppressed its anti-apoptotic activities. We conclude that BIRC5 is induced via a functional cooperation between MYCN and E2F1.

Molecular characterization and classification of neuroblastoma

For many decades, neuroblastoma has remained a challenging disease for both clinicians and researchers. Now, techniques that efficiently specify both comprehensive genetic and gene-expression alterations of neuroblastoma tumors have provided molecular markers that indicate tumor behavior and patient outcome with very high accuracy. Once the anticipated value of these markers has been confirmed in ongoing studies, patients may profit from more accurate risk assessment by integrating these markers into clinical routine. Moreover, disclosing further tumor-initiating events, such as the recently revealed oncogenic mutations of ALK, will further promote the elucidation of the genetic etiology of the disease. Together with recent information on altered signaling pathways in aggressively growing tumors, this knowledge will help to establish therapeutic strategies specifically targeting molecular key factors of neuroblastoma tumor progression.

Heterogeneity of the MYCN oncogene in neuroblastoma

PURPOSE

MYCN amplification is an important therapy-stratifying marker in neuroblastoma. Fluorescence in situ hybridization with signal detection on the single-cell level allows a critical judgement of MYCN intratumoral heterogeneity.

EXPERIMENTAL DESIGN

The MYCN status was investigated by fluorescence in situ hybridization at diagnosis and relapse. Heterogeneity was defined as the simultaneous presence of amplified cells (>/=5 cells per slide) and nonamplified cells within one tumor or sequential change of the amplification status during the course of the disease. Likewise, heterogeneity can be detected between primary tumor and metastasis.

RESULTS

From 1,341 patients analyzed, 1,071 showed no amplification, 250 showed homogeneous amplification, and 20 patients showed MYCN heterogeneity. Of the patients with heterogeneity, 12 of 20 had clusters of MYCN amplifications, 3 of 20 had amplified single cells, 3 of 20 showed MYCN amplifications in the bone marrow but not in the primary tumor, and 2 of 20 acquired MYCN amplification during the course of the disease. All stage 4 patients were treated according to high-risk protocols; 7 of 8 later progressed. Four patients with localized disease were treated according to high-risk protocol because of MYCN-amplified clusters; 1 of 4 later progressed. One patient treated with mild chemotherapy experienced progression. Seven patients with localized/4S disease underwent no chemotherapy: 4 of 5 patients with MYCN heterogeneity at diagnosis remained disease-free, and 1 of 5 experienced local progression. Two patients had normal MYCN status at diagnosis but acquired MYCN amplification during the course of the disease.

CONCLUSION

MYCN heterogeneity is rare. Our results suggest that small amounts of MYCN-amplified cells are not correlated to adverse outcomes. More patients with heterogeneity are warranted to clarify the role of MYCN heterogeneity for risk classification.

Subclassification and individual survival time prediction from gene expression data of neuroblastoma patients by using CASPAR

PURPOSE

To predict individual survival times for neuroblastoma patients from gene expression data using the cancer survival prediction using automatic relevance determination (CASPAR) algorithm.

EXPERIMENTAL DESIGN

A first set of oligonucleotide microarray gene expression profiles comprising 256 neuroblastoma patients was generated. Then, CASPAR was combined with a leave-one-out cross-validation to predict individual times for both the whole cohort and subgroups of patients with unfavorable markers, including stage 4 disease (n = 67), unfavorable genetic alterations, intermediate-risk or high-risk stratification by the German neuroblastoma trial, and patients predicted as unfavorable by a recently described gene expression classifier (n = 83). Prediction accuracy of individual survival times was assessed by Kaplan-Meier analyses and time-dependent receiver operator characteristics curve analyses. Subsequently, classification results were validated in an independent cohort (n = 120).

RESULTS

CASPAR separated patients with divergent outcome in both the initial and the validation cohort [initial set, 5y-OS 0.94 +/- 0.04 (predicted long survival) versus 0.38 +/- 0.17 (predicted short survival), P < 0.0001; validation cohort, 5y-OS 0.94 +/- 0.07 (long) versus 0.40 +/- 0.13 (short), P < 0.0001]. Time-dependent receiver operator characteristics analyses showed that CASPAR-predicted individual survival times were highly accurate (initial set, mean area under the curve for first 10 years of overall survival prediction 0.92 +/- 0.04; validation set, 0.81 +/- 0.05). Furthermore, CASPAR significantly discriminated short (<5 years) from long survivors (>5 years) in subgroups of patients with unfavorable markers with the exception of MYCN-amplified patients (initial set). Confirmatory results with high significance were observed in the validation cohort [stage 4 disease (P = 0.0049), NB2004 intermediate-risk or high-risk stratification (P = 0.0017), and unfavorable gene expression prediction (P = 0.0017)].

CONCLUSIONS

CASPAR accurately forecasts individual survival times for neuroblastoma patients from gene expression data.

Localized infant neuroblastomas often show spontaneous regression: results of the prospective trials NB95-S and NB97

PURPOSE

The excellent prognosis of localized neuroblastoma in infants, the overdiagnosis observed in neuroblastoma screening studies, and several case reports of regression of localized neuroblastoma prompted us to initiate a prospective cooperative trial on observation of localized neuroblastoma without cytotoxic treatment.

PATIENTS AND METHODS

For infants with localized neuroblastoma without MYCN amplification, chemotherapy was scheduled only in cases with threatening symptoms; otherwise, the tumor was either resected or observed by ultrasound and magnetic resonance imaging (MRI).

RESULTS

Of 340 eligible participants, 190 underwent resection, 57 were treated with chemotherapy, and 93 were observed with gross residual tumor. Of those 93 patients with unresected tumors, spontaneous regression was seen in 44, local progression in 28, progression to stage 4S in seven, and progression to stage 4 in four. Time to regression was quite variable, with first signs of regression noted 1 to 18 months after diagnosis and in 15 of 44 patients even after the first year of life. So far, complete regression was observed in 17 of 44 patients 4 to 20 months after diagnosis. Known clinical risk factors were not able to differentiate between patients with regression and regional or metastatic progression. Overall survival (OS; 3-year OS, 0.99 +/- 0.01) and metastases-free survival (rate at 3 years, 0.94 +/- 0.03) for patients with unresected tumors was excellent and was not different from patients treated with surgery or chemotherapy.

CONCLUSION

Spontaneous regression is regularly seen in infants with localized neuroblastoma and is not limited to the first year of life. A wait-and-see strategy is justified in those patients.

Molecular biology of neuroblastoma

Neuroblastoma is one of the most frequently occurring solid tumours in children, especially in the first year of life, when it accounts for 50% of all tumours. It is the second most common cause of death in children, only preceded by accidents. The most peculiar characteristic of neuroblastoma is its clinical heterogeneity. Approximately half of the cases are classified as high risk, with overall survival rates around 40% despite intensive multimodal therapy. Nevertheless, other subsets of neuroblastomas will undergo spontaneous regression and others will show very slow progression. Despite many advances in the past three decades, neuroblastoma has remained an enigmatic challenge to clinical and basic scientists. Elucidation of the exact molecular pathways of neuroblastoma will enable researchers and clinicians to stratify the disease and adapt therapy to the risk of relapse or progression. This review focuses on recent advances in our understanding of the biology of this complex paediatric tumour. Neuroblastoma is already one of the first examples for the use of tumoral genetic markers as a tool for defining tumour behaviour and to aid clinical staging.

Comparative proteomic expression profile in all-trans retinoic acid differentiated neuroblastoma cell line

Neuroblastoma (NB) is an infant tumor which frequently differentiates into neurons. We used two-dimensional differential in-gel electrophoresis (2D-DIGE) to analyze the cytosolic and nuclear protein expression patterns of LAN-5 cells following neuronal differentiating agent all-trans-retinoic acid treatment. We identified several candidate proteins, from which G beta2 and Prefoldin 3 may have a role on NB development. These results strength the use of proteomics to discover new putative protein targets in cancer.

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.

Multilocus loss of heterozygosity allelotypes identify a genetic pathway associated with progression from low to high stage disease in neuroblastoma

Neuroblastoma is a heterogeneous tumour with a variety of clinical phenotypes, ranging from a localised tumour with excellent outcome (stage 1) to a metastatic, usually fatal malignancy (stage 4). In order to investigate the genetic relationship between these tumour subtypes, a loss of heterozygosity (LOH) analysis was carried out. Composite LOH allelotypes incorporating data from 96 loci on 5 chromosomes (1p, 3p, 4p, 11q, 14q), were constructed for 62 neuroblastomas. Neuroblastomas with similar allelotypes were clustered into groups and allelotype patterns correlated with clinical features. Three distinct genetic subgroups of neuroblastoma were observed. The largest group (50% of tumours) was characterised by specific allelotype patterns indicative of a stepwise accumulation of genetic alterations (11q LOH-->1p, 4p, and/or 14q LOH-->3p LOH), associated with progression from low to high stage disease. These tumours are distinct from MYCN amplified neuroblastomas which have a more rapid and aggressive disease course, and also a proportion of low stage tumours, often ganglioneuromas or ganglioneuroblastomas, with restricted growth potential.

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.

Reduced expression of CAMTA1 correlates with adverse outcome in neuroblastoma patients

PURPOSE

A distal portion of 1p is frequently deleted in human neuroblastomas, and it is generally assumed that this region harbors at least one gene relevant for neuroblastoma development. A 1p36.3 commonly deleted region, bordered by D1S2731 and D1S214 has been defined. The present study surveys whether expression of genes mapping to this region is associated with tumor behavior.

EXPERIMENTAL DESIGN

Candidate genes localized within the deleted region were identified by sequence data analysis. Their expression was assessed in a cohort of 49 primary neuroblastomas using cDNA microarray analysis. Gene expression patterns associated with known prognostic markers and patient outcome were further evaluated by quantitative real-time reverse transcription-PCR in a cohort of 102 neuroblastomas.

RESULTS

The commonly deleted region spans 261 kb and encompasses two genes, FLJ10737 and CAMTA1. We found no evidence for an association of FLJ10737 expression with established prognostic variables or outcome. In contrast, low CAMTA1 expression characterized tumors with 1p deletion, MYCN amplification, and advanced tumor stages 3 and 4. Moreover, low CAMTA1 expression was significantly associated with poor outcome (P < 0.001). In multivariate analysis of event-free survival, the prognostic information of low CAMTA1 expression was independent of 1p status, MYCN status, tumor stage, and age of the patient at diagnosis (hazard ratio, 3.52; 95% confidence interval, 1.21-10.28; P = 0.02).

CONCLUSIONS

Our data suggest that assessment of CAMTA1 expression may improve the prognostic models for neuroblastoma and that it will be important to define the biological function of CAMTA1 in this disease.

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.

Quantitative Real-Time PCR for Quick Simultaneous Determination of Therapy-Stratifying Markers MYCN Amplification, Deletion 1p and 11q

Amplification of the oncogene MYCN as well as deletions in 1p and 11q are important prognostic and in part therapy-stratifying factors in human neuroblastoma. Due to the increasing clinical relevance of these molecular markers, accurate and fast assessment of the status of MYCN, 1p, and 11q is essential. As 2 techniques are recommended to avoid artefacts and to circumvent technical limitations, we developed a real-time q-PCR assay using genomic DNA from frozen and paraffin-embedded tissue as template as an alternative to LOH analyses and Southern blot (SB) and in addition to fluorescence in situ hybridization (FISH). Determination of deletion or amplification was achieved by comparing the copy number of a target gene (TG from the region of interest) to an unaffected reference gene (RG) within the same chromosome. PCR raw data were normalized to a serial dilution standard curve and a ratio TG/RG was created. The ratio to define a deletion was set as 0.5 (= expected ratio 1 TG copy/2 RG copies), the amplification threshold was set as >10.0. Data were compared to results obtained by FISH and were consistent in 10 of 13 (77%) tumors with deletion 1p, 18 of 20 (90%) with deletion 11q, 12 of 12 (100%) with MYCN amplification, and 146 of 151 (97%) samples without any aberration. Three tumors with aberrations in 1p and 2 tumors with aberrations in 11q were detectable by FISH but not by PCR. Three cases indicated a deletion 11q, 1 tumor a deletion 1p by PCR only. Specificity was 98% for 1p and MYCN each and 92% for 11q. Sensitivity was 77% for 1p, 90% for 11q, and 100% for MYCN. The discrepant results were mostly caused by heterogeneous cell populations of the investigated tissue; the use of real-time q-PCR for the detection of chromosomal aberrances in NB enables a fast and reliable assessment of the 3 most relevant chromosomal aberrations simultaneously. As the assay does not require reference tissue, can be performed with small amounts of DNA, and allows the investigation of paraffin-embedded material for the MYCN-status, it can be regarded alternative to LOH or SB analyses and in addition to FISH.

Characterization of karyotypic events and evolution in neuroblastoma

BACKGROUND

Neuroblastoma (NB) is cytogenetically characterized by a number of non-random events. However, knowledge is limited concerning the timing of occurrence and inter-action of many of these events.

METHODS

Karyotypic patterns were obtained from a study group of 49 NB tumors that had been analyzed by conventional cytogenetics combined with FISH and in some instances SKY.

RESULTS

All chromosomes were involved in a numerical and structural aberration in at least one tumor. There was a positive correlation between the occurrence of MYCN and del(1p) and between del(1p) and 17q. Aberrations involving chromosomes X, 3, 19, and del(1p) could be considered early events, whereas those involving chromosomes 9, 13, 15, 18, 20, and 21 were often late events.

CONCLUSIONS

This study suggests that the karyotypic patterns characterizing NB are complex. There are aberrations that can be grouped into early or late karyotypic events, but others, such as gain of 17q, are variable.

MYCN-status in neuroblastoma: characteristics of tumours showing amplification, gain, and non-amplification

While the role of MYCN-amplification (MNA) for risk assessment in neuroblastoma is undisputed, the phenomenon of gene copy excess below the amplification threshold is rarely described. To discuss biological characteristics and the clinical impact of the so-called MYCN-gain versus amplified or non-amplified cases, we investigated the MYCN status of 659 patients uniformly analysed by fluorescence in situ hybridisation. The number of MYCN-amplified tumours in our cohort was 18% (116/659); an additional 38 tumours (6%) displayed MYCN-gain. Both alterations were associated with an advanced stage disease, an increased patient age and further chromosomal alterations. Most of the amplified neuroblastomas displayed 1p aberrations, whereas MYCN-gain tumours correlated with 11q alterations. In contrast to the amplified cases, tumours with gain displayed no increased MYCN RNA levels. MNA versus non-amplification discriminated between good and poor outcomes, independent of stage, age and the degree of amplification. However, patients with amplified tumours showed a significantly better outcome when this was combined with non-stage 4 disease and age <1 year versus stage 4 and age < 1 year. Although MYCN-gain was associated with poor event-free-survival (EFS) in stages 1-3, 4S (P=0.005), this might be related to associated genetic aberrations and not to the MYCN-gain itself. A survival difference between neuroblastomas with gain and single copy MYCN could not be delineated. In conclusion, MNA predicts a poor outcome for neuroblastoma patients of all stages and age. MYCN-gain is also a characteristic feature of advanced stage tumours and older patients, but is not associated with higher MYCN expression and appears not to be discriminative in predicting patient outcome.