Predictive and prognostic markers in neuro-oncology

Prognostic and Predictive Value of a Long Non-coding RNA Signature in Glioma: A lncRNA Expression Analysis

The current histologically based grading system for glioma does not accurately predict which patients will have better outcomes or benefit from adjuvant chemotherapy. We proposed that combining the expression profiles of multiple long non-coding RNAs (lncRNAs) into a single model could improve prediction accuracy. We included 1,094 glioma patients from three different datasets. Using the least absolute shrinkage and selection operator (LASSO) Cox regression model, we built a multiple-lncRNA-based classifier on the basis of a training set. The predictive and prognostic accuracy of the classifier was validated using an internal test set and two external independent sets. Using this classifier, we classified patients in the training set into high- or low-risk groups with significantly different overall survival (OS, HR = 8.42, 95% CI = 4.99–14.2, p < 0.0001). The prognostic power of the classifier was then assessed in the other sets. The classifier was an independent prognostic factor and had better prognostic value than clinicopathological risk factors. The patients in the high-risk group were found to have a favorable response to adjuvant chemotherapy (HR = 0.4, 95% CI = 0.25–0.64, p < 0.0001). We built a nomogram that integrated the 10-lncRNA-based classifier and four clinicopathological risk factors to predict 3 and 5 year OS. Gene set variation analysis (GSVA) showed that pathways related to tumorigenesis, undifferentiated cancer, and epithelial–mesenchymal transition were enriched in the high-risk groups. Our classifier built on 10-lncRNAs is a reliable prognostic and predictive tool for OS in glioma patients and could predict which patients would benefit from adjuvant chemotherapy.

Relationship between Malignant Brain Tumors and Values of Homocysteine, Folic Acid and Vitamin B12

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Homocysteine (Hcy) has a detrimental influence on human neurons, considering that human GBM cells undergo cell death already at D,L-Hcy concentrations in culture medium of 50 μM. Th is data demonstrate that Hcy is a potent gliotoxic agent capable of inducing the death of human glial cells already at concentrations reached in brain during hyperhomocysteinemia. The one retrospective study found that the serum vitamin B12 level can be used to predict survival time in metastatic cancer patients including neurological cancer. Cancer risk increases with elevated vitamin B12 level, mostly within the first year of the follow-up period, suggesting that vitamin B12 level could be used as a cancer diagnostic marker. In addition, the relationship between elevated vitamin B12 level and poor cancer survival time has been reported. Previous investigation suggests that the folate supplementation could be used as an adjuvant in antiglioma therapy to limit the low DNA methylation level because this confers a poor prognosis in glioblastoma multiforme patients. Taking into account all presented data, it can be concluded that effect of homocystein, folic acid and vitamin B12 on formation, development and outcome of treatment in patients with carcinoma is very intriguing question, whose response requires additional both experimental and clinical research. There lack of data in the literature on the incidence of elevated levels of Hcy in the blood, as well as the disorders of folic acid and vitamin B12, at malignant tumors of the brain.

Prognostic role of microRNA-21 expression in gliomas: a meta-analysis

MicroRNA-21 (miRNA-21) has recently been shown to be a promising prognostic tumor biomarker. However, few studies have not supported this idea and have shown inconsistent data. Thus, we conducted a meta-analysis to elucidate the predictive value of miRNA-21 in gliomas. The relevant studies were identified by performing online search in PubMed, EMBASE and Web of Science databases up to Apr 2016. This meta-analysis study included seven eligible studies, consisting of 1121 gliomas and 533 glioblastoma multiforme (GBM) patients. Heterogeneity between studies was assessed using Egger's and Begg's test. Hazard ratios (HRs) with 95 % confidence intervals (CIs) for overall survival (OS), which compared the expression levels of miRNA-21 in patients with gliomas, were extracted and estimated. Our analysis revealed that the high expression of miRNA-21 is associated with the worse OS in gliomas. Further subgroup analysis indicated that increased expression of miRNA-21 was also associated with OS in GBM patients. Moreover, we observed a correlation between miRNA-21 expression and the World Health Organization defined gliomas grading system (WHO grade). Besides, high miRNA-21 expression was significantly correlated with lowered OS both in the Asian group and non-Asian group. In the cut-off subgroup analysis, both mean cut off value and median cut off value were significantly associated with OS. The expression level of miRNA-21 was not high in low KPS (Karnofsky score) group. miRNA-21 appears to be a promising biomarker for predicting the progression of patients with gliomas or GBM. However, due to the limited sample size, further prospective or retrospective multi-center well designed studies with adequate sample size should be conducted to verify its definite prognostic value.

Impact on prognosis of the regional distribution of MGMT methylation with respect to the CpG island methylator phenotype and age in glioma patients

Clinical and molecular prognostic factors in gliomas include age, IDH mutation, the glioma CpG island methylator phenotype (G-CIMP+) and promoter methylation of the O(6)-methylguanine DNA-methyltransferase (MGMT) gene. Among these markers, a predictive value was reported in glioblastomas (GBM) for MGMT promoter methylation, in particular in elderly GBM patients. In this study, methylation data from 46 glioma samples with the Illumina 450K platform were obtained and extended using external data to include a total of 247 glioma samples. Methylation analysis of the whole MGMT gene with this platform revealed two strongly survival-associated CpG regions within the promoter and the gene body, which were confirmed in a reported dataset of high grade-gliomas. Methylation at the promoter (CpG 25, cg12981137 and the prognostic model MGMT-STP27) and at the gene body CpG 165 (cg07933035), were significantly associated with better overall survival, and strongly correlated with G-CIMP+ status. In this series, the prognostic value of MGMT methylation at the promoter was not observed in G-CIMP- cases, although around 50 % of them were MGMT-methylated. These results were also obtained in an homogeneously-treated series of chemoradiated G-CIMP- GBMs analyzed by MSP and qMSP, and confirmed in a reported pyrosequencing-analyzed series of gliomas. Interestingly, in contrast to the MGMT promoter, gene body methylation was of prognostic value in G-CIMP-patients older than 65 years. Our study highlights the relevance of the prognostic value of the different regions of methylation throughout the MGMT gene that could be affected by specific G-CIMP profiles and age groups.

Can in-vitro chemoresponse assays help find new treatment regimens for malignant gliomas?

Various in-vitro chemosensitivity and resistance assays (CSRAs) have been demonstrated to be helpful decision aids for non-neurological tumors. Here, we evaluated the performance characteristics of two CSRAs for glioblastoma (GB) cells. The chemoresponse of fresh GB cells from 30 patients was studied in vitro using the ATP tumor chemoresponse assay and the chemotherapy resistance assay (CTR-Test). Both assay platforms provided comparable results. Of seven different chemotherapeutic drugs and drug combinations tested in vitro, treosulfan plus cytarabine (TARA) was the most effective, followed by nimustine (ACNU) plus teniposide (VM26) and temozolomide (TMZ). Whereas ACNU/VM26 and TMZ have proven their clinical value for malignant gliomas in large randomized studies, TARA has not been successful in newly diagnosed gliomas. This seeming discrepancy between in vitro and clinical result might be explained by the pharmacological behavior of treosulfan. Our results show reasonable agreement between two cell-based CSRAs. They appear to confirm the clinical effectiveness of drugs used in GB treatment as long as pharmacological preconditions such as overcoming the blood-brain barrier are properly considered.

Establishment and characterization of primary glioblastoma cell lines from fresh and frozen material: a detailed comparison

Background

Development of clinically relevant tumor model systems for glioblastoma multiforme (GBM) is important for advancement of basic and translational biology. High molecular heterogeneity of GBM tumors is well recognized, forming the rationale for molecular tests required before administration of several of the novel therapeutics rapidly entering the clinics. One model that has gained wide acceptance is the primary cell culture model. The laborious and time consuming process is rewarded with a relative high success rate (about 60%). We here describe and evaluate a very simple cryopreservation procedure for GBM tissue prior to model establishment that will considerably reduce the logistic complexity.

Methods

Twenty-seven GBM samples collected ad hoc were prepared for primary cell culture freshly from surgery (#1) and after cryopreservation (#2).

Results

Take rates after cryopreservation (59%) were as satisfactory as from fresh tissue (63%; p = 1.000). We did not observe any relevant molecular or phenotypic differences between cell lines established from fresh or vitally frozen tissue. Further, sensitivity both towards standard chemotherapeutic agents (Temozolomide, BCNU and Vincristine) and novel agents like the receptor tyrosine kinase inhibitor Imatinib did not differ.

Conclusions

Our simple cryopreservation procedure facilitates collection, long-time storage and propagation (modeling) of clinical GBM specimens (potentially also from distant centers) for basic research, (pre-) clinical studies of novel therapies and individual response prediction.

Expression of p53, epidermal growth factor receptor, Ki-67 and O6-methylguanine-DNA methyltransferase in human gliomas

The present study aimed to evaluate the expression of p53, Ki-67, epidermal growth factor receptor (EGFR) and O⁶-methylguanine-DNA methyltransferase (MGMT), and to analyze the correlation between their expression and the histological grade of the tumors in 152 patients with gliomas. The tumors were classified according to the recommendations of the World Health Organization (WHO; 2007) into grade I (n=9), grade II (n=56), grade III (n=52) and grade IV (n=35). The expression of p53, Ki-67, EGFR and MGMT was analyzed using immunohistochemistry. The frequency of p53 immunopositivity was significantly lower in grade I gliomas than in grades II, III and IV. The frequency of EGFR immunopositivity was significantly higher in grade III and IV gliomas compared with grades I and II. The mean Ki-67 labelling index (LI) significantly increased in the higher glioma grades. The expression of MGMT in grade I and II tumors was not significantly different from that of grade III and IV tumors. The present data indicate that the expression of EGFR and Ki-67 is significantly correlated with the histological grade of the glioma, but that the expression of p53 and MGMT is not associated with the tumor grade.

Oncogene addiction in gliomas: implications for molecular targeted therapy

Oncogene addiction is a phenomenon that the survival of cancer cells depends on an activated oncogene or inactivation of tumor suppressor gene, and is regarded as the 'Achilles heel' of the successful molecular targeted therapies in cancer. However, the role of oncogene addiction in gliomas has not been elucidated systematically. In this review, we summarize the current experimental and clinical evidence for the concept of oncogene addiction and describe the mechanisms explaining oncogene addiction in gliomas. And the clinical implications for oncogene addiction in molecular targeted therapy are further emphasized. In addition, we discuss future direction for defining complex "oncogene addiction network" through the integrated analysis of multiple platforms in the flow of genetic information in gliomagenesis.

Robust detection of EGFR copy number changes and EGFR variant III: technical aspects and relevance for glioma diagnostics

Epidermal growth factor receptor (EGFR) is commonly affected in cancer, generally in the form of an increase in DNA copy number and/or as mutation variants [e.g., EGFR variant III (EGFRvIII), an in-frame deletion of exons 2-7]. While detection of EGFR aberrations can be expected to be relevant for glioma patients, such analysis has not yet been implemented in a routine setting, also because feasible and robust assays were lacking. We evaluated multiplex ligation-dependent probe amplification (MLPA) for detection of EGFR amplification and EGFRvIII in DNA of a spectrum of 216 diffuse gliomas. EGFRvIII detection was verified at the protein level by immunohistochemistry and at the RNA level using the conventionally used endpoint RT-PCR as well as a newly developed quantitative RT-PCR. Compared to these techniques, the DNA-based MLPA assay for EGFR/EGFRvIII analysis tested showed 100% sensitivity and specificity. We conclude that MLPA is a robust assay for detection of EGFR/EGFRvIII aberrations. While the exact diagnostic, prognostic and predictive value of such EGFR testing remains to be seen, MLPA has great potential as it can reliably and relatively easily be performed on routinely processed (formalin-fixed, paraffin-embedded) tumor tissue in combination with testing for other relevant glioma markers.

Methylation Status of the O6-Methylguanine-Deoxyribonucleic Acid Methyltransferase Gene Promoter in World Health Organization Grade III Gliomas

OBJECTIVE

We analyzed the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter in World Health Organization (WHO) grade III gliomas in association with other molecular markers to evaluate their prevalence.

METHODS

The samples of a total of 36 newly WHO grade III glioma patients including 19 anaplastic oligodendrogliomas (AO), 7 anaplastic oligoastrocytomas (AOA), and 10 anaplastic astrocytomas (AA) were analyzed. The methylation status of the MGMT gene promoter was confirmed by methylation-specific polymerase chain reaction. The 1p/19q chromosomal deletion status and EGFR amplification were assessed by Fluorescence In-Situ Hybridization. MGMT, EGFR, EGFRvIII, and p53 expression were analyzed by immunohistochemical staining.

RESULTS

The MGMT gene promoter was methylated in 32 (88.9%) and unmethylated in 4 (11.2%). Among them, all of the AO and AOA had methylated MGMT gene promoter without exception. Significant associations between MGMT gene promoter hypermethylation and 1p/19q deletion was observed (p = 0.003). Other molecular markers failed to show significant associations between MGMT gene promoter statuses.

CONCLUSION

There was extensive epigenetic silencing of MGMT gene in high grade gliomas with oligodendroglial component. Together with frequent 1p/19q co-deletion in oligodendroglial tumors, this may add plausible explanations supporting the relative favorable prognosis in oligodendroglial tumors compared with pure astrocytic tumors.

Pharmacokinetics of erlotinib for the treatment of high-grade glioma in a pediatric patient with cystic fibrosis: case report and review of the literature

A 12-year-old girl with cystic fibrosis was diagnosed with a high-grade glioma after radiographic and biopsy results confirmed the primary intracranial lesion. She was treated with single-agent erlotinib during and after daily localized radiation therapy. Pharmacokinetic studies were conducted to assess the effect of pancreatic enzyme deficiency and intestinal malabsorption secondary to cystic fibrosis on the bioavailability of orally administered erlotinib, a lipophilic drug. Pharmacokinetic analysis of plasma samples from days 1 and 8 demonstrated that absorption of oral erlotinib was not affected by the patient's cystic fibrosis when the drug was given concomitantly with pancreatic enzyme replacement. When pediatric patients with cystic fibrosis are receiving erlotinib or other lipophilic oral drugs, continued supplementation of pancreatic enzymes is recommended, with therapeutic drug monitoring of plasma drug concentrations when feasible, and close observation for therapeutic responses and adverse effects.

Determination of EGFR status in gliomas: usefulness of immunohistochemistry and fluorescent in situ hybridization

Epidermal growth factor receptor (EGFR) is produced during the molecular pathogenesis of glioma, and new anti-EGFR molecules are available for therapeutics. Consequently, analyses of the EGFR gene and protein are frequently used for glioma characterization. We compare the accuracy and the usefulness of 2 currently used techniques for histologic classification of gliomas. Fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) techniques were used to assess EGFR gene amplification and protein abundance in a series of 35 gliomas, including World Health Organization (WHO) grade I, II, and III astrocytomas (AI, AII, AIII), grade II and III tumors with oligodendroglial component (OII, OIII) and grade IV glioblastomas (GBs). EGFR gene amplification was found in one-third of the tumors studied. It was frequent in GB and OIII but was never found in AI, AII, AIII, and OII tumors. IHC and FISH provided similar findings for grade of tumor, despite the fact that, in contrast to the FISH gene amplification, EGFR protein was overexpressed in AIII and in GB. EGFR gene amplification was never observed in tumors not containing EGFR protein: therefore FISH is unnecessary when IHC shows no EGFR protein expression. EGFR gene amplification seems to be restricted to high-grade tumors, WHO grade IV astrocytomas, and grade III oligodendroglial tumors.

Phase II study of protracted daily temozolomide for low-grade gliomas in adults

PURPOSE

Resistance to temozolomide chemotherapy is partly mediated by O(6)-methylguanine-DNA methlytransferase (MGMT). Protracted treatment with temozolomide potentially overcomes MGMT resistance and improves outcome. We conducted a phase II study of protracted daily temozolomide in adults with low-grade gliomas.

EXPERIMENTAL DESIGN

Patients with newly diagnosed oligodendroglioma or oligoastrocytoma with a MIB-1 index of >5% or recurrent low-grade gliomas received temozolomide (75 mg/m(2)/day in 11-week cycles of 7 weeks on/4 weeks off). Treatment continued for a total of six cycles or until tumor progression or unacceptable toxicity. Primary end point was best overall response rate; secondary end points were progression-free survival, overall survival, and toxicity. We correlated response with MGMT promoter methylation and chromosome 1p/19q deletion status.

RESULTS

Forty-four patients were treated (14 female, 30 male) with a median follow-up of 39.4 months. Median age was 43 years (range, 20-68 years) and median Karnofsky performance status was 90 (range, 70-100). The regimen was well tolerated. No patients had a complete response (0%), 9 had partial response (20%), 33 had stable disease (75%), and 2 had progressive disease (5%). A total of 21 patients eventually progressed with an overall median progression-free survival of 38 months. Patients with methylated MGMT promoter had a longer overall survival (P = 0.008). Deletion of either 1p or 19q chromosomes also predicted longer overall survival (hazard ratio, 0.17; 95% confidence interval, 0.03-0.93; log-rank P = 0.02).

CONCLUSIONS

A protracted course of daily temozolomide is a well-tolerated regimen and seems to produce effective tumor control. This compares favorably with historical data on the standard 5-day temozolomide regimen.

O(6)-methylguanine DNA methyltransferase immunoexpression in nonfunctioning pituitary adenomas: are progressive tumors potential candidates for temozolomide treatment?

BACKGROUND

Currently, no effective alternative treatment exists for progressive, regrowing, nonfunctioning pituitary adenomas (NFPA) that are resistant to conventional multimodality therapy. Temozolomide (TMZ) was proposed as a treatment option for pituitary carcinomas and aggressive pituitary adenomas. Recently, it was suggested that the responsiveness of pituitary tumors to TMZ depends on the immunoexpression of O(6)-methylguanine DNA methyltransferase (MGMT). Therefore, the authors of this report assessed MGMT expression in a series of patients with progressive, regrowing NFPAs to evaluate whether TMZ may serve as alternative treatment option.

METHODS

On the basis of postoperative magnetic resonance imaging, 45 patients with NFPAs were allocated to either a group with progressive, regrowing tumors (n = 24) or a tumor-free group (n = 21), which served as a control. MGMT expression was assessed semiquantitatively by immunohistochemistry (low expression was defined as <or=50% immunostained adenoma cells, and high expression was defined as >50% immunostained adenoma cells) and was compared between the 2 groups.

RESULTS

At the time of initial surgery, low MGMT expression was observed in 12 of 24 patients (50%) in the study group with progressive, regrowing NFPAs. In the control group of tumor-free patients, only 5 of 21 patients (24%) exhibited low MGMT expression. A comparable distribution of MGMT expression was observed in the specimens from repeat surgeries. A shorter interval to second surgery was observed in patients who had low MGMT expression.

CONCLUSIONS

The current data has suggested that half of the patients with progressive, regrowing NFPAs exhibit low MGMT expression and are potential candidates for treatment with TMZ. These findings provide a rationale for the use of TMZ as an alternative treatment approach in this subgroup if conventional therapy, including reoperation, radiosurgery, and radiotherapy, fails.

Cerebral blood volume measurements by perfusion-weighted MR imaging in gliomas: ready for prime time in predicting short-term outcome and recurrent disease?

BACKGROUND AND PURPOSE

Current classification and grading of primary brain tumors has significant limitations. Our aim was to determine whether the relative cerebral volume (rCBV) measurements in gliomas may serve as an adjunct to histopathologic grading, with a hypothesis that rCBV values are more accurate in predicting 1-year survival and recurrence.

MATERIALS AND METHODS

Thirty-four patients with gliomas (WHO grade I-IV, 27 astrocytomas, 7 tumors with oligodendroglial components) underwent contrast-enhanced MR rCBV measurements before treatment. The region of interest and the single pixel with the maximum CBV value within the tumors were normalized relative to the contralateral normal tissue (rCBV(mean) and rCBV(max), respectively). Karnofsky performance score and progression-free survival (PFS) were recorded. Receiver operating characteristic curves and Kaplan-Meier survival analysis were conducted for CBV and histologic grade (WHO grade).

RESULTS

Significant correlations were detected only when patients with oligodendrogliomas and oligoastrocytomas were excluded. The rCBV(mean) and rCBV(max) in the astrocytomas were 3.5 +/- 2.9 and 3.7 +/- 2.7. PFS correlated with rCBV parameters (r = -0.54 to -0.56, P < or = .009). WHO grade correlated with rCBV values (r = 0.65, P < or = .0002). rCBV(max) > 4.2 was found to be a significant cutoff value for recurrence prediction with 77.8% sensitivity and 94.4% specificity (P = .0001). rCBV(max) < or = 3.8 was a significant predictor for 1-year survival (93.7% sensitivity, 72.7% specificity, P = .0002). The relative risk for shorter PFS was 11.1 times higher for rCBV(max) > 4.2 (P = .0006) and 6.7 times higher for WHO grade > II (P = .05). The combined CBV-WHO grade classification enhanced the predictive value for recurrence/progression (P < .0001).

CONCLUSIONS

rCBV values in astrocytomas but not tumors with oligodendroglial components are predictive for recurrence and 1-year survival and may be more accurate than histopathologic grading.

Molecular profiling in glioblastoma: prelude to personalized treatment

The purpose of this review is to provide an up-to-date summary of the current knowledge and understanding of the molecular alterations and pathways relevant to the clinical outcome of glioblastoma patients and their potential use in designing personalized treatment for these patients. This article also discusses the potential of molecular profiling as a diagnostic modality, possible therapeutic implications of MGMT promoter methylation, the targeted inhibition of angiogenesis, and assessment of the tumor's molecular background with respect to PI3K/AKT pathway activation and associated molecules (EGFR, EGFRvIII, PTEN).

Designer therapies for glioblastoma multiforme

Primary brain tumors account for less than 2% of all cancers in adults; however, they are often associated with neurologic morbidity and high mortality. Glioblastoma multiforme (GBM) has been a focus of new therapy development in neurooncology because it is the most common primary brain tumor in adults. Standard-of-care therapy for newly diagnosed GBM includes surgical resection, radiotherapy, and temozolomide, administered both during and after radiotherapy. However, most patients develop tumor recurrence or progression after this multimodality treatment. Repeat resection and stereotactic radiosurgery upon recurrence may improve outcome only in selected patients. Most salvage chemotherapies offer only palliation. Recent advances in our understanding of the molecular abnormalities of GBM have generated new therapeutic venues of molecularly targeted agents (designer drugs) against key components of cellular pathways critical for cancer initiation and maintenance. Such drugs may offer the potential advantage to increase therapeutic efficacy and decrease systemic toxicity compared with traditional cytotoxic agents. Nonetheless, first-generation targeted agents have failed to demonstrate survival benefits in unselected GBM patient populations. Several mechanisms of treatment failure of the first-generation designer drugs have been proposed, whereas new strategies have been developed to increase effectiveness of these agents. Here we will discuss the recent development and the strategies to optimize the effectiveness of designer therapy for GBM.