bims-malgli Biomed News
on Biology of malignant gliomas
Issue of 2020‒08‒09
thirteen papers selected by
Oltea Sampetrean
Keio University
  1. MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas.
  2. Epigenetic Targeting of Mcl-1 Is Synthetically Lethal with Bcl-xL/Bcl-2 Inhibition in Model Systems of Glioblastoma.
  3. Proteasome inhibition for the treatment of glioblastoma.
  4. Autologous CMV-specific T cells are a safe adjuvant immunotherapy for primary glioblastoma multiforme.
  5. Role of exosomes in malignant glioma: microRNAs and proteins in pathogenesis and diagnosis.
  6. Molecular Heterogeneity and Immunosuppressive Microenvironment in Glioblastoma.
  7. Temporospatial genomic profiling in glioblastoma identifies commonly altered core pathways underlying tumor progression.
  8. All Myeloid-Derived Suppressor Cells Are Not Created Equal: How Gender Inequality Influences These Cells and Affects Cancer Therapy.
  9. The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation.
  10. A tailored next-generation sequencing panel identified distinct subtypes of wildtype IDH and TERT promoter glioblastomas.
  11. The Role of RNA and DNA Aptamers in Glioblastoma Diagnosis and Therapy: A Systematic Review of the Literature.
  12. Immune phenotyping of diverse syngeneic murine brain tumors identifies immunologically distinct types.
  13. A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology.
  1. Nat Commun. 2020 Aug 04. 11(1): 3883
    MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas.
    Barbara Oldrini, Nuria Vaquero-Siguero, Quanhua Mu, Paula Kroon, Ying Zhang, Marcos Galán-Ganga, Zhaoshi Bao, Zheng Wang, Hanjie Liu, Jason K Sa, Junfei Zhao, Hoon Kim, Sandra Rodriguez-Perales, Do-Hyun Nam, Roel G W Verhaak, Raul Rabadan, Tao Jiang, Jiguang Wang, Massimo Squatrito.
      Temozolomide (TMZ) is an oral alkylating agent used for the treatment of glioblastoma and is now becoming a chemotherapeutic option in patients diagnosed with high-risk low-grade gliomas. The O-6-methylguanine-DNA methyltransferase (MGMT) is responsible for the direct repair of the main TMZ-induced toxic DNA adduct, the O6-Methylguanine lesion. MGMT promoter hypermethylation is currently the only known biomarker for TMZ response in glioblastoma patients. Here we show that a subset of recurrent gliomas carries MGMT genomic rearrangements that lead to MGMT overexpression, independently from changes in its promoter methylation. By leveraging the CRISPR/Cas9 technology we generated some of these MGMT rearrangements in glioma cells and demonstrated that the MGMT genomic rearrangements contribute to TMZ resistance both in vitro and in vivo. Lastly, we showed that such fusions can be detected in tumor-derived exosomes and could potentially represent an early detection marker of tumor recurrence in a subset of patients treated with TMZ.
    DOI:  https://doi.org/10.1038/s41467-020-17717-0
  2. Cancers (Basel). 2020 Aug 01. pii: E2137. [Epub ahead of print]12(8):
    Epigenetic Targeting of Mcl-1 Is Synthetically Lethal with Bcl-xL/Bcl-2 Inhibition in Model Systems of Glioblastoma.
    Enyuan Shang, Trang T T Nguyen, Chang Shu, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D Siegelin.
      Apoptotic resistance remains a hallmark of glioblastoma (GBM), the most common primary brain tumor in adults, and a better understanding of this process may result in more efficient treatments. By utilizing chromatin immunoprecipitation with next-generation sequencing (CHIP-seq), we discovered that GBMs harbor a super enhancer around the Mcl-1 locus, a gene that has been known to confer cell death resistance in GBM. We utilized THZ1, a known super-enhancer blocker, and BH3-mimetics, including ABT263, WEHI-539, and ABT199. Combined treatment with BH3-mimetics and THZ1 led to synergistic growth reduction in GBM models. Reduction in cellular viability was accompanied by significant cell death induction with features of apoptosis, including disruption of mitochondrial membrane potential followed by activation of caspases. Mechanistically, THZ1 elicited a profound disruption of the Mcl-1 enhancer region, leading to a sustained suppression of Mcl-1 transcript and protein levels, respectively. Mechanism experiments suggest involvement of Mcl-1 in the cell death elicited by the combination treatment. Finally, the combination treatment of ABT263 and THZ1 resulted in enhanced growth reduction of tumors without induction of detectable toxicity in two patient-derived xenograft models of GBM in vivo. Taken together, these findings suggest that combined epigenetic targeting of Mcl-1 along with Bcl-2/Bcl-xL is potentially therapeutically feasible.
    Keywords:  BH3-mimetics; Mcl1; THZ1; epigenome; non-coding regions; super-enhancer
    DOI:  https://doi.org/10.3390/cancers12082137
  3. Expert Opin Investig Drugs. 2020 Aug 04.
    Proteasome inhibition for the treatment of glioblastoma.
    Patrick Roth, Warren P Mason, Paul G Richardson, Michael Weller.
      Introduction Glioblastoma is a primary brain tumor with a poor prognosis despite multimodal therapy including surgery, radiotherapy and alkylating chemotherapy. Novel therapeutic options are therefore urgently needed; however, there has been various drug failures in late-stage clinical development. The proteasome represents a key target for anti-cancer therapy as successfully shown in multiple myeloma and other hematologic malignancies. Areas covered This review article summarizes the preclinical and clinical development of proteasome inhibitors in the context of glioblastoma. Expert opinion Early clinical trials with bortezomib ended with disappointing results because this agent does not cross the blood-brain barrier. In contrast to bortezomib and other proteasome inhibitors, marizomib is a novel drug that displays strong inhibitory properties on all enzymatic subunits of the proteasome and, most importantly, crosses the blood-brain barrier, making it a potentially very active novel agent against intrinsic brain tumors. While preclinical studies have demonstrated significant anti-glioma activity, its clinical benefit has yet to be proven. Exploiting the biological effects of proteasome inhibitors in combination with other therapeutic strategies may represent a key next step in their clinical development.
    Keywords:  Glioblastoma; bortezomib; brain tumor; chemotherapy; marizomib; neuro-oncology; proteasome
    DOI:  https://doi.org/10.1080/13543784.2020.1803827
  4. J Clin Invest. 2020 Aug 04. pii: 138649. [Epub ahead of print]
    Autologous CMV-specific T cells are a safe adjuvant immunotherapy for primary glioblastoma multiforme.
    Corey Smith, Katie E Lineburg, J Paulo Martins, George Ambalathingal, Michelle A Neller, Beth Morrison, Katherine K Matthews, Sweera Rehan, Pauline Crooks, Archana Panikkar, Leone Beagley, Laetitia Le Texier, Sriganesh Srihari, David Walker, Rajiv Khanna.
      BACKGROUND: The recent failure of checkpoint-blockade therapies for glioblastoma multiforme (GBM) in late-phase clinical trials has directed interest towards adoptive cellular immunotherapies (ACT). In this open-label, first-in-human trial, we have assessed the safety and therapeutic potential of cytomegalovirus (CMV)-specific ACT in an adjuvant setting for patients with primary GBM, with an ultimate goal to prevent or delay recurrence and prolong overall survival.METHODS: Twenty-eight patients with primary GBM were recruited to this prospective study, 25 of whom were treated with in vitro-expanded autologous CMV-specific T cells. Participants were monitored for safety, progression-free survival (PFS), overall survival (OS) and immune reconstitution.
    RESULTS: No participants showed evidence of ACT-related toxicities. Of 25 evaluable participants, ten were alive at the completion of follow-up, while five were disease free. Reconstitution of CMV-specific T-cell immunity was evident and CMV-specific ACT may trigger bystander effect leading to additional T-cell responses to non-viral tumour-associated antigens through epitope spreading. Long-term follow-up of participants treated before recurrence showed significantly improved OS when compared to those who progressed before ACT (median 23 months, range 7-65 vs. median 14 months, range 5-19; p=0.018). Gene expression analysis of the ACT products indicated that a favourable T-cell gene signature was associated with improved long-term survival.
    CONCLUSION: Data presented in this study demonstrate that CMV-specific ACT can be safely used as an adjuvant therapy for primary GBM and, if offered before recurrence, this therapy may improve overall survival of GBM patients.
    TRIAL REGISTRATION: anzctr.org.au: ACTRN12615000656538Funding Source:National Health & Medical Research Council (Australia)Trial registration: anzctr.org.au: ACTRN12615000656538Funding Source: Philanthropic funding &National Health & Medical Research Council (Australia).
    Keywords:  Cancer immunotherapy; Immunology; Immunotherapy; Oncology; T cells
    DOI:  https://doi.org/10.1172/JCI138649
  5. Cell Commun Signal. 2020 Aug 03. 18(1): 120
    Role of exosomes in malignant glioma: microRNAs and proteins in pathogenesis and diagnosis.
    Amir B Ghaemmaghami, Maryam Mahjoubin-Tehran, Ahmad Movahedpour, Korosh Morshedi, Amirhossein Sheida, Seyed Pouya Taghavi, Hamed Mirzaei, Michael R Hamblin.
      Malignant gliomas are the most common and deadly type of central nervous system tumors. Despite some advances in treatment, the mean survival time remains only about 1.25 years. Even after surgery, radiotherapy and chemotherapy, gliomas still have a poor prognosis. Exosomes are the most common type of extracellular vesicles with a size range of 30 to 100 nm, and can act as carriers of proteins, RNAs, and other bioactive molecules. Exosomes play a key role in tumorigenesis and resistance to chemotherapy or radiation. Recent evidence has shown that exosomal microRNAs (miRNAs) can be detected in the extracellular microenvironment, and can also be transferred from cell to cell via exosome secretion and uptake. Therefore, many recent studies have focused on exosomal miRNAs as important cellular regulators in various physiological and pathological conditions. A variety of exosomal miRNAs have been implicated in the initiation and progression of gliomas, by activating and/or inhibiting different signaling pathways. Exosomal miRNAs could be used as therapeutic agents to modulate different biological processes in gliomas. Exosomal miRNAs derived from mesenchymal stem cells could also be used for glioma treatment. The present review summarizes the exosomal miRNAs that have been implicated in the pathogenesis, diagnosis and treatment of gliomas. Moreover, exosomal proteins could also be involved in glioma pathogenesis. Exosomal miRNAs and proteins could also serve as non-invasive biomarkers for prognosis and disease monitoring. Video Abstract.
    Keywords:  Biomarkers; Exosomes; Gliomas; MicroRNAs; Proteins; Therapy; pathogenesis
    DOI:  https://doi.org/10.1186/s12964-020-00623-9
  6. Front Immunol. 2020 ;11 1402
    Molecular Heterogeneity and Immunosuppressive Microenvironment in Glioblastoma.
    Syreeta DeCordova, Abhishek Shastri, Anthony G Tsolaki, Hadida Yasmin, Lukas Klein, Shiv K Singh, Uday Kishore.
      Glioblastoma (GBM) is the most aggressive primary brain tumor in adults, with a poor prognosis, despite surgical resection combined with radio- and chemotherapy. The major clinical obstacles contributing to poor GBM prognosis are late diagnosis, diffuse infiltration, pseudo-palisading necrosis, microvascular proliferation, and resistance to conventional therapy. These challenges are further compounded by extensive inter- and intra-tumor heterogeneity and the dynamic plasticity of GBM cells. The complex heterogeneous nature of GBM cells is facilitated by the local inflammatory tumor microenvironment, which mostly induces tumor aggressiveness and drug resistance. An immunosuppressive tumor microenvironment of GBM provides multiple pathways for tumor immune evasion. Infiltrating immune cells, mostly tumor-associated macrophages, comprise much of the non-neoplastic population in GBM. Further understanding of the immune microenvironment of GBM is essential to make advances in the development of immunotherapeutics. Recently, whole-genome sequencing, epigenomics and transcriptional profiling have significantly helped improve the prognostic and therapeutic outcomes of GBM patients. Here, we discuss recent genomic advances, the role of innate and adaptive immune mechanisms, and the presence of an established immunosuppressive GBM microenvironment that suppresses and/or prevents the anti-tumor host response.
    Keywords:  astrocytes; brain tumor; glioblastoma; immunity; microenvironment; microglia
    DOI:  https://doi.org/10.3389/fimmu.2020.01402
  7. Neurooncol Adv. 2020 Jan-Dec;2(1):2(1): vdaa078
    Temporospatial genomic profiling in glioblastoma identifies commonly altered core pathways underlying tumor progression.
    Mylan R Blomquist, Shannon Fortin Ensign, Fulvio D'Angelo, Joanna J Phillips, Michele Ceccarelli, Sen Peng, Rebecca F Halperin, Francesca P Caruso, Luciano Garofano, Sara A Byron, Winnie S Liang, David W Craig, John D Carpten, Michael D Prados, Jeffrey M Trent, Michael E Berens, Antonio Iavarone, Harshil Dhruv, Nhan L Tran.
      Background: Tumor heterogeneity underlies resistance and disease progression in glioblastoma (GBM), and tumors most commonly recur adjacent to the surgical resection margins in contrast non-enhancing (NE) regions. To date, no targeted therapies have meaningfully altered overall patient survival in the up-front setting. The aim of this study was to characterize intratumoral heterogeneity in recurrent GBM using bulk samples from primary resection and recurrent samples taken from contrast-enhancing (EN) and contrast NE regions.Methods: Whole exome and RNA sequencing were performed on matched bulk primary and multiple recurrent EN and NE tumor samples from 16 GBM patients who received standard of care treatment alone or in combination with investigational clinical trial regimens.
    Results: Private mutations emerge across multi-region sampling in recurrent tumors. Genomic clonal analysis revealed increased enrichment in gene alterations regulating the G2M checkpoint, Kras signaling, Wnt signaling, and DNA repair in recurrent disease. Subsequent functional studies identified augmented PI3K/AKT transcriptional and protein activity throughout progression, validated by phospho-protein levels. Moreover, a mesenchymal transcriptional signature was observed in recurrent EN regions, which differed from the proneural signature in recurrent NE regions.
    Conclusions: Subclonal populations observed within bulk resected primary GBMs transcriptionally evolve across tumor recurrence (EN and NE regions) and exhibit aberrant gene expression of common signaling pathways that persist despite standard or targeted therapy. Our findings provide evidence that there are both adaptive and clonally mediated dependencies of GBM on key pathways, such as the PI3K/AKT axis, for survival across recurrences.
    Keywords:  PI3K signaling; clonal evolution; contrast enhancement; glioblastoma; temporospatial heterogeneity
    DOI:  https://doi.org/10.1093/noajnl/vdaa078
  8. Cancer Discov. 2020 Aug;10(8): 1100-1102
    All Myeloid-Derived Suppressor Cells Are Not Created Equal: How Gender Inequality Influences These Cells and Affects Cancer Therapy.
    Dmitry I Gabrilovich.
      In this issue of Cancer Discovery, Bayik and colleagues demonstrated sexual dimorphism in accumulation of different populations of myeloid-derived suppressor cells in glioblastoma and showed that they could be targeted by different agents.See related article by Bayik et al., p. 1210.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0494
  9. Genome Biol. 2020 Aug 06. 21(1): 195
    The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation.
    Adam Kosti, Patricia Rosa de Araujo, Wei-Qing Li, Gabriela D A Guardia, Jennifer Chiou, Caihong Yi, Debashish Ray, Fabiana Meliso, Yi-Ming Li, Talia Delambre, Mei Qiao, Suzanne S Burns, Franziska K Lorbeer, Fanny Georgi, Markus Flosbach, Sarah Klinnert, Anne Jenseit, Xiufen Lei, Carolina Romero Sandoval, Kevin Ha, Hong Zheng, Renu Pandey, Aleksandra Gruslova, Yogesh K Gupta, Andrew Brenner, Erzsebet Kokovay, Timothy R Hughes, Quaid D Morris, Pedro A F Galante, Stefano Tiziani, Luiz O F Penalva.
      BACKGROUND: RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiation and growth. Identification and characterization of oncogenic RBPs and their regulatory networks provide new opportunities for targeted therapy.RESULTS: We identify the RNA-binding protein SERBP1 as a novel regulator of glioblastoma (GBM) development. High SERBP1 expression is prevalent in GBMs and correlates with poor patient survival and poor response to chemo- and radiotherapy. SERBP1 knockdown causes delay in tumor growth and impacts cancer-relevant phenotypes in GBM and glioma stem cell lines. RNAcompete identifies a GC-rich region as SERBP1-binding motif; subsequent genomic and functional analyses establish SERBP1 regulation role in metabolic routes preferentially used by cancer cells. An important consequence of these functions is SERBP1 impact on methionine production. SERBP1 knockdown decreases methionine levels causing a subsequent reduction in histone methylation as shown for H3K27me3 and upregulation of genes associated with neurogenesis, neuronal differentiation, and function. Further analysis demonstrates that several of these genes are downregulated in GBM, potentially through epigenetic silencing as indicated by the presence of H3K27me3 sites.
    CONCLUSIONS: SERBP1 is the first example of an RNA-binding protein functioning as a central regulator of cancer metabolism and indirect modulator of epigenetic regulation in GBM. By bridging these two processes, SERBP1 enhances glioma stem cell phenotypes and contributes to GBM poorly differentiated state.
    Keywords:  Cancer metabolism; Epigenetic regulation; GBM; One carbon cycle; RNA-binding protein; SERBP1
    DOI:  https://doi.org/10.1186/s13059-020-02115-y
  10. Cancer Sci. 2020 Aug 04.
    A tailored next-generation sequencing panel identified distinct subtypes of wildtype IDH and TERT promoter glioblastomas.
    Nayuta Higa, Toshiaki Akahane, Seiya Yokoyama, Hajime Yonezawa, Hiroyuki Uchida, Tomoko Takajo, Mari Kirishima, Taiji Hamada, Kei Matsuo, Shingo Fujio, Tomoko Hanada, Hiroshi Hosoyama, Masanori Yonenaga, Akihisa Sakamoto, Tsubasa Hiraki, Akihide Tanimoto, Koji Yoshimoto.
      Central nervous system tumors are classified based on an integrated diagnosis combining histology and molecular characteristics, including IDH1/2 and H3-K27M mutations, as well as 1p/19q codeletion. Here, we aimed to develop and assess the feasibility of a glioma-tailored 48-gene next-generation sequencing (NGS) panel for integrated glioma diagnosis. We designed a glioma-tailored 48-gene NGS panel for detecting 1p/19q codeletion and mutations in IDH1/2, TP53, PTEN, PDGFRA, NF1, RB1, CDKN2A/B, CDK4, and the TERT promoter (TERTp). We analyzed 106 glioma patients (grade II: 19 cases, grade Ⅲ: 23 cases, grade Ⅳ: 64 cases) using this system. The 1p/19q codeletion was detected precisely in oligodendroglial tumors using our NGS panel. In a cohort of 64 grade Ⅳ gliomas, we identified 56 IDH-wildtype glioblastomas. Within these IDH-wildtype glioblastomas, 33 samples (58.9%) showed a mutation in TERTp. Notably, PDGFRA mutations and their amplification were more commonly seen in TERTp-wildtype glioblastomas (43%) than in TERTp-mutant glioblastomas (6%) (p = 0.001). Hierarchical molecular classification of IDH-wildtype glioblastomas revealed three distinct groups of IDH-wildtype glioblastomas. One major cluster was characterized by mutations in PDGFRA, amplification of CDK4 and PDGFRA, homozygous deletion of CDKN2A/B, and absence of TERTp mutations. This cluster was significantly associated with older age (p = 0.021), higher Ki-67 score (p = 0.007), poor prognosis (p=0.012), and a periventricular tumor location. We report the development of a glioma-tailored NGS panel for detecting 1p/19q codeletion and driver gene mutations on a single platform. Our panel identified distinct subtypes of IDH- and TERTp-wildtype glioblastomas with frequent PDGFRA alterations.
    Keywords:  1p/19q codeletion; PDGFRA alterations; TERT promoter; glioblastoma; next-generation sequencing
    DOI:  https://doi.org/10.1111/cas.14597
  11. Cancers (Basel). 2020 Aug 05. pii: E2173. [Epub ahead of print]12(8):
    The Role of RNA and DNA Aptamers in Glioblastoma Diagnosis and Therapy: A Systematic Review of the Literature.
    Silvia Nuzzo, Valentina Brancato, Alessandra Affinito, Marco Salvatore, Carlo Cavaliere, Gerolama Condorelli.
      Glioblastoma (GBM) is the most lethal primary brain tumor of the central nervous system in adults. Despite advances in surgical and medical neuro-oncology, the median survival is about 15 months. For this reason, initial diagnosis, prognosis, and targeted therapy of GBM represent very attractive areas of study. Aptamers are short three-dimensional structures of single-stranded nucleic acids (RNA or DNA), identified by an in vitro process, named systematic evolution of ligands by exponential enrichment (SELEX), starting from a partially random oligonucleotide library. They bind to a molecular target with high affinity and specificity and can be easily modified to optimize binding affinity and selectivity. Thanks to their properties (low immunogenicity and toxicity, long stability, and low production variability), a large number of aptamers have been selected against GBM biomarkers and provide specific imaging agents and therapeutics to improve the diagnosis and treatment of GBM. However, the use of aptamers in GBM diagnosis and treatment still represents an underdeveloped topic, mainly due to limited literature in the research world. On these bases, we performed a systematic review aimed at summarizing current knowledge on the new promising DNA and RNA aptamer-based molecules for GBM diagnosis and treatment. Thirty-eight studies from 2000 were included and investigated. Seventeen involved the use of aptamers for GBM diagnosis and 21 for GBM therapy. Our findings showed that a number of DNA and RNA aptamers are promising diagnostic and therapeutic tools for GBM management.
    Keywords:  aptamer; diagnosis; glioblastoma; nucleic acid; therapy
    DOI:  https://doi.org/10.3390/cancers12082173
  12. Nat Commun. 2020 Aug 06. 11(1): 3912
    Immune phenotyping of diverse syngeneic murine brain tumors identifies immunologically distinct types.
    Jasneet Kaur Khalsa, Nina Cheng, Joshua Keegan, Ameen Chaudry, Joseph Driver, Wenya Linda Bi, James Lederer, Khalid Shah.
      Immunotherapy has emerged as a promising approach to treat cancer, however, its efficacy in highly malignant brain-tumors, glioblastomas (GBM), is limited. Here, we generate distinct imageable syngeneic mouse GBM-tumor models and utilize RNA-sequencing, CyTOF and correlative immunohistochemistry to assess immune-profiles in these models. We identify immunologically-inert and -active syngeneic-tumor types and show that inert tumors have an immune-suppressive phenotype with numerous exhausted CD8 T cells and resident macrophages; fewer eosinophils and SiglecF+ macrophages. To mimic the clinical-settings of first line of GBM-treatment, we show that tumor-resection invigorates an anti-tumor response via increasing T cells, activated microglia and SiglecF+ macrophages and decreasing resident macrophages. A comparative CyTOF analysis of resected-tumor samples from GBM-patients and mouse GBM-tumors show stark similarities in one of the mouse GBM-tumors tested. These findings guide informed choices for use of GBM models for immunotherapeutic interventions and offer a potential to facilitate immune-therapies in GBM patients.
    DOI:  https://doi.org/10.1038/s41467-020-17704-5
  13. Acta Neuropathol Commun. 2020 Aug 05. 8(1): 124
    A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology.
    Julia Lorenz, Tanja Rothhammer-Hampl, Saida Zoubaa, Elisabeth Bumes, Tobias Pukrop, Oliver Kölbl, Selim Corbacioglu, Nils O Schmidt, Martin Proescholdt, Peter Hau, Markus J Riemenschneider.
      Recent updates in the classification of central nervous system (CNS) tumors have increased the need for molecular testing. Assessment of multiple alterations in parallel, complex combinations of gene sequence and chromosomal changes, as well as therapy prediction by identification of actionable mutations are the major challenges. We here report on a customized next generation sequencing (NGS)-based DNA panel assay that combines diagnostic and predictive testing and -as a comprehensive approach- allows for simultaneous single nucleotide variant (SNP) / small insertion/deletion (InDel), copy number variation (CNV) and loss of heterozygosity (LOH) detection. We analyzed formalin-fixed and paraffin-embedded (FFPE) DNA from a total of 104 patients with CNS tumors. After amplicon capture-based library preparation, sequencing was performed on the relatively cost-efficient Illiumina MiniSeq platform and evaluated with freely available bioinformatical tools. 57 genes for exonic SNP/InDel calling (19 of those in intronic regions for CNV analysis), 3 chromosomal arms and 4 entire chromosomes for CNV and LOH analysis were covered. Results were extensively validated. Our approach yielded high accuracy, sensitivity and specificity. It led to refined diagnoses in a relevant number of analyzed cases, reliably enabled complex subclassifications (e.g. for medulloblastomas) and identified actionable targets for clinical use. Thus, our single-platform approach is an efficient and powerful tool to comprehensively support molecular testing in neurooncology. Future functionality is guaranteed as novel upcoming biomarkers can be easily incorporated in a modular panel design.
    Keywords:  Glioblastoma; Glioma; Integrated diagnoses; Medulloblastoma; Meningioma; Next generation sequencing; Targeted therapy
    DOI:  https://doi.org/10.1186/s40478-020-01000-w
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