The 2021 WHO Classification of Central Nervous System Tumors recommended evaluation of cyclin‐dependent kinase inhibitor 2A/B (CDKN2A/B) deletion in addition to codeletion of 1p/19q to characterize ...IDH‐mutant gliomas. Here, we demonstrated the use of a nanopore‐based copy‐number variation sequencing (nCNV‐seq) approach to simultaneously identify deletions of CDKN2A/B and 1p/19q. The nCNV‐seq approach was initially evaluated on three distinct glioma cell lines and then applied to 19 IDH‐mutant gliomas (8 astrocytomas and 11 oligodendrogliomas) from patients. The whole‐arm 1p/19q codeletion was detected in all oligodendrogliomas with high concordance among nCNV‐seq, FISH, DNA methylation profiling, and whole‐genome sequencing. For the CDKN2A/B deletion, nCNV‐seq detected the loss in both astrocytoma and oligodendroglioma, with strong correlation with the CNV profiles derived from whole‐genome sequencing (Pearson correlation (r) = 0.95, P < 2.2 × 10−16 to r = 0.99, P < 2.2 × 10−16) and methylome profiling. Furthermore, nCNV‐seq can differentiate between homozygous and hemizygous deletions of CDKN2A/B. Taken together, nCNV‐seq holds promise as a new, alternative approach for a rapid and simultaneous detection of the molecular signatures of IDH‐mutant gliomas without capital expenditure for a sequencer.
The 2021 WHO classification of CNS tumors recommended detection of 1p/19q co‐deletion and CDKN2A/B homozygous deletion to characterize IDH‐mutant gliomas. A crucial challenge remained as how to evaluate CDKN2A/B status in routine pathology laboratory. We described a new approach, Nanopore‐based CNV sequencing (nCNV‐seq), that can determine the 1p/19q co‐deletion and CDKN2A/B loss with excellent concordance against other diagnostic methods including WGS and DNA methylation profiling in 19 IDH‐mutant gliomas. In addition, modified nCNV‐seq analysis can differentiate homozygous deletion from hemizygous deletion of CDKN2A/B. Therefore, the nCNV‐seq holds promise as a new, alternative approach for characterization of IDH‐mutant gliomas without capital expenditure for a sequencer.
Objective To investigate the relationship between 3 hypoxic markers, carbonic anhydrase-9 (CA-9), hypoxia-inducible factor (HIF)-1α, and HIF-2α and the traditional genetic markers, deletions of ...chromosomes 1p and 19q and Isocitrate dehydrogenase 1 (IDH1) R132H mutation in oligodendrogliomas. Methods Thirty-one oligodendrogliomas (27 World Health Organization Grade WHO II and 4 WHO Grade III) were processed into tissue microarray. Fluorescence in situ hybridization was exploited to detect chromosome deletion, whereas immunohistochemistry was performed to assess IDH1R132H mutation, CA-9, HIF-1α, and HIF-2α expression. Results The frequencies of 1p/19q co-deletion and IDH1 R132H mutation were 68% and 71%, respectively. High expression of CA-9 was observed in 42% and was associated with longer survival ( P = 0.04) in WHO Grade II oligodendroglioma. High CA-9 expression also identified 62% of 1p/19q-codeleted oligodendroglioma ( P = 0.001). In addition, all tumors with high CA-9 expression displayed 1p/19q-codeletion. HIF-1α and HIF-2α provided no additional prognostic value for survival. Conclusions High expression of CA-9, a marker for hypoxia and acidosis, is associated with favorable prognosis in oligodendroglioma. In addition, it may serve as a simple screening test for 1p/19q co-deletion if validated in larger cohorts.
High-grade (WHO grade II and III) meningiomas represent a small subset of meningiomas with aggressive biology and high rate of recurrence. The mainstay treatment for high-grade meningiomas is surgery ...whereas the role of adjuvant radiotherapy (RT) remains controversial. We retrospectively evaluated the impact of RT following resection on survival of 65 patients with high-grade meningiomas at our institution between 2006 and 2010. Of 65 patients, 44 (68%) were female. The median age of diagnosis was 51.3 years. Of 46 patients who underwent gross total resection (GTR), 16 (34.8%) patients received RT, whereas 14 (73.7%) of 19 patients who underwent subtotal resection (STR) received RT. At a median follow up 66.6 months, the 5-year OS and 5-year PFS rates for all 65 patients were 65.4% and 53.6%, respectively. Postoperative RT did not improve OS or PFS in unselected high-grade meningiomas. However, adjuvant RT following STR significantly improved PFS compared with STR alone (P = 0.018) with the 5-year PFS rates with and without adjuvant RT of 71% and 40%, respectively. The 5-year OS rates for STR patients with and without RT were 86% and 40%, respectively. In the GTR group, adjuvant RT was not associated with significant survival benefits. In conclusion, adjuvant RT after STR for high-grade meningiomas improved local disease control and survival compared with STR alone.
•Cryptococcal meningoencephalitis (CM) is a complication of cryptococcal infection of the CNS.•Brainstem infarction complicated by CM is extremely uncommon.•Pathogenesis of vasculopathy in CM is ...uncertain.•Few studies suggested a poor prognosis of CM complicated with vasculopathy.•Treatment regimen was selected based on immune status of patients.
Cryptococcal meningoencephalitis is one of the most common central nervous system infections affecting immunocompromised patients. However, brainstem involvement is extremely rare and may represent a diagnostic challenge to clinicians. We report a non-HIV infected, chronically immunosuppressed, patient with fatal disseminated cryptococcosis presented with subcutaneous masses at both thighs and progressive brainstem dysfunction. Magnetic resonance imaging demonstrated multiple brainstem infarcts likely derived from small vessel vasculopathy. Anti-fungal treatment led to partial neurologic improvement but the patient succumbed to a fatal sepsis from hospital-acquired pneumonia.
The revised WHO guidelines for classifying and grading brain tumors include several copy number variation (CNV) markers. The turnaround time for detecting CNVs and alterations throughout the entire ...genome is drastically reduced with the customized read incremental approach on the nanopore platform. However, this approach is challenging for non-bioinformaticians due to the need to use multiple software tools, extract CNV markers and interpret results, which creates barriers due to the time and specialized resources that are necessary. To address this problem and help clinicians classify and grade brain tumors, we developed GLIMMERS: glioma molecular markers exploration using long-read sequencing, an open-access tool that automatically analyzes nanopore-based CNV data and generates simplified reports.
GLIMMERS is available at https://gitlab.com/silol_public/glimmers under the terms of the MIT license.
Infection of susceptible mice with Theiler’s murine encephalomyelitis virus results in neurological dysfunction from progressive central nervous system demyelination that is pathologically similar to ...the human disease, multiple sclerosis. We hypothesized that the development of neuropathology proceeds down a final common pathway that can be accurately quantified within a single spinal cord lesion. To test this hypothesis, we conducted quantitative ultrastructural analyses of individual demyelinated spinal cord lesions from chronically infected mice to determine whether pathological variables assessed within a single lesion accurately predicted global assessments of morphological and functional disease course. Within lesions we assessed by electron microscopy the frequencies of normally myelinated, remyelinated, and demyelinated axons, as well as degenerating axons and intra-axonal mitochondria. The frequency of medium and large remyelinated fibers within a single lesion served as a powerful indicator of axonal preservation and correlated with preserved neurological function. The number of degenerating axons and increased intra-axonal mitochondria also correlated strongly with global measures of disease course, such as total lesion load, spinal cord atrophy, and neurological function. This is the first study to demonstrate that functional severity of disease course is evident within a single demyelinated lesion analyzed morphometrically at the ultrastructural level.
Malignant gliomas are the most prevalent type of primary brain tumor in adults. Despite progress in brain tumor therapy, the prognosis of malignant glioma patients remains dismal. The median survival ...of patients with glioblastoma multiforme, the most common grade of malignant glioma, is 10-12 months. Conventional therapy of surgery, radiation and chemotherapy is largely palliative. Essentially, tumor recurrence is inevitable. Salvage treatments upon recurrence are palliative at best and rarely provide significant survival benefit. Therapies targeting the underlying molecular pathogenesis of brain tumors are urgently required. Common genetic abnormalities in malignant glioma specimens are associated with aberrant activation or suppression of cellular signal transduction pathways and resistance to radiation and chemotherapy. Several low molecular weight signal transduction inhibitors have been examined in preclinical and clinical malignant glioma trials. The efficacy of these agents as monotherapies has been modest, at best; however, small subsets of patients who harbor specific genetic changes in their tumors may display favorable clinical responses to defined small molecule inhibitors. Multitargeted kinase inhibitors or combinations of agents targeting different mitogenic pathways may overcome the resistance of tumors to single-agent targeted therapies. Well designed studies of small molecule kinase inhibitors will include assessment of safety, drug delivery, target inhibition and correlative biomarkers to define mechanisms of response or resistance to these agents. Predictive biomarkers will enrich for patients most likely to respond in future clinical trials. Additional clinical studies will combine novel targeted therapies with radiation, chemotherapies and immunotherapies.
•The WHO classification for gliomas uses phenotypic and genotypic data for diagnosis.•This approach presents difficulties for countries with limited laboratory resources.•A simplified approach is ...presented based on morphology and limited molecular assays.•With this approach, we were able to reach the WHO diagnosis in 117/118 cases.
The most recent WHO classification (2016) for gliomas introduced integrated diagnoses requiring both phenotypic and genotypic data. This approach presents difficulties for countries with limited resources for laboratory testing. The present study describes a series of 118 adult Thai patients with diffuse gliomas, classified by the WHO 2016 classification. The purpose was to demonstrate how a diagnosis can still be achieved using a simplified approach that combines clinical, morphological, immunohistochemical, and fewer molecular assays than typically performed. This algorithm starts with tumor location (midline vs. non-midline) with diffuse midline glioma identified by H3 K27M immunostaining. All other tumors are placed into one of 6 categories, based on morphologic features rather than specific diagnoses. Molecular testing is limited to IDH1/IDH2 mutations, plus co-deletion of 1p/19q for cases with oligodendroglial features and TERT promoter mutation for cases without such features. Additional testing for co-deletion of 1p/19q, TERT promoter mutation and BRAF mutations are only used in selected cases to refine diagnosis and prognosis. With this approach, we were able to reach the integrated diagnosis in 117/118 cases, saving 50 % of the costs of a more inclusive testing panel. The demographic data and tumor subtypes were found to be similar to series from other regions of the world. To the best of our knowledge, this is to the first reported series of diffuse gliomas in South-East Asia categorized by the WHO 2016 classification system.
Vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR) signaling are established contributors to malignant glioma (MG) biology. We, therefore, evaluated bevacizumab, a ...humanized anti-VEGF monoclonal antibody, in combination with the EGFR tyrosine kinase inhibitor erlotinib, in this phase 2 study for recurrent MG patients (www.ClinicalTrials.gov, NCT00671970). Fifty-seven patients (n = 25, glioblastoma GBM; n = 32, anaplastic glioma AG) were enrolled. The primary endpoint was 6-month progression-free survival (PFS-6). Overall survival (OS), radiographic response, pharmacokinetics, and correlative biomarkers were the secondary endpoints. Patients were stratified based on the concurrent use of enzyme-inducing antiepileptic drugs (EIAEDs). Bevacizumab (10 mg/kg) was given intravenously every 2 weeks. Erlotinib was orally administered daily at 200 mg/day for patients not on EIAEDs and 500 mg/day for patients on EIAEDs. PFS-6 and median OS were 28% and 42 weeks for GBM patients and 44% and 71 weeks for AG patients, respectively. Twelve (48%) GBM patients and 10 (31%) AG patients achieved a radiographic response. Erlotinib pharmacokinetic exposures were comparable between EIAED and non-EIAED groups. Rash, mucositis, diarrhea, and fatigue were common but mostly grades 1 and 2. Among GBM patients, grade 3 rash, observed in 32%, was associated with survival benefit, whereas elevated hypoxia-inducible factor-2 alpha and VEGF receptor-2 levels were associated with poor survival. Bevacizumab plus erlotinib was adequately tolerated in recurrent MG patients. However, this regimen was associated with similar PFS benefit and radiographic response when compared with other historical bevacizumab-containing regimens.
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