Combining Gene Expression Profiles and Clinical Parameters for Risk Stratification in Medulloblastomas

Elevated Kir2.1/nuclear N2ICD defines a highly malignant subtype of non-WNT/SHH medulloblastomas

Medulloblastoma (MB) is one of the most common childhood malignant brain tumors (WHO grade IV), traditionally divided into WNT, SHH, Group 3, and Group 4 subgroups based on the transcription profiles, somatic DNA alterations, and clinical outcomes. Unlike WNT and SHH subgroup MBs, Group 3 and Group 4 MBs have similar transcriptomes and lack clearly specific drivers and targeted therapeutic options. The recently revised WHO Classification of CNS Tumors has assigned Group 3 and 4 to a provisional non-WNT/SHH entity. In the present study, we demonstrate that Kir2.1, an inwardly-rectifying potassium channel, is highly expressed in non-WNT/SHH MBs, which promotes tumor cell invasion and metastasis by recruiting Adam10 to enhance S2 cleavage of Notch2 thereby activating the Notch2 signaling pathway. Disruption of the Notch2 pathway markedly inhibited the growth and metastasis of Kir2.1-overexpressing MB cell-derived xenograft tumors in mice. Moreover, Kir2.1^high/nuclear N2ICD^high MBs are associated with the significantly shorter lifespan of the patients. Thus, Kir2.1^high/nuclear N2ICD^high can be used as a biomarker to define a novel subtype of non-WNT/SHH MBs. Our findings are important for the modification of treatment regimens and the development of novel-targeted therapies for non-WNT/SHH MBs.

A Five-Gene Risk Score Model for Predicting the Prognosis of Multiple Myeloma Patients Based on Gene Expression Profiles

Multiple myeloma is a heterogeneous plasma cell malignancy that remains incurable because of the tendency of relapse for most patients. Survival outcomes may vary widely due to patient and disease variables; therefore, it is necessary to establish a more accurate prognostic model to improve prognostic precision and guide clinical therapy. Here, we developed a risk score model based on myeloma gene expression profiles from three independent datasets: GSE6477, GSE13591, and GSE24080. In this model, highly survival-associated five genes, including EPAS1, ERC2, PRC1, CSGALNACT1, and CCND1, are selected by using the least absolute shrinkage and selection operator (Lasso) regression and univariate and multivariate Cox regression analyses. At last, we analyzed three validation datasets (including GSE2658, GSE136337, and MMRF datasets) to examine the prognostic efficacy of this model by dividing patients into high-risk and low-risk groups based on the median risk score. The results indicated that the survival of patients in low-risk group was greatly prolonged compared with their counterparts in the high-risk group. Therefore, the five-gene risk score model could increase the accuracy of risk stratification and provide effective prediction for the prognosis of patients and instruction for individualized clinical treatment.

3D hydrogels reveal medulloblastoma subgroup differences and identify extracellular matrix subtypes that predict patient outcome

Medulloblastoma (MB) is the most common malignant brain tumour in children and is subdivided into four subgroups: WNT, SHH, Group 3, and Group 4. These molecular subgroups differ in their metastasis patterns and related prognosis rates. Conventional 2D cell culture methods fail to recapitulate these clinical differences. Realistic 3D models of the cerebellum are therefore necessary to investigate subgroup‐specific functional differences and their role in metastasis and chemoresistance. A major component of the brain extracellular matrix (ECM) is the glycosaminoglycan hyaluronan. MB cell lines encapsulated in hyaluronan hydrogels grew as tumour nodules, with Group 3 and Group 4 cell lines displaying clinically characteristic laminar metastatic patterns and levels of chemoresistance. The glycoproteins, laminin and vitronectin, were identified as subgroup‐specific, tumour‐secreted ECM factors. Gels of higher complexity, formed by incorporation of laminin or vitronectin, revealed subgroup‐specific adhesion and growth patterns closely mimicking clinical phenotypes. ECM subtypes, defined by relative levels of laminin and vitronectin expression in patient tissue microarrays and gene expression data sets, were able to identify novel high‐risk MB patient subgroups and predict overall survival. Our hyaluronan model system has therefore allowed us to functionally characterize the interaction between different MB subtypes and their environment. It highlights the prognostic and pathological role of specific ECM factors and enables preclinical development of subgroup‐specific therapies. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Role of FUT8 expression in clinicopathology and patient survival for various malignant tumor types: a systematic review and meta-analysis

Dysregulation of α(1,6)-fucosyltransferase (FUT8) plays significant roles in development of a variety of malignant tumor types. We collected as many relevant articles and microarray datasets as possible to assess the prognostic value of FUT8 expression in malignant tumors. For this purpose, we systematically searched PubMed, Embase, Web of Science, Springer, Chinese National Knowledge Infrastructure (CNKI), and Wan Fang, and eventually identified 7 articles and 35 microarray datasets (involving 6124 patients and 10 tumor types) for inclusion in meta-analysis. In each tumor type, FUT8 expression showed significant (p< 0.05) correlation with one or more clinicopathological parameters; these included patient gender, molecular subgroup, histological grade, TNM stage, estrogen receptor, progesterone receptor, and recurrence status. In regard to survival prognosis, FUT8 expression level was associated with overall survival in non-small cell lung cancer (NSCLC), breast cancer, diffuse large B cell lymphoma, gastric cancer, and glioma. FUT8 expression was also correlated with disease-free survival in NSCLC, breast cancer, and colorectal cancer, and with relapse-free survival in pancreatic ductal adenocarcinoma. For most tumor types, survival prognosis of patients with high FUT8 expression was related primarily to clinical features such as gender, tumor stage, age, and pathological category. Our systematic review and meta-analysis confirmed the association of FUT8 with clinicopathological features and patient survival rates for numerous malignant tumor types. Verification of prognostic value of FUT8 in these tumor types will require a large-scale study using standardized methods of detection and analysis.

Medulloblastoma: From Myth to Molecular

Current therapies for medulloblastoma were introduced primarily in the 1980s and consist of predominantly cytotoxic, nontargeted approaches. Mortality from medulloblastoma remains significant. In addition, many survivors suffer from severe treatment-related effects of radiation and cytotoxic chemotherapy. Further intensification of nonspecific therapy is unlikely to offer additional benefits, because survival rates have reached a plateau. Recent publications in medulloblastoma have revolved largely around the recognition that medulloblastoma per se does not exist, but rather, that there are a group of histologically similar but clinically and molecularly distinct entities that have been grouped under that rubric. Distinguishing the four molecular subgroups of medulloblastoma-wingless (WNT), sonic hedgehog (SHH), group 3, and group 4-in the daily treatment of patients, as well in the setting of clinical trials, is an important challenge in the near term for the pediatric neuro-oncology community. The preponderance of morbidity in treating patients with medulloblastoma is secondary to the treatment or prophylaxis of leptomeningeal metastases, and the cause of most deaths is leptomeningeal metastases. Recurrence of medulloblastoma is a nearly universally fatal event, with no significant salvage rate. The extent of spatial and temporal intratumoral heterogeneity as medulloblastoma metastasizes to leptomeninges and as it evolves in the face of radiation and cytotoxic chemotherapy is just beginning to be understood as a major barrier to therapeutic success. Pediatric neuro-oncology clinicians and scientists must now determine how best to incorporate rapid changes in our biologic understanding of medulloblastoma into the next generation of upfront clinical trials, with the goal of both improving survival for the highest-risk patients and improving quality of life for survivors.

Medulloblastoma: Molecular Classification-Based Personal Therapeutics

Recent advances in cancer genomics have revealed 4 distinct subgroups of medulloblastomas, each with unique transcription profiles, DNA alterations and clinical outcome. Molecular classification of medulloblastomas improves predictions of clinical outcome, allowing more accurate matching of intensity of conventional treatments with chemotherapy and radiation to overall prognosis and setting the stage for the introduction of targeted therapies.

Pharmacogenomic biomarkers for personalized medicine

Pharmacogenomics examines how the benefits and adverse effects of a drug vary among patients in a target population by analyzing genomic profiles of individual patients. Personalized medicine prescribes specific therapeutics that best suit an individual patient. Much current research focuses on developing genomic biomarkers to identify patients, to identify which patients would benefit from a treatment, have an adverse response, or no response at all, prior to treatment according to relevant differences in risk factors, disease types and/or responses to therapy. This review describes the use of the two personalized medicine biomarkers, prognostic and predictive, to classify patients into subgroups for treatment recommendation.

Bone metastases in medulloblastoma--single institution experience

BACKGROUND

Medulloblastoma has one of the highest rates of metastasis outside the central nervous system (CNS). Bone metastases are the most common lesions, although lymph node and visceral spread have also been reported.

OBJECTIVE

To present patients with bone metastasis in medulloblastoma and discuss their radiologic appearances and treatment approach.

PATIENTS AND METHODS

From 1993 to 2008, 82 patients diagnosed with medulloblastoma were treated at the Institute for Oncology and Radiology of Serbia. Three (3.6%) developed extraneural metastasis (ENM). In primary treatment, patients were treated with surgery, craniospinal radiotherapy with local boost to tumor bed, and adjuvant chemotherapy [lomustine (CCNU) and vincristine]. Of the three patients with ENM, all developed bone metastases at the time of relapse. Relapse occurred within 17 to 42 months of initial diagnosis. Patients received secondary chemotherapy and palliative radiotherapy to the affected bone in two cases.

RESULTS

Among these three patients, case 1 had initially a solitary lytic lesion. Case 2 had diffuse blastic lesions and also bone marrow involvement. Case 3 had multiple mixed lytic-sclerotic lesions but later developed lymph node metastasis and metastases to both breasts, as well. All patients were without concurrent CNS involvement at the time of ENM. Unfortunately, after initial partial response, the three patients died at 24, 13, and 18 months after detection of metastases, respectively.

CONCLUSION

With prolonged survival times in children with medulloblastoma, more emphasis should be placed on the possibility of systemic involvement. A greater understanding of the pathogenesis of the systemic metastases may be valuable in designing future, more aggressive multimodal therapy.

Assessment of reproducibility of cancer survival risk predictions across medical centers

BACKGROUND

Two most important considerations in evaluation of survival prediction models are 1) predictability - ability to predict survival risks accurately and 2) reproducibility - ability to generalize to predict samples generated from different studies. We present approaches for assessment of reproducibility of survival risk score predictions across medical centers.

METHODS

Reproducibility was evaluated in terms of consistency and transferability. Consistency is the agreement of risk scores predicted between two centers. Transferability from one center to another center is the agreement of the risk scores of the second center predicted by each of the two centers. The transferability can be: 1) model transferability - whether a predictive model developed from one center can be applied to predict the samples generated from other centers and 2) signature transferability - whether signature markers of a predictive model developed from one center can be applied to predict the samples from other centers. We considered eight prediction models, including two clinical models, two gene expression models, and their combinations. Predictive performance of the eight models was evaluated by several common measures. Correlation coefficients between predicted risk scores of different centers were computed to assess reproducibility - consistency and transferability.

RESULTS

Two public datasets, the lung cancer data generated from four medical centers and colon cancer data generated from two medical centers, were analyzed. The risk score estimates for lung cancer patients predicted by three of four centers agree reasonably well. In general, a good prediction model showed better cross-center consistency and transferability. The risk scores for the colon cancer patients from one (Moffitt) medical center that were predicted by the clinical models developed from the another (Vanderbilt) medical center were shown to have excellent model transferability and signature transferability.

CONCLUSIONS

This study illustrates an analytical approach to assessing reproducibility of predictive models and signatures. Based on the analyses of the two cancer datasets, we conclude that the models with clinical variables appear to perform reasonable well with high degree of consistency and transferability. There should have more investigations on the reproducibility of prediction models including gene expression data across studies.

Impact of genetic targets on primary brain tumor therapy: what's ready for prime time?

Primary brain tumors constitute a substantial public health problem with 66,290 cases diagnosed in the US in 2012, and 13,700 deaths recorded. With discovery of genetic factors associated with specific brain tumor subtypes, the goal of therapy is changing from treating a class of tumors to developing individualized therapies catering to the molecular composition of the actual tumor. For oligodendrogliomas, the loss of 1p/19q due to an unbalanced translocation improves both survival and the response to therapy, and is thus both a prognostic and a predictive marker. Several additional genetic alterations such as EGFR amplification, MGMT methylation, PDGFR activation, and 9p and 10q loss, have improved our understanding of the characteristics of these tumors and may help guide therapy in the future. For astrocytic tumors, MGMT is associated with a better prognosis and an improved response to temozolomide, and for all glial tumors, mutations in the IDH1 gene are possibly the most potent of good prognostic markers. Three of these markers - 1p/19q deletions, MGMT methylation status, and mutations in the IDH1 gene - are so potent that a new brain tumor subtype, the "triple negative" glioma (1p/19q intact, MGMT unmethylated, IDH1 non-mutated) has entered common parlance. Newer markers, such as CD 133, require additional investigation to determine their prognostic and predictive utility. In medulloblastomas, markers of WNT activation, MYCC/MCYN amplification, and TrkC expression levels are reliable prognostic indicators, but do not yet drive specific treatment selection. Many other proposed markers, such as 17q gain, TP53 mutations, and hMOF protein expression show promise, but are not yet ready for prime time. In this chapter, we focus on the markers that have shown convincing prognostic, predictive, and diagnostic value, and discuss potential markers that are being currently being intensively investigated. We also discuss serum profiling of tumors in an effort to discover additional potential markers.

Assessment of performance of survival prediction models for cancer prognosis

BACKGROUND

Cancer survival studies are commonly analyzed using survival-time prediction models for cancer prognosis. A number of different performance metrics are used to ascertain the concordance between the predicted risk score of each patient and the actual survival time, but these metrics can sometimes conflict. Alternatively, patients are sometimes divided into two classes according to a survival-time threshold, and binary classifiers are applied to predict each patient's class. Although this approach has several drawbacks, it does provide natural performance metrics such as positive and negative predictive values to enable unambiguous assessments.

METHODS

We compare the survival-time prediction and survival-time threshold approaches to analyzing cancer survival studies. We review and compare common performance metrics for the two approaches. We present new randomization tests and cross-validation methods to enable unambiguous statistical inferences for several performance metrics used with the survival-time prediction approach. We consider five survival prediction models consisting of one clinical model, two gene expression models, and two models from combinations of clinical and gene expression models.

RESULTS

A public breast cancer dataset was used to compare several performance metrics using five prediction models. 1) For some prediction models, the hazard ratio from fitting a Cox proportional hazards model was significant, but the two-group comparison was insignificant, and vice versa. 2) The randomization test and cross-validation were generally consistent with the p-values obtained from the standard performance metrics. 3) Binary classifiers highly depended on how the risk groups were defined; a slight change of the survival threshold for assignment of classes led to very different prediction results.

CONCLUSIONS

1) Different performance metrics for evaluation of a survival prediction model may give different conclusions in its discriminatory ability. 2) Evaluation using a high-risk versus low-risk group comparison depends on the selected risk-score threshold; a plot of p-values from all possible thresholds can show the sensitivity of the threshold selection. 3) A randomization test of the significance of Somers' rank correlation can be used for further evaluation of performance of a prediction model. 4) The cross-validated power of survival prediction models decreases as the training and test sets become less balanced.

The micro-RNA 199b-5p regulatory circuit involves Hes1, CD15, and epigenetic modifications in medulloblastoma

Micro-RNA (miR) 199b-5p targets Hes1 in medulloblastoma, one of the downstream effectors of both the canonical Notch and noncanonical Sonic Hedgehog pathways. In medulloblastoma patients, expression of miR-199b-5p is significantly decreased in metastatic cases, thus suggesting a downregulation mechanism. We studied this mechanism, which is mediated mostly by Hes1 and epigenetic promoter modifications. The miR-199b-5p promoter region was characterized, which identified a Hes1 binding site, thus demonstrating a negative feedback loop of regulation. MiR-199b-5p was shown to be downregulated in several medulloblastoma cell lines and in tumors by epigenetic methylation of a cytosine-phosphate-guanine island upstream of the miR-199b-5p promoter. Furthermore, the cluster of differention (CD) carbohydrate antigen CD15, a marker of medulloblastoma tumor-propagating cells, is an additional direct target of miR-199b-5p. Most importantly, regulation of miR-199b-5p expression in these CD15+/CD133+ tumor-propagating cells was influenced by only Hes1 expression and not by any epigenetic mechanism of regulation. Moreover, reverse-phase protein array analysis showed both the Akt and extracellular-signal-regulated kinase pathways as being mainly negatively regulated by miR-199b-5p expression in several medulloblastoma cell lines and in primary cell cultures. We present here the finely tuned regulation of miR-199b-5p in medulloblastoma, underlining its crucial role by its additional targeting of CD15.

Medulloblastoma and primitive neuroectodermal tumors

Medulloblastomas and sPNETs remain highly problematic tumors to treat. Prognosis has improved over the past two decades, but many children who survive treatment have significant long-term sequelae. The improvements in outcome have been due to advances in surgical techniques, the wider use of chemotherapy, and the more judicious use of radiotherapy. For further improvements,the recent impressive discoveries concerning molecular mechanisms of embryonal tumor origin, development,and growth will need to be translated into molecularly based, risk-adapted therapy.

[Medulloblastomas: review]

INTRODUCTION

The term of "medulloblastoma" refers to cerebellar tumors belonging to the family of primitive neuro-ectodermic tumors (PNET). Medulloblastomas represent 40% of cerebellar tumors, 15 to 20% of brain tumors and the first cause of malignant brain tumors in childhood. Seventy to 80% of cases are diagnosed in children versus 20 to 30% in adults.

UPDATED KNOWLEDGE

Diagnosis is based on clinical and radiological exams, and proved on pathological analysis in association with molecular biology. Treatment comprises surgery, craniospinal radiotherapy except for children under five years of age and chemotherapy according to age and high-risk criteria. Medulloblastoma is a rare case of a central nervous system tumor which is radio- and chemo-sensitive. Treatment goals are, on one hand, to improve the survival rates and, on the other hand, to avoid late neurocognitive, neuroendocrine and orthopedic side effects related to radiation therapy, notably in children. The prognosis is relatively good, with a five year survival rate over 75% after complete resection of a localized tumor although sequelae may still compromise outcome.

PERSPECTIVES AND CONCLUSION

Management of patients with medulloblastoma implies a multidisciplinary approach combining the contributions of neurosurgery, neuroradiology, pediatric oncology, neuro-oncology and radiotherapy teams.

Chromosome 17 alterations identify good-risk and poor-risk tumors independently of clinical factors in medulloblastoma

Current risk stratification schemas for medulloblastoma, based on combinations of clinical variables and histotype, fail to accurately identify particularly good- and poor-risk tumors. Attempts have been made to improve discriminatory power by combining clinical variables with cytogenetic data. We report here a pooled analysis of all previous reports of chromosomal copy number related to survival data in medulloblastoma. We collated data from previous reports that explicitly quoted survival data and chromosomal copy number in medulloblastoma. We analyzed the relative prognostic significance of currently used clinical risk stratifiers and the chromosomal aberrations previously reported to correlate with survival. In the pooled dataset metastatic disease, incomplete tumor resection and severe anaplasia were associated with poor outcome, while young age at presentation was not prognostically significant. Of the chromosomal variables studied, isolated 17p loss and gain of 1q correlated with poor survival. Gain of 17q without associated loss of 17p showed a trend to improved outcome. The most commonly reported alteration, isodicentric chromosome 17, was not prognostically significant. Sequential multivariate models identified isolated 17p loss, isolated 17q gain, and 1q gain as independent prognostic factors. In a historical dataset, we have identified isolated 17p loss as a marker of poor outcome and 17q gain as a novel putative marker of good prognosis. Biological markers of poor-risk and good-risk tumors will be critical in stratifying treatment in future trials. Our findings should be prospectively validated independently in future clinical studies.

Evidence in medulloblastomas

Medulloblastoma is the most common infratentorial malignant tumour under 15 years of age. In recent protocols, the patients are stratified for treatment in standard risk or high risk, according to the clinical variables as age, localized or disseminated disease, degree of surgical resection and more recently expected biological behaviour based on retrospective and prospective studies of former samples analyzed. The objectives for future treatments are reduce morbidity without jeopardizing survival.

OTX2 is critical for the maintenance and progression of Shh-independent medulloblastomas

OTX2 is a developmentally regulated transcription factor involved in early morphogenesis of the central nervous system. This gene is amplified and overexpressed in medulloblastoma cell lines, but the nature and extent of its genetic alterations in primary tumors have not been evaluated. Analysis of a large cohort of primary medulloblastomas revealed frequent focal copy number gain of a region minimally containing OTX2 as a single gene. OTX2 copy number gain was restricted to tumor subtypes that did not express a molecular signature of Wnt or Shh pathway activation. FISH analysis revealed copy number gain in a subset of cells within medulloblastoma samples, suggesting a late event in tumor progression. Gain of OTX2 copy number was associated with the presence of anaplastic histologic features and shorter survival in medulloblastoma patients. In support of a functional role, ectopic OTX2 expression enhanced proliferation and tumorigenicity of immortalized primary cells, whereas OTX2 knockdown in medulloblastoma cells prolonged the survival of animals bearing xenograft tumors. Mechanistic investigations revealed upregulation of MYC as a potential mechanism whereby OTX2 promotes tumor progression. Our findings define OTX2 as an important oncogenic driver in medulloblastoma.

The evolving role of surgery in the management of pediatric brain tumors

Surgery is an integral component and typically the first line of therapy for children with central nervous system tumors. The outcome with regard to surgical morbidity and disease control can be greatly influenced by the initial care that these children receive. Conventional aims of neurosurgery including tumor removal, management of hydrocephalus, and diagnostic sampling have been radically modified with innovative technologies such as navigational guidance, functional mapping, endoscopic surgery, second-look surgery, and physiologic imaging. The overall role of the pediatric neurosurgeon in caring for children with nervous system tumors is also expanding to include unconventional responsibilities including disease staging, tissue procurement, and drug delivery. It is thus anticipated that the pediatric neurosurgeon will be increasingly relied upon for oncologic therapeutic strategies and should thus remain abreast of forthcoming information and technologies.

Update on diagnostic practice: tumors of the nervous system

CONTEXT

Changes in the practice of diagnosing brain tumors are formally reflected in the evolution of the World Health Organization classification. Beyond this classification, the practice of diagnostic pathology is also changing with the availability of new tests and the introduction of new treatment options.

OBJECTIVE

Glioblastomas, oligodendrogliomas, glioneuronal tumors, and primitive pediatric tumors are discussed in an exemplary way to illustrate these changes.

DATA SOURCES

Review of relevant publications through Medline database searches.

CONCLUSIONS

The example of glioblastomas shows how new predictive markers may help identify subgroups of tumors that respond to certain therapy regimens. The development of new treatment strategies also leads to different questions in the assessment of brain tumors, as seen in the example of pseudoprogression or the changes in tumor growth pattern in patients taking bevacizumab. Oligodendrogliomas illustrate how the identification of 1p/19q loss as a cytogenetic aberration aids our understanding of these tumors and changes diagnostic practice but also introduces new challenges in classification. Glioneuronal tumors are an evolving group of lesions. Besides a growing list of usually low-grade entities with well-defined morphologic features, these also include more poorly defined cases in which a component of infiltrating glioma is often associated with focal neuronal elements. The latter is biologically interesting but of uncertain clinical significance. Oligodendrogliomas and glioneuronal tumors both illustrate the importance of effective communication between the pathologist and the treating oncologist in the discussion of these patients. Finally, the discussion of primitive pediatric tumors stresses the clinical importance of the distinction between different entities, like atypical teratoid rhabdoid tumor, "central" (supratentorial) primitive neuroectodermal tumor, "peripheral" primitive neuroectodermal tumor, and medulloblastoma. In medulloblastomas, the recognition of different variants is emerging as a prognostic factor that may in the future also predict therapy responsiveness.

Pediatric brain tumors: current treatment strategies and future therapeutic approaches

Pediatric CNS tumors are the most common solid tumors of childhood and the second most common cancer after hematological malignancies accounting for approximate 20 to 25% of all primary pediatric tumors. With over 3,000 new cases per year in the United States, childhood CNS tumors are the leading cause of death related to cancer in this population. The prognosis for these patients has improved over the last few decades, but current therapies continue to carry a high risk of significant side effects, especially for the very young. Currently a combination of surgery, radiation, and chemotherapy is often used in children greater than 3 years of age. This article will outline current and future therapeutic strategies for the most common pediatric CNS tumors, including primitive neuroectodermal tumors such as medulloblastoma, as well as astrocytomas and ependymomas.

Current treatment approaches for infants with malignant central nervous system tumors

The management of brain tumors in very young children remains a challenge for neuro-oncologists in large part because of the greater vulnerability of the developing brain to treatment-related toxicity. Nearly three decades of infant brain tumor clinical trials have led to significant progress in the delineation of prognostic factors and improvements in outcome. Innovative strategies that employ high-dose chemotherapy, intrathecal chemotherapy, modified focal irradiation, or combinations of these have been used to delay or avoid the use of conventional craniospinal irradiation in order to minimize the risk for deleterious neurocognitive impairment in survivors. However, it is difficult to evaluate the impact of such approaches on intellectual and functional outcome, and results to date are limited. This review covers the most recent therapeutic advances for the most common histological subtypes of malignant infant brain tumors: medulloblastoma, supratentorial primitive neuroectodermal tumor, ependymoma, atypical teratoid rhabdoid tumor, choroid plexus carcinoma, and high-grade glioma. Survival and neurocognitive outcome are emphasized.

Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci

PURPOSE

Medulloblastoma is the most common malignant brain tumor in children. Current treatment decisions are based on clinical variables. Novel tumor-derived biomarkers may improve the risk stratification of medulloblastoma patients.

PATIENTS AND METHODS

A model for the molecular risk stratification was proposed from an array-based comparative genomic hybridization (array-CGH) screen (n = 80). Fluorescence in situ hybridization (FISH) analyses for chromosome arms 6q, 17p, and 17q and the MYC and MYCN loci were performed in an independent validation set (n = 260). Copy number aberrations were correlated with clinical, histologic, and survival data.

RESULTS

Gain of 6q and 17q and genomic amplification of MYC or MYCN were each associated with poor outcome in the array-CGH study (n = 80). In contrast, all patients with 6q-deleted tumors survived. Given these findings, the following hierarchical molecular staging system was defined: (1) MYC/MYCN amplification, (2) 6q gain, (3) 17q gain, (4) 6q and 17q balanced, and (5) 6q deletion. The prognostic value of this staging system was investigated by FISH analysis (n = 260). The addition of molecular markers to clinical risk factors resulted in the identification of a large proportion of patients (72 of 260 patients; 30%) at high risk for relapse and death who would be considered standard risk by application of clinical variables alone.

CONCLUSION

Genomic aberrations in medulloblastoma are powerful independent markers of disease progression and survival. By adding genomic markers to established clinical and histologic variables, outcome prediction can be substantially improved. Because the analyses can be conducted on routine paraffin-embedded material, it will be especially feasible to use this novel molecular staging system in large multicenter clinical trials.

Survival of patients with adult medulloblastoma: a population-based study

BACKGROUND

Adult medulloblastoma accounts for less than 1% of adult intracranial tumors. Previous survival studies have been inconclusive because of small sample sizes and patient ascertainment bias.

METHODS

The Surveillance, Epidemiology, and End Results (SEER) 17 registries database, released April 2007, was used to assess survival rates and prognostic factors in this disease. SEER*Stat was used to calculate observed and relative 2-, 5-, 10-, 15-, and 20-year survival and Cox Proportion Hazard Regression modeling was used to evaluate prognostic variables.

RESULTS

Four hundred fifty-four patients with adult medulloblastoma were diagnosed from 1973-2004 in the 17 regions covered by SEER. The 2-, 5-, and 10-year relative survival rates were 79.9, 64.9, and 52.1%, respectively. The overall median survival was 127 months (10.6 years). The survival of this disease has improved in the last 3 decades. The median survival of those diagnosed <or= 1980 and from 1981-1990 were 39 (3.3 years) and 127 months (10.6 years), respectively, and has not been reached for those diagnosed from 1991-2000 and after 2000. In multivariable regression modeling, diagnoses after the 1980s, age of diagnosis before 20, gross total resection, and radiation were favorable prognostic factors, whereas large cell histology was associated with poor survival.

CONCLUSIONS

This is the largest and most representative survival study to date, but further assessments are needed to evaluate the potential of using molecular genetic markers, together with clinical and histopathologic variables, in predicting survival. This may have to take place in the context of a large consortium.

Outcome of pediatric pineoblastoma after surgery, radiation and chemotherapy

INTRODUCTION

Pineoblastomas are a category of supratentorial primitive neuroectodermal tumors (sPNETs) occurring in the pineal gland; some studies support the impression that patients with pineoblastomas have a worse prognosis than those with other sPNETs.

METHODS

We reviewed the medical records and tissue sections of all patients with the diagnosis of pineoblastoma that were treated at the Dana-Farber Cancer Institute/Children's Hospital Boston Pediatric Brain Tumor Program between 1986 and 2005.

RESULTS

Thirteen patients with the pathologic diagnosis of pineoblastoma were treated at our Hospital; 11 of these cases had complete records suitable for study. The median age was 8 years 8 months (5 F, 6 M). Surgical, radiation and chemotherapeutic regimens varied from case to case. Three patients had gross total resection and are alive and free of disease, versus four of eight with subtotal resection or biopsy only. Patients who received CSI and multi-agent chemotherapy had improved overall survival.

CONCLUSIONS

Seven of eleven patients with pineoblastoma are currently alive and free of disease, reflecting an improved outcome and longer survival than previously appreciated. Gross total surgical resection appeared to correlate with improved survival, as did treatment with craniospinal irradiation and multi-agent chemotherapy. Further study of this group of patients as a distinct diagnostic entity will be necessary to determine optimal therapy.

Expression of MAGE and GAGE genes in medulloblastoma and modulation of resistance to chemotherapy. Laboratory investigation

OBJECT

Cancer testis antigens (CTAs) were initially identified by their ability to elicit autologous T-cell-mediated immune responses in patients with melanoma. The CTA genes are widely expressed in a variety of human cancers, such as melanoma, breast cancer, lung cancer, esophageal cancer, and hepatocellular carcinoma; however, their expression in pediatric brain tumors, such as medulloblastoma (MB), has not been the subject of in-depth analysis. The MAGE proteins are members of the CTA family and have been shown to correlate with tumor development, aggressive clinical course, or resistance to chemotherapeutic agents. The authors undertook this study to examine the expression and role of MAGE proteins in human MB cell lines and specimens.

METHODS

From a transcriptional profiling study in which 47,000 genes in MB cell lines were examined, the authors identified members of the MAGE and GAGE families as being highly expressed. A series of MB tumors was examined using both immunohistochemistry and Western blot analysis with antibodies to the MAGE-A family, MAGE-A1, and GAGE proteins.

RESULTS

Western blot analysis showed expression of these 3 proteins (MAGE-A family, MAGE-A1, and GAGE) in 62, 46, and 84%, respectively, of MB specimens examined. In addition, a correlation was observed between the expression of MAGE and GAGE genes and resistance of MB cells to chemotherapeutic agents. The functional significance of this correlation was examined in MAGE knockdown studies, and increased drug-induced cytotoxicity was observed in UW426 MB cells following treatment with chemotherapeutic drugs. Cleaved caspase-3 was found in UW426/MAGE small interfering (si)RNA-inhibited cells treated with cisplatin, but not in UW426 cells treated with cisplatin alone at the same concentration.

CONCLUSIONS

These data show that MAGE and GAGE family members are expressed in MB cell lines and specimens, and that inhibition of MAGE and GAGE genes by siRNA increases apoptosis of MB cells and sensitizes them to certain chemotherapeutic agents such as cisplatin and etoposide.

Clinical and Molecular Parameters for Risk Stratification in Mexican Children with Medulloblastoma

BACKGROUND

Clinical, histological, and more recently, molecular factors have been described as important in survival of the patient with medulloblastoma. Best survival results include aggressive chemotherapeutic protocols. More exact risk analysis may differentiate patients who require aggressive treatments from those with low risk who may respond adequately to less aggressive protocols.

METHODS

Twenty six patients were included over a 10-year period and were followed for at least 5 years. Personal variables were obtained from their clinical records. Immunochemistry studies were performed on their formalin-fixed paraffin-embedded tissues. Statistical analysis included chi(2) test, odds risk, linear regression models, and Kaplan-Meier survival analysis.

RESULTS

Metastatic disease and chemotherapy with VP16-carboplatin reduce the patient's probability of survival, whereas anaplastic histology increases the probability of death. Global survival and disease-free survival were 66.6 and 45.02%, respectively. Only two patients overexpressed the ERBB2 protein, and no significant difference was found in survival in terms of ERBB2 overexpression.

CONCLUSIONS

Risk stratification has become very important in medulloblastoma. We found an increased hazard of death when metastatic disease was present. Gene expression in Mexican children requires a larger sample in order to be analyzed.

Emerging treatments and gene expression profiling in high-risk medulloblastoma

The past decades have seen an increase in the survival rates of patients with standard-risk medulloblastoma. Efforts have, therefore, been focused on obtaining better results in the treatment of patients with high-risk tumors. In addition to consolidated therapies, novel approaches such as small molecules, monoclonal antibodies, and antiangiogenic therapies that aim to improve outcomes and quality of life are now available through new breakthroughs in the molecular biology of medulloblastoma. The advent of innovative anticancer drugs tested in brain tumors has important consequences for personalized therapy. Gene expression profiling of medulloblastoma can be used to identify the genes and signaling transduction pathways that are crucial for the tumorigenesis process, thereby revealing both new targets for therapy and sensitive/resistance phenotypes. The interpretation of microarray data for new treatments of patients with high-risk medulloblastoma, as well as other poor prognosis tumors, should be developed through a consensus multidisciplinary approach involving oncologists, neurosurgeons, radiotherapists, biotechnologists, bioinformaticists, and other professionals.

Principes et intérêts pour l’étude des maladies neurologiques et technologie des puces ADN

INTRODUCTION

DNA microarray is a powerful technology which can rapidly provide a high throughput and detailed view of the entire genome and transcriptome. In this review we discuss the basic principles behind gene expression microarrays, CGH arrays and DNA microarray genotyping, and their potential applications to neurological diseases.

STATE OF THE ART

Microarray gene expression profiling is a reliable technology that has already been used with great success in the molecular classification of cancer. It is a very promising technology in the field of Neurooncology. One of the interesting characteristics of DNA microarrays is also that they can be used in a non-hypothesis-driven manner to discover new genomic characteristics that will enable to establish new pathophysiological hypotheses. Such a strategy has already yielded interesting new insights in the study of multiple sclerosis, Alzheimer disease or neuromuscular diseases. With DNA microarray genotyping it is now possible to detect mutations in many genes simultaneously.

CONCLUSIONS

In Neurooncology DNA microarrays should help to establish a more accurate classification of brain tumors and recent studies have shown how gene expression profiling of brain tumors allows to uncover previously unrecognized patient subsets that differ in their survival. The applications of microarrays for the study of neurological diseases, like multiple sclerosis, Alzheimer disease or neuromuscular diseases are also promising both for generating new pathophysiological hypotheses and for enabling new molecular classifications. DNA microarray genotyping is a powerful technology that should help to discover genetic factors associated with multifactorial neurological disorders and help to diagnose complex neurogenetic diseases. This technology should also facilitate the realization of pharmacogenomic studies in neurological diseases.

Combining Clinical and Genomic Covariates via Cov-TGDR

Clinical covariates such as age, gender, tumor grade, and smoking history have been extensively used in prediction of disease occurrence and progression. On the other hand, genomic biomarkers selected from microarray measurements may provide an alternative, satisfactory way of disease prediction. Recent studies show that better prediction can be achieved by using both clinical and genomic biomarkers. However, due to different characteristics of clinical and genomic measurements, combining those covariates in disease prediction is very challenging. We propose a new regularization method, Covariate-Adjusted Threshold Gradient Directed Regularization (Cov-TGDR), for combining different type of covariates in disease prediction. The proposed approach is capable of simultaneous biomarker selection and predictive model building. It allows different degrees of regularization for different type of covariates. We consider biomedical studies with binary outcomes and right censored survival outcomes as examples. Logistic model and Cox model are assumed, respectively. Analysis of the Breast Cancer data and the Follicular lymphoma data show that the proposed approach can have better prediction performance than using clinical or genomic covariates alone.

Molecular genetics of pediatric central nervous system tumors

Recent advances in molecular biology have enhanced our understanding of the pathogenesis of brain tumors, particularly in children. The use of molecular diagnostic tools is quickly becoming a standard component in the diagnosis and classification of brain tumors in children, in addition to providing insight leading to treatment stratification and improved outcome prediction. All new protocols involving treatments for brain tumors in children include studies of biomarkers and biologic correlates as a means to identify new targets for therapeutics and possible intervention strategies.

Current concepts in the molecular genetics of pediatric brain tumors: implications for emerging therapies

BACKGROUND

The revolution in molecular biology that has taken place over the past 2 decades has provided researchers with new and powerful tools for detailed study of the molecular mechanisms giving rise to the spectrum of pediatric brain tumors. Application of these tools has greatly advanced our understanding of the molecular pathogenesis of these lesions.

REVIEW

After familiarizing readers with some promising new techniques in the field of oncogenomics, this review will present the current state of knowledge as it pertains to the molecular biology of pediatric brain neoplasms. Along the way, we hope to highlight specific instances where the detailed mechanistic knowledge acquired thus far may be exploited for therapeutic advantage.

Molecular changes in brain tumors: prognostic and therapeutic impact

PURPOSE OF REVIEW

This review focuses on recent advances in the molecular biology of the main primary brain tumors (gliomas, medulloblastomas, and ependymomas), with particular emphasis on prognostic markers and potential therapeutic targets.

RECENT FINDINGS

Current biologic markers are useful for predicting prognosis (e.g. 1p/19q codeletion in grade 2 and 3 gliomas, nuclear beta-catenin expression in medulloblastoma) or response to the treatment (e.g. the methyl guanyl methyl transferase promoter methylation status). Recent gene profiling studies have identified specific molecular signatures that permit a molecular classification and that also provide new, potentially useful prognostic markers. The studies have also shown a striking parallel between central nervous system ontogenesis and the oncogenesis of brain tumors. By elucidating the underlying activated molecular pathways, these approaches provide the basis for a biologic therapy to target the critically activated pathways.

SUMMARY

Important advances have been made in the biologic understanding, molecular subclassification, and identification of prognostic markers in brain tumors, thereby improving the current classifications. Such data provide a rational basis for current and future targeted biologically based strategies.

Medulloblastoma outcome is adversely associated with overexpression of EEF1D, RPL30, and RPS20 on the long arm of chromosome 8

Background

Medulloblastoma is the most common malignant brain tumor of childhood. Improvements in clinical outcome require a better understanding of the genetic alterations to identify clinically significant biological factors and to stratify patients accordingly. In the present study, we applied cytogenetic characterization to guide the identification of biologically significant genes from gene expression microarray profiles of medulloblastoma.

Methods

We analyzed 71 primary medulloblastomas for chromosomal copy number aberrations (CNAs) using comparative genomic hybridization (CGH). Among 64 tumors that we previously analyzed by gene expression microarrays, 27 were included in our CGH series. We analyzed clinical outcome with respect to CNAs and microarray results. We filtered microarray data using specific CNAs to detect differentially expressed candidate genes associated with survival.

Results

The most frequent lesions detected in our series involved chromosome 17; loss of 16q, 10q, or 8p; and gain of 7q or 2p. Recurrent amplifications at 2p23-p24, 2q14, 7q34, and 12p13 were also observed. Gain of 8q is associated with worse overall survival (p = 0.0141), which is not entirely attributable to MYC amplification or overexpression. By applying CGH results to gene expression analysis of medulloblastoma, we identified three 8q-mapped genes that are associated with overall survival in the larger group of 64 patients (p < 0.05): eukaryotic translation elongation factor 1D (EEF1D), ribosomal protein L30 (RPL30), and ribosomal protein S20 (RPS20).

Conclusion

The complementary use of CGH and expression profiles can facilitate the identification of clinically significant candidate genes involved in medulloblastoma growth. We demonstrate that gain of 8q and expression levels of three 8q-mapped candidate genes (EEF1D, RPL30, RPS20) are associated with adverse outcome in medulloblastoma.

Early gene expression profile in mouse brain after exposure to ionizing radiation

Acute changes in the gene expression profile in mouse brain after exposure to ionizing radiation were studied using microarray analysis. RNA was isolated at 0.25, 1, 5 and 24 h after exposure to 20 Gy and at 5 h after exposure of the whole brain of adult mice to 2 or 10 Gy. RNA was hybridized onto 15K cDNA microarrays, and data were analyzed using GeneSpring and Significant Analysis of Microarray. Radiation modulated the expression of 128, 334, 325 and 155 genes and ESTs at 0.25, 1, 5 and 24 h after 20 Gy and 60 and 168 at 5 h after 2 and 10 Gy, respectively. The expression profiles showed dose- and time-dependent changes in both expression levels and numbers of differentially modulated genes and ESTs. Seventy-eight genes were modulated at two or more times. Differentially modulated genes were associated with 12 different classes of molecular function and 24 different biological pathways and showed time- and dose-dependent changes. The change in expression of four genes (Jak3, Dffb, Nsep1 and Terf1) after irradiation was validated using quantitative real-time PCR. Up-regulation of Jak3 was observed in another mouse strain. In mouse brain, there was an increase of Jak3 immunoreactivity after irradiation. In conclusion, changes in the gene profile in the brain after irradiation are complex and are dependent on time and dose, and genes with diverse functions and pathways are modulated.

Distinctive clinical course and pattern of relapse in adolescents with medulloblastoma

PURPOSE

To report the clinical course of adolescents with medulloblastoma, with specific emphasis on prognosis and pattern of relapse.

METHODS AND MATERIALS

We retrospectively studied the clinical course and outcomes of children aged 10-20 years with medulloblastoma, treated at centers throughout Canada between 1986 and 2003. To better assess time to relapse, a cohort of patients aged 3-20 years at diagnosis was generated.

RESULTS

A total of 72 adolescents were analyzed. Five-year overall survival and event-free survival rates were 78.3%+/-5.4% and 68.0%+/-6.2%, respectively. Late relapses occurred at a median of 3.0 years (range, 0.3-6.8 years). In univariate analysis, conventional risk stratification and the addition of chemotherapy to craniospinal radiation did not have prognostic significance. Female patients had improved overall survival (p=0.007). Time to relapse increased with age in a linear fashion. After relapse, patients faired poorly regardless of treatment modality. Patients who did not receive chemotherapy initially had improved progression-free survival at relapse (p=0.05).

CONCLUSIONS

Our study suggests that adolescents with medulloblastoma might have a unique prognosis and pattern of relapse, dissimilar to those in younger children. They might benefit from different risk stratifications and prolonged follow-up. These issues should be addressed in future prospective trials.

Standard-Risk Medulloblastoma Treated by Adjuvant Chemotherapy Followed by Reduced-Dose Craniospinal Radiation Therapy: A French Society of Pediatric Oncology Study

Objective

The primary objective of this study was to decrease the late effects of prophylactic radiation without reducing survival in standard-risk childhood medulloblastoma.

Patients and Methods

Inclusion criteria were as follows: children between the ages of 3 and 18 years with total or subtotal tumor resection, no metastasis, and negative postoperative lumbar puncture CSF cytology. Two courses of eight drugs in 1 day followed by two courses of etoposide plus carboplatin (500 and 800 mg/m2 per course, respectively) were administered after surgery. Radiation therapy had to begin 90 days after surgery. Delivered doses were 55 Gy to the posterior fossa and 25 Gy to the brain and spinal canal.

Results

Between November 1991 and June 1998, 136 patients (median age, 8 years; median follow-up, 6.5 years) were included. The overall survival rate and 5-year recurrence-free survival rate were 73.8% ± 7.6% and 64.8% ± 8.1%, respectively. Radiologic review showed that 4% of patients were wrongly included. Review of radiotherapy technical files demonstrated a correlation between the presence of a major protocol deviation and treatment failure. The 5-year recurrence-free survival rate of patients included in this study with all optimal quality controls of histology, radiology, and radiotherapy was 71.8% ± 10.5%. In terms of sequelae, 31% of patients required growth hormone replacement therapy and 25% required special schooling.

Conclusion

Reduced-dose craniospinal radiation therapy can be proposed in standard-risk medulloblastoma provided staging and radiation therapy are performed under optimal conditions.

Expression of MATH1, a marker of cerebellar granule cell progenitors, identifies different medulloblastoma sub-types

In order to look for genetic markers helpful for the biological risk stratification of medulloblastomas (MBs) we assayed by real-time PCR expression levels of the following genes: MATH1, encoding a critical transcription factor for the differentiation of cerebellar granular cells (CGCs); PEDF, that encodes a trophic factor for CGCs and is located in a region of frequent allelic imbalance in MBs; and BIRC5, encoding the antiapoptotic protein survivin, usually overexpressed in malignancies. Expression levels of TRKC, higher in MBs with a more favorable prognosis, were also studied. Twenty-three patients were considered: MATH1 expression was strong in 14/23 and undetectable in the others. PEDF was up-regulated in 8/23, TRKC in 9/23, and BIRC5 in 23/23. MATH1 expression was significantly correlated with adult age (p < 0.0001), tumor location in hemispheres rather than the vermis (p < 0.0004), and PEDF and TRKC up-regulation (p < 0.008 and p < 0.04, respectively). During development MATH1 is selectively expressed in the external germinal layer (EGL) of the cerebellum. Thus, MATH1 expression identifies a subgroup of MBs that derive from the EGL and arise during adult age into cerebellar hemispheres. MATH1 mRNA-positive MBs express high levels of PEDF and show a trend towards longer survival, in agreement with increased expression of TRKC. BIRC5 expression, which is strong in all MBs and absent in normal cerebellum, lacks any prognostic value but could be explored for selective targeting of therapeutic factors to MBs.

Brain tumors in children

Pediatric brain tumors are a challenging group of very divergent diseases. Considerable controversy exists concerning the accurate diagnosis and treatment of these patients. Aggressive therapy is often needed to cure aggressive and potentially lethal disease, yet late effects, especially injury to the developing brain, remain a profound problem. The discipline of pediatric neuro-oncology remains one of the most productive areas for continued clinical and basic research because of these and other challenges.

Prognosis-Related Molecular Markers in Pediatric Central Nervous System Tumors

In the wake of recent progress in understanding the genetic pathways involved in the development of brain tumors, a major goal is to correlate molecular data with clinical outcome, survival, and response to treatment modalities. This is of particular importance among the pediatric population. Reliable prognostic factors could potentially permit a tailoring of therapy in that only patients with the most aggressive tumors would receive the most intense treatments. A survey of publications about prognosis-related molecular features among pediatric brain tumors revealed 74 series, of which 46 presented statistically significant outcome-associated parameters as defined by a p value <0.05. Most investigations revealing significant prognosis-related features were performed on medulloblastomas (34 publications), followed by astrocytic tumors (6 publications) and ependymomas (5 publications). Promising approaches and molecular markers include gene expression profiles, DNA ploidy, loss of heterozygosity and chromosomal aberrations as detected by CGH and FISH (1q, 17p, 17q), as well as oncogenes/ tumor suppressor genes and their proteins (TP53, PTEN, c-erbB2, N-myc, c-myc), growth factor and hormonal receptors (PDGFRA, VEGF, EGFR, HER2, HER4, ErbB-2, hTERT, TrkC), cell cycle genes (p27) and cell adhesion molecules, as well as factors potentially related to therapeutic resistance (multi-drug resistance, DNA topoisomerase IIalpha, metallothionein, P-glycoprotein, tenascin). This review discusses the predictive potential of molecular markers for clinical outcome and their influence on therapeutic decision-making among children with brain tumors.

DNA-microarray analysis of brain cancer: molecular classification for therapy

Primary brain tumours are among the most lethal of all cancers, largely as a result of their lack of responsiveness to current therapy. Numerous new therapies hold great promise for the treatment of patients with brain cancer, but the main challenge is to determine which treatment is most likely to benefit an individual patient. DNA-microarray-based technologies, which allow simultaneous analysis of expression of thousands of genes, have already begun to uncover previously unrecognized patient subsets that differ in their survival. Here, we review the progress made so far in using DNA microarrays to optimize brain cancer therapy.