Alterations In Brain Tumors Research Articles

PATH-65. INTEGRATING DNA METHYLATION AND SEQUENCING TECHNOLOGIES FOR ADVANCED BRAIN TUMOR DIAGNOSIS

Abstract DNA methylation has emerged as an indispensable tool in neuropathological diagnostics, improving the diagnosis of various brain tumor entities. At our institution, methylation arrays as well as DNA and RNA sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) tissue blocks have become routine diagnostic practices for several years. In this study, we present an integration of DNA methylation analyses with targeted gene panel sequencing and RNA sequencing data in an extensive cohort comprising 5749 cases. The cohort encompassing both adult and pediatric patients with central nervous system (CNS) tumors. Only those cases conclusively classified by the Heidelberg brain tumor classifier (v12.5, cutoff > 0.9) and possessing available sequencing data were included in the analyses. The study includes several rare and less characterized brain tumor entities, unveiling frequent mutations and gene fusions that will improve the diagnostic process. Our study offers an unparalleled comprehensive overview of the prevalence of genetic alterations in brain tumors, precisely defined by their unique methylation classes. The profound implications of our results extend far beyond diagnosis alone, significantly augmenting the evaluation of targeted treatment options for patients undergoing DNA methylation analyses.

Imaging 2-hydroxyglutarate and other brain oncometabolites pertinent to critical genomic alterations in brain tumors.

The 2021 World Health Organization (WHO) Classification of Tumors of the Central Nervous System (CNS) and recent smaller annual updates have shown that alterations in tumor genetics are essential to determining tumor diagnosis, biological activity, and potential treatment options. This review summarizes the most important mutations and oncometabolites, with a focus on the central role played by 2-hydroxyglutarate in isocitrate dehydrogenase mutant tumors, as well as their corresponding imaging counterparts using standard and advanced imaging techniques.

Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma.

Changes in metabolism are known to contribute to tumour phenotypes. If and how metabolic alterations in brain tumours contribute to patient outcome is still poorly understood. Epigenetics impact metabolism and mitochondrial function. The aim of this study is a characterisation of metabolic features in molecular subgroups of isocitrate dehydrogenase mutant (IDHmut) and isocitrate dehydrogenase wildtype (IDHwt) gliomas. We employed DNA methylation pattern analyses with a special focus on metabolic genes, large-scale metabolism panel immunohistochemistry (IHC), qPCR-based determination of mitochondrial DNA copy number and immune cell content using IHC and deconvolution of DNA methylation data. We analysed molecularly characterised gliomas (n=57) for in depth DNA methylation, a cohort of primary and recurrent gliomas (n=22) for mitochondrial copy number and validated these results in a large glioma cohort (n=293). Finally, we investigated the potential of metabolic markers in Bevacizumab (Bev)-treated gliomas (n=29). DNA methylation patterns of metabolic genes successfully distinguished the molecular subtypes of IDHmut and IDHwt gliomas. Promoter methylation of lactate dehydrogenase A negatively correlated with protein expression and was associated with IDHmut gliomas. Mitochondrial DNA copy number was increased in IDHmut tumours and did not change in recurrent tumours. Hierarchical clustering based on metabolism panel IHC revealed distinct subclasses of IDHmut and IDHwt gliomas with an impact on patient outcome. Further quantification of these markers allowed for the prediction of survival under anti-angiogenic therapy. A mitochondrial signature was associated with increased survival in all analyses, which could indicate tumour subgroups with specific metabolic vulnerabilities.

Mapping an Extended Neurochemical Profile at 3 and 7 T Using Accelerated High-Resolution Proton Magnetic Resonance Spectroscopic Imaging.

The aim of this study was to compare high-resolution free induction decay magnetic resonance spectroscopic imaging (FID-MRSI) at 3 T and 7 T in the brain of healthy subjects and to showcase the clinical potential of accelerated FID-MRSI at 7 T in 2 brain tumor cases. In this institutional review board-approved study, 10 healthy volunteers (8 men/2 women; age: 31 ± 6 years) were measured at 3 T and 7 T (Trio and 7T-Magnetom; Siemens Healthcare, Germany) and 2 patients (a 38-year-old man and a 37-year-old man), 1 with an anaplastic oligoastrocytoma (grade III) and 1 with a low-grade glioma (oligodendroglioma), were measured at 7 T.Free induction decay MR spectroscopic imaging with 3.4 × 3.4 mm in-plane resolution was acquired in 30 minutes/6 minutes (nonaccelerated/accelerated) at both field strengths. In addition, single-slice or multi-slice FID-MRSI at 7 T was measured in the 2 tumor patients at 7 T within 6 minutes/13.3 minutes. Signal-to-noise ratio, Cramer-Rao lower bounds, and parallel imaging efficiency were assessed. High-resolution maps were created for 9 different brain metabolites. At 7 T, 7 of 9 metabolites were reliably mapped over the whole slice but only 3 at 3 T. Parallel imaging efficiency was significantly improved at 7 T. Signal-to-noise ratios were +75%/+66% (P < 0.05) for N-acetylaspartate and +97%/+74%(P < 0.05) for glutamine + glutamate [Glx], and full-widths at half maximum were +112%/+109%(P < 0.05) higher at 7 T than at 3 T (nonaccelerated/accelerated) for N-acetylaspartate. Cramer-Rao lower bounds were more than double at 3 T (P < 0.05). At 7 T, FID-MRSI allowed the assessment of an extended neurochemical profile and yielded better metabolic maps in only approximately 6 minutes at 7 T than in approximately 30 minutes at 3 T. We found several potentially therapy-relevant neurochemical alterations in brain tumors that highlighted the potential of fast clinical FID-MRSI at 7 T.

Retrospective Analysis of Molecular and Immunohistochemical Characterization of 381 Primary Brain Tumors.

The classification of brain tumors has traditionally depended on microscopic examination of hematoxylin and eosin-stained tissue sections. The increased understanding of clinically relevant genetic alterations has led to the incorporation of molecular signatures as part of the diagnosis of brain malignancies. Advances in sequencing technologies have facilitated the use of next-generation sequencing (NGS) assays in clinical laboratories. We performed a retrospective analysis of sequencing results for 381 brain tumors tested by NGS at our institution using a validated, commercially available panel. The results of the NGS assay were analyzed in conjunction with the results of immunohistochemical stains. A genetic alteration was detected in approximately two thirds of the cases. The most commonly mutated genes were TP53 (37.2%), IDH1 (29.4%), PIK3CA (8%), PTEN (8%), and EGFR (7.5%). BRAF mutations were detected in ∼3% of the cases, including 50% of gangliogliomas and ∼20% of gliosarcomas. No mutations were detected in 6 medulloblastomas. PIK3CA and CTNNB1 mutations were detected in 1 rosette-forming glioneuronal tumor and 1 adamantinomatous craniopharyngioma, respectively. Approximately 23% of cases showed amplification of 1 or more of the genes included in the NGS panel. This analysis demonstrates the utility of NGS for detecting genetic alterations in brain tumors in the clinical setting.

Metabolic Reprogramming in Brain Tumors.

Next-generation sequencing has substantially enhanced our understanding of the genetics of primary brain tumors by uncovering several novel driver genetic alterations. How many of these genetic modifications contribute to the pathogenesis of brain tumors is not well understood. An exciting paradigm emerging in cancer biology is that oncogenes actively reprogram cellular metabolism to enable tumors to survive and proliferate. We discuss how some of these genetic alterations in brain tumors rewire metabolism. Furthermore, metabolic alterations directly impact epigenetics well beyond classical mechanisms of tumor pathogenesis. Metabolic reprogramming in brain tumors is also influenced by the tumor microenvironment contributing to drug resistance and tumor recurrence. Altered cancer metabolism can be leveraged to noninvasively image brain tumors, which facilitates improved diagnosis and the evaluation of treatment effectiveness. Many of these aspects of altered metabolism provide novel therapeutic opportunities to effectively treat primary brain tumors.

OT-10 * IMPLEMENTATION OF NEXT GENERATION COPY NUMBER AND MUTATIONAL ANALYSIS IN ROUTINE NEUROPATHOLOGY: MOLECULAR INVERSION PROFILING IS A HELPFUL TOOL IN DIFFERENTIAL DIAGNOSTICS AND PROGNOSTIFICATION OF PEDIATRIC BRAIN TUMORS

Brain tumor entities are characterized by specific copy number alterations (CNA), allelic losses/disbalances and recurrend mutations. Emerging technologies including SNP arrays, whole exome and whole genome sequencing are not suitable for degraded DNA derived from formalin-fixed, paraffin embedded (FFPE) samples. The aim of our study was to analyse the sensitivity and robustness of molecular inversion profiling (MIP) as a tool to identify these alterations in brain tumors and to compare this method to FISH and multiplex ligation probe analysis (MLPA). Genomic DNA extracted from up to 20 years old FFPE materials from more than 1300 brain tumors covering most WHO entities were analyzed by MIP profiling (Oncoscan V2/V3, Affymetrix). MIP revealed genome-wide copy number information from as little as 20 ng of degraded DNA; drop-out rate was <5%. In contrast to FISH and MLPA, MIP allowed a genome-wide analysis, adding significant information to the differential diagnosis. Characteristic CNA were detected, including BRAF duplications in pilocytic astrocytomas, chromosome 22 loss in ATRT, chromosome 10 loss, 7 gain and amplifications of PDGFR or EGFR in glioblastoma, 1p19q codeletion in oligodendroglial tumors, chromosome 2 gain and C19MC amplification in ependymoblastoma. Novel prognostic markers including MYCN amplification in CNS-PNET were identified. Established prognostic markers including MYC/MYCN amplifications in medulloblastomas and chromosome 1q gain in ependymomas were easily detected and validated by orthogonal methods. Extended chromosomal alterations including widespread hyperploidy in plexus papillomas or complex alterations such as chromosomal scattering of whole chromosomes (chromotripsis) in TP53 deficient medulloblastomas were easily uncovered. MIP also detected copy-neutral LOH and recurrent tumor-associated mutations (e.g BRAFV600E, IDH gene mutations). Our data indicate that MIP is a sensitive and robust method to assess CNA, allelic imbalances/losses and specific recurrent point mutations in FFPE tumor material, and therefore represents a novel tool for precise neuropathological tumor diagnostics and prognostic stratification.

Heavy Metals and Epigenetic Alterations in Brain Tumors

Heavy metals and their derivatives can cause various diseases. Numerous studies have evaluated the possible link between exposure to heavy metals and various cancers. Recent data show a correlation between heavy metals and aberration of genetic and epigenetic patterns. From a literature search we noticed few experimental and epidemiological studies that evaluate a possible correlation between heavy metals and brain tumors. Gliomas arise due to genetic and epigenetic alterations of glial cells. Changes in gene expression result in the alteration of the cellular division process. Epigenetic alterations in brain tumors include the hypermethylation of CpG group, hypomethylation of specific genes, aberrant activation of genes, and changes in the position of various histones. Heavy metals are capable of generating reactive oxygen assumes that key functions in various pathological mechanisms. Alteration of homeostasis of metals could cause the overproduction of reactive oxygen species and induce DNA damage, lipid peroxidation, and alteration of proteins. In this study we summarize the possible correlation between heavy metals, epigenetic alterations and brain tumors. We report, moreover, the review of relevant literature.

BRAF alterations in brain tumours: molecular pathology and therapeutic opportunities.

To summarize the current knowledge on v-RAF murine sarcoma viral oncogene homologue B1 (BRAF) aberrations in tumours of the central nervous system. BRAF alterations are found in variable frequencies across a wide spectrum of diverse central nervous system neoplasms. BRAF V600 point mutations (most commonly of the V600E type) are most common in pleomorphic xanthoastrocytoma (approximately 60% of cases), gangliogliomas (50%), dysembryoplastic neuroepithelial tumours (30%), Langerhans cell histiocytosis (50%), melanoma brain metastases (50%) and papillary craniopharyngiomas (96%) and are also detectable in a fraction of glioblastomas (overall mutation rate of 2-12%, with a higher rate of approximately 50% in epithelioid glioblastomas). BRAF fusions (most commonly KIAA1549: BRAF) are typical for pilocytic astrocytomas and are almost absent from other tumour types. Clinical trials have established tyrosine-kinase inhibitors of BRAF as feasible treatment option in selected patients with mutation-bearing brain metastases of melanoma. Preclinical studies, some case reports and small patient series have documented tumour responses of primary brain tumours with BRAF aberrations to BRAF inhibition. Molecular testing for BRAF alterations in brain tumours may be of clinical relevance for differential diagnostic considerations in some situations or to guide selection of patients for targeted therapy with specific inhibitors. Prospective clinical trials evaluating the efficacy of BRAF inhibitors in central nervous system tumours are strongly supported by the available evidence.

MC13-0007 Metabolomic profile of multiple myeloma patients

Purpose/Objective: We evaluated whether cell-free circulating DNA can be used as a noninvasive approach for detection of genetic/epigenetic alterations in brain tumors during the course of the disease. Materials and Methods: Paired tumor-serum samples from 37 primary patients with glioblastoma and 21 primary benign meningiomas were analyzed. 19 non-cancer individuals serum were used as control. The median interval between surgery and serum sampling was 1.5 month. The methylation status of O6-methyl guanine methyltransferase (MGMT) was studied by methylationspecific PCR. The mRNA expression of CCNB1 was studied by qRT-PCR. Promoter hypermethylation in MGMT was detected at high frequencies in paraffin-embedded (FFPE) tumor sections and serum in glioblastoma. Results: Statistically significant tumor-serum concordance was found for MGMT methylation in patients (r=0.87, p<0.01). None of the control serum showed aberrant methylation. Hypermethylation in serum DNA was all accompanied with methylation in the corresponding tumor tissues with 100% specificity. Highly elevated MGMT methylation levels in serum were the sole independent factors predicting inferior overall survival in this cohort. Over-expression of CCNB1 was also detected in FFPE and serum in meningioma patients. None of the control serum showed over-express. CCNB1 expression was significantly higher in patients with tumor recurrence (p<0.01). Conclusions: CCNB1 serum mRNA was a potential prognostic factor predicting meningioma recurrence.

MC13-0006 Cell-free circulating DNA can be used as a noninvasive approach for detection of genetic/epigenetic alterations in brain tumors

MC13-0006 Cell-free circulating DNA can be used as a noninvasive approach for detection of genetic/epigenetic alterations in brain tumors

Genetic and Modifying Factors that Determine the Risk of Brain Tumors

Some modifying factors may determine the risk of brain tumors. Until now, it could not be attempted to identify people at risk and also to improve significantly disease progression. Current therapy consists of surgical resection, followed by radiation therapy and chemotherapy. Despite of these treatments, the prognosis for patients is poor. In this review, we highlight general aspects concerning genetic alterations in brain tumors, namely astrocytomas, glioblastomas, oligodendrogliomas, medulloblastomas and ependymomas. The influence of these genetic alterations in patients' prognosis is discussed. Mutagen sensitivity is associated with cancer risk. The convincing studies that linked DNA damages and DNA repair alterations with brain tumors are also described. Another important modifying factor is immunity. General immune response against cancer, tumor microenvironment and immune response, mechanisms of tumor escape, CNS tumor immunology, immune defects that impair anti-tumor systemic immunity in brain tumor patients and local immuno-suppressive factors within CNS are also reviewed. New hope to treatment perspectives, as dendritic-cell-based vaccines is summarized too. Concluding, it seems well established that there is association between brain tumor risk and mutagen sensitivity, which is highly heritable. Primary brain tumors cause depression in systemic host immunity; local immuno-suppressive factors and immunological characteristics of tumor cells may explain the poor prognosis and DNA damages responses can alert immune system. However, it is necessary to clarify if individuals with both constitutional defects in immune functions and genetic instability have higher risk of developing brain tumors. Cytogenetic prospective studies and gene copy number variations analysis also must be performed in peripheral lymphocytes from brain tumor patients.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

BTECH: A Platform to Integrate Genomic, Transcriptomic and Epigenomic Alterations in Brain Tumors

The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor initiation and progression remain largely unknown. Unfortunately, most of these data are scattered in multiple databases and supplementary materials of publications, thus making their retrieval, evaluation, comparison and visualization a rather arduous task. Here we report the development and implementation of an open access database (BTECH), a community resource for the deposition of a wide range of molecular data derived from brain tumor studies. This comprehensive database integrates multiple datasets, including transcript profiles, epigenomic CpG methylation data, DNA copy number alterations and structural chromosomal rearrangements, tumor-associated gene lists, SNPs, genomic features concerning Alu repeats and general genomic annotations. A genome browser has also been developed that allows for the simultaneous visualization of the different datasets and the various annotated features. Besides enabling an integrative view of diverse datasets through the genome browser, we also provide links to the original references for users to have a more accurate understanding of each specific dataset. This integrated platform will facilitate uncovering interactions among genetic and epigenetic factors associated with brain tumor development. BTECH is freely available at http://cmbteg.childrensmemorial.org/.Electronic supplementary materialThe online version of this article (doi:10.1007/s12021-010-9091-9) contains supplementary material, which is available to authorized users.

Serum DNA can define tumor-specific genetic and epigenetic markers in gliomas of various grades

We evaluated whether cell-free circulating DNA can be used as a noninvasive approach for detection of genetic/epigenetic alterations in brain tumors during the course of the disease. Paired tumor-serum samples from 70 patients with either high-grade astrocytomas (n = 41) or oligodendrogliomas of various grades were analyzed. The median interval between surgery and serum sampling was 1 month (range 0.5-168 months). DNA was extracted from whole blood, serum, and paraffin-embedded tumor sections. Loss of heterozygosity (LOH) in chromosomes 1p, 19q, and 10q was assessed by polymerase chain reaction (PCR)-based microsatellite analysis. The methylation status of O(6)-methyl guanine methyltransferase (MGMT) and phosphatase and tensin homolog promoters was studied by methylation-specific PCR. LOH and/or methylation that could identify DNA as tumor-specific was found in 80.5% of astrocytic tumors and in all oligodendrogliomas. The rate of serum detection of these biomarkers was 51% and 55%, respectively, with specificity around 100%. The rate of serum detection did not differ between low- and high-grade oligodendrogliomas. Statistically significant tumor-serum concordance was found for MGMT methylation in both astrocytic tumors (83%; P < .001) and oligodendroglial tumors (72%; P < .003) and for LOH of 10q (79%; P < .002) and 1p (62%; P < .03) in oligodendrogliomas. We conclude that serum DNA in glial tumors is informative for both LOH and aberrant gene promoter methylation analysis during the course of the disease. The sensitivity is moderate and specificity is high for both low- and high-grade tumors. Future studies should identify a panel of biomarkers that bear the highest potential for clinical application.

Therapy-Induced Morphological Alterations in Brain Tumors

Routine therapeutic options for tumors of the brain or spinal cord comprise surgery, radiation and/or chemotherapy, all of which are associated with several possible complications. The most important consequences of brain tumor therapy are hemorrhage, acute brain swelling with external herniation of parts of the brain, CSF leaks, and coagulopathies. The anatomical location of surgical manipulation may have additional special effects, like diabetes insipidus following pituitary or adjacent base of the brain surgery. New techniques of radiotherapy applied in neuro- oncology such as gamma knife (stereotactic radiosurgery), intracavital brachytherapy, three dimensional conformal radiation, are also associated with iatrogenic changes in the brain. Pathologic changes induced by various radio- therapeutic modalities are discussed in this review, with special emphasis on terminology, timing and the importance of pathologic examination for assessing the tumor response to therapy, signs of peritumoral tissue damage and tumor recurrence. Therapy-induced secondary neoplastic lesions are also discussed.

Molecular Epigenetics and Genetics in Neuro-Oncology

Gliomas arise through genetic and epigenetic alterations of normal brain cells, although the exact cell of origin for each glioma subtype is unknown. The alteration-induced changes in gene expression and protein function allow uncontrolled cell division, tumor expansion, and infiltration into surrounding normal brain parenchyma. The genetic and epigenetic alterations are tumor subtype and tumor-grade specific. Particular alterations predict tumor aggressiveness, tumor response to therapy, and patient survival. Genetic alterations include deletion, gain, amplification, mutation, and translocation, which result in oncogene activation and tumor suppressor gene inactivation, or in some instances the alterations may simply be a consequence of tumorigenesis. Epigenetic alterations in brain tumors include CpG island hypermethylation associated with tumor suppressor gene silencing, gene-specific hypomethylation associated with aberrant gene activation, and genome-wide hypomethylation potentially leading to loss of imprinting, chromosomal instability, and cellular hyperproliferation. Other epigenetic alterations, such as changes in the position of histone variants and changes in histone modifications are also likely to be important in the molecular pathology of brain tumors. Given that histone deacetylases are targets for drugs that are already in clinical trial, surprisingly little is known about histone acetylation in primary brain tumors. Although a majority of epigenetic alterations are independent of genetic alterations, there is interaction on specific genes, signaling pathways and within chromosomal domains. Next-generation sequencing technology is now the method of choice for genomic and epigenome profiling, allowing more comprehensive understanding of genetic and epigenetic contributions to tumorigenesis in the brain.

Somatic alterations in brain tumors

Mutations in TP53 and RB1 have been shown to participate in the development of malignant brain tumors. Emerging evidence shows that mutations are involved in LGI1 in brain tumor progression. Herein we present data from the sequencing of a series of high- and low-grade gliomas with matched normal DNA. We report on 35 unique missense mutations in TP53, RB1 and LGI1 genes and use available information for each mutation in order to classify them as likely to be 'driver' or 'passenger' mutations. The identification of putatively deleterious mutations in LGI1 supports the notion that this locus may play a role in brain cancer development.

Genetic Alterations in Brain Tumors Following 1,3-Butadiene Exposure in B6C3F1 Mice

The nervous system of the B6C3F1 mouse has rarely been a target for chemical carcinogenesis in the National Toxicology Program (NTP) bioassays. However, 6 malignant gliomas and 2 neuroblastomas were observed in B6C3F1 mice exposed to 625 ppm 1,3-butadiene (NTP technical reports 288 and 434). These mouse brain tumors were evaluated with regard to the profile of genetic alterations that are observed in human brain tumors. Alterations in the p53 tumor suppressor gene were common. Missense mutations were observed in 3/6 malignant gliomas and 2/2 neuroblastomas and were associated with loss of heterozygosity. Most of the mutations occurred in exons 5-8 of the p53 gene and were G-->A transitions, and did not involve CpG sites. Loss of heterozygosity at the Ink4a/Arf gene locus was observed in 5/5 malignant gliomas and 1/1 neuroblastoma, while the PTEN(phosphatase and tensin homologue) gene locus was unaffected by deletions. One of 2 neuroblastomas had a mutation in codon 61 of H-ras, while H-ras mutations were not observed in the malignant gliomas examined. Only 1 brain tumor has been reported from control mice of over 500 NTP studies. This malignant glioma showed no evidence of alterations in the p53 gene or K- and H-ras mutations. It is likely that the specific genetic alterations observed were induced or selected for by 1,3-butadiene treatment that contributed to the development of mouse brain tumors. The observed findings are similar in part to the genetic alterations reported in human brain tumors.

Small Molecule and Monoclonal Antibody Therapies in Neurooncology

The prognosis for most patients with primary brain tumors remains poor. Recent advances in molecular and cell biology have led to a greater understanding of molecular alterations in brain tumors. These advances are being translated into new therapies that will hopefully improve the prognosis for patients with brain tumors. We reviewed the literature on small molecule targeted agents and monoclonal antibodies used in brain tumor research and brain tumor clinical trials for the past 20 years. Brain tumors commonly express molecular abnormalities. These alterations can lead to the activation of cell pathways involved in cell proliferation. This knowledge has led to interest in novel anti-brain-tumor therapies targeting key components of these pathways. Many drugs and monoclonal antibodies have been developed that modulate these pathways and are in various stages of testing. The use of targeted therapies against brain tumors promises to improve the prognosis for patients with brain tumors. However, as the molecular pathogenesis of brain tumors has not been linked to a single genetic defect or target, molecular agents may need to be used in combinations or in tandem with cytotoxic agents. Further study of these agents in well-designed cooperative clinical trials is needed.