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1.
Nature ; 576(7785): 112-120, 2019 12.
Article in English | MEDLINE | ID: mdl-31748746

ABSTRACT

The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear1,2. Here we analysed temporally separated DNA-sequencing data and matched clinical annotation from 222 adult patients with glioma. By analysing mutations and copy numbers across the three major subtypes of diffuse glioma, we found that driver genes detected at the initial stage of disease were retained at recurrence, whereas there was little evidence of recurrence-specific gene alterations. Treatment with alkylating agents resulted in a hypermutator phenotype at different rates across the glioma subtypes, and hypermutation was not associated with differences in overall survival. Acquired aneuploidy was frequently detected in recurrent gliomas and was characterized by IDH mutation but without co-deletion of chromosome arms 1p/19q, and further converged with acquired alterations in the cell cycle and poor outcomes. The clonal architecture of each tumour remained similar over time, but the presence of subclonal selection was associated with decreased survival. Finally, there were no differences in the levels of immunoediting between initial and recurrent gliomas. Collectively, our results suggest that the strongest selective pressures occur during early glioma development and that current therapies shape this evolution in a largely stochastic manner.


Subject(s)
Glioma/genetics , Adult , Chromosomes, Human, Pair 1 , Chromosomes, Human, Pair 19 , Disease Progression , Glioma/pathology , Humans , Isocitrate Dehydrogenase/genetics , Mutation , Polymorphism, Single Nucleotide , Recurrence
2.
J Neurooncol ; 161(3): 451-467, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36757526

ABSTRACT

INTRODUCTION: Brain tumors cause morbidity and mortality in part through peritumoral brain edema. The current main treatment for peritumoral brain edema are corticosteroids. Due to the increased recognition of their side-effect profile, there is growing interest in finding alternatives to steroids but there is little formal study of animal models of peritumoral brain edema. This study aims to summarize the available literature. METHODS: A systematic search was undertaken of 5 literature databases (Medline, Embase, CINAHL, PubMed and the Cochrane Library). The generic strategy was to search for various terms associated with "brain tumors", "brain edema" and "animal models". RESULTS: We identified 603 reports, of which 112 were identified as relevant for full text analysis that studied 114 peritumoral brain edema animal models. We found significant heterogeneity in the species and strain of tumor-bearing animals, tumor implantation method and edema assessment. Most models did not produce appreciable brain edema and did not test for observable manifestations thereof. CONCLUSION: No animal model currently exists that enable the investigation of novel candidates for the treatment of peritumoral brain edema. With current interest in alternative treatments for peritumoral brain edema, there is an unmet need for clinically relevant animal models.


Subject(s)
Brain Edema , Brain Neoplasms , Animals , Humans , Magnetic Resonance Imaging/methods , Brain Neoplasms/pathology , Edema/complications , Brain Edema/complications , Brain/pathology
3.
Histopathology ; 81(2): 159-167, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35322456

ABSTRACT

The Delphi method is a well-established research tool, used for consensus building across a number of fields. Despite its widespread use, and popularity in many medical specialities, there is a paucity of literature on the use of the Delphi method in Histopathology. This literature review seeks to critique the Delphi methodology and explore its potential applications to histopathology-based clinical and research questions. We review those published studies that have utilized the Delphi methodology in Histopathology settings and specifically outline the advantages and limitations of this technique, highlighting situations where its application can be most effective.


Subject(s)
Consensus , Delphi Technique , Humans , Surveys and Questionnaires
4.
Br J Neurosurg ; : 1-8, 2020 Dec 30.
Article in English | MEDLINE | ID: mdl-33377401

ABSTRACT

PURPOSE: Both phenotypic and genotypic variations now underpin glioma classification, thus helping to more accurately guide their clinical management. However, WHO Grade III anaplastic astrocytoma (AA) remains an unpredictable, heterogeneous entity; displaying a variable prognosis, clinical course and treatment response. This study aims to examine whether additional tumour characteristics influence either overall survival (OS) or 3-year survival in AA. MATERIALS AND METHODS: Data were collected on all newly diagnosed cases of AA between 2003 and 2014, followed up for a minimum of 3 years. Molecular information was obtained from case records and if missing, was re-analysed. Histological slides were independently examined for Ki-67 proliferation index, cellularity and number of mitotic figures. Kaplan-Meier and Cox regression analyses were used to assess OS. RESULTS: In total, 50 cases were included with a median OS of 14.5 months (range: 1-150 months). Cumulative 3-year survival was 31.5%. Median age was 50 years (range: 24 - 77). Age, IDH1 mutation status, lobar location, oncological therapy and surgical resection were significant independent prognostic indicators for OS. In cases demonstrating an OS ≥ 3 years (n = 15), Ki-67 index, number of mitotic figures and percentage areas of 'high cellularity' were significantly reduced, i.e. more characteristic of lower-grade/WHO Grade II glioma. CONCLUSIONS: IDH1 status, age, treatment and location remain the most significant prognostic indicators for patients with AA. However, Ki-67 index, mitotic figures and cellularity may help identify AA cases more likely to survive < 3 years, i.e. AA cases more similar to glioblastoma and those cases more likely to survive > 3 years, i.e. more similar to a low-grade glioma.

5.
BMC Cancer ; 19(1): 139, 2019 Feb 11.
Article in English | MEDLINE | ID: mdl-30744596

ABSTRACT

BACKGROUND: Intracranial and intraspinal tumours are the most numerous solid tumours in children. Some recently defined subtypes are relatively frequent in childhood. Many cancer registries routinely ascertain CNS tumours of all behaviours, while others only cover malignant neoplasms. Some behaviour codes have changed between revisions of the International Classification of Diseases for Oncology, including pilocytic astrocytoma, downgraded to uncertain behaviour in ICD-O-3. METHODS: We used data from the population-based National Registry of Childhood Tumours, which routinely included non-malignant CNS tumours, to document the occurrence of CNS tumours among children aged < 15 years in Great Britain during 2001-2010 and to document the descriptive epidemiology of childhood CNS tumours over the 40-year period 1971-2010, during which several new entities were accommodated in successive editions of the WHO Classification and revisions of ICD-O. Eligible cases were all those with a diagnosis included in Groups III (CNS tumours) and Xa (CNS germ-cell tumours) of the International Classification of Childhood Cancer, Third Edition. The population at risk was derived from annual mid-year estimates by sex and single year of age compiled by the Office for National Statistics and its predecessors. Incidence rates were calculated for age groups 0, 1-4, 5-9 and 10-14 years, and age-standardised rates were calculated using the weights of the world standard population. RESULTS: Age-standardised incidence in 2001-10 was 40.1 per million. Astrocytomas accounted for 41%, embryonal tumours for 17%, other gliomas for 10%, ependymomas for 7%, rarer subtypes for 20% and unspecified tumours for 5%. Incidence of tumours classified as malignant and non-malignant by ICD-O-3 increased by 30 and 137% respectively between 1971-75 and 2006-10. CONCLUSIONS: Total incidence was similar to that in other large western countries. Deficits of some, predominantly low-grade, tumours or differences in their age distribution compared with the United States and Nordic countries are compatible with delayed diagnosis. Complete registration regardless of tumour behaviour is essential for assessing burden of disease and changes over time. This is particularly important for pilocytic astrocytoma, because of its recent downgrading to non-malignant and time trends in the proportion of astrocytomas with specified subtype.


Subject(s)
Central Nervous System Neoplasms/epidemiology , Central Nervous System Neoplasms/pathology , Adolescent , Age Factors , Central Nervous System Neoplasms/history , Child , Child, Preschool , Female , History, 20th Century , History, 21st Century , Humans , Incidence , Infant , Infant, Newborn , Male , Neoplasms, Second Primary/epidemiology , Neoplasms, Second Primary/etiology , Population Surveillance , Registries , United Kingdom/epidemiology
6.
Int J Cancer ; 142(8): 1620-1626, 2018 04 15.
Article in English | MEDLINE | ID: mdl-29194603

ABSTRACT

Many traits of cancer progression (e.g., development of metastases or resistance to therapy) are facilitated by tumour evolution: Darwinian selection of subclones with distinct genotypes or phenotypes that enable such progression. Characterising these subclones provide an opportunity to develop drugs to better target their specific properties but requires the accurate identification of somatic mutations shared across multiple spatiotemporal tumours from the same patient. Current best practices for calling somatic mutations are optimised for single samples, and risk being too conservative to identify shared mutations with low prevalence in some samples. We reasoned that datasets from multiple matched tumours can be used for mutual validation and thus propose an adapted two-stage approach: (1) low-stringency mutation calling to identify mutations shared across samples irrespective of the weight of evidence in a single sample; (2) high-stringency mutation calling to further characterise mutations present in a single sample. We applied our approach to three-independent cohorts of paired primary and recurrent glioblastoma tumours, two of which have previously been analysed using existing approaches, and found that it significantly increased the amount of biologically relevant shared somatic mutations identified. We also found that duplicate removal was detrimental when identifying shared somatic mutations. Our approach is also applicable when multiple datasets e.g. DNA and RNA are available for the same tumour.


Subject(s)
Glioblastoma/genetics , Genotype , Humans , Mutation/genetics , Neoplasm Recurrence, Local/genetics , Phenotype
7.
Acta Neuropathol ; 136(4): 557-567, 2018 10.
Article in English | MEDLINE | ID: mdl-30123935

ABSTRACT

The deposition of the amyloid ß-protein (Aß) in senile plaques is one of the histopathological hallmarks of Alzheimer's disease (AD). Aß-plaques arise first in neocortical areas and, then, expand into further brain regions in a process described by 5 phases. Since it is possible to identify amyloid pathology with radioactive-labeled tracers by positron emission tomography (PET) the question arises whether it is possible to distinguish the neuropathological Aß-phases with amyloid PET imaging. To address this question we reassessed 97 cases of the end-of-life study cohort of the phase 3 [18F]flutemetamol trial (ClinicalTrials.gov identifiers NCT01165554, and NCT02090855) by combining the standardized uptake value ratios (SUVRs) with pons as reference region for cortical and caudate nucleus-related [18F]flutemetamol-retention. We tested them for their prediction of the neuropathological pattern found at autopsy. By defining threshold levels for cortical and caudate nucleus SUVRs we could distinguish different levels of [18F]flutemetamol uptake termed PET-Aß phase estimates. When comparing these PET-Aß phase estimates with the neuropathological Aß-phases we found that PET-Aß phase estimate 0 corresponded with Aß-phases 0-2, 1 with Aß-phase 3, 2 with Aß-phase 4, and 3 with Aß-phase 5. Classification using the PET-Aß phase estimates predicted the correct Aß-phase in 72.16% of the cases studied here. Bootstrap analysis was used to confirm the robustness of the estimates around this association. When allowing a range of ± 1 phase for a given Aß-phase correct classification was given in 96.91% of the cases. In doing so, we provide a novel method to convert SUVR-levels into PET-Aß phase estimates that can be easily translated into neuropathological phases of Aß-deposition. This method allows direct conclusions about the pathological distribution of amyloid plaques (Aß-phases) in vivo. Accordingly, this method may be ideally suited to detect early preclinical AD-patients, to follow them with disease progression, and to provide a more precise prognosis for them based on the knowledge about the underlying pathological phase of the disease.


Subject(s)
Amyloid beta-Protein Precursor/metabolism , Aniline Compounds , Benzothiazoles , Plaque, Amyloid/diagnostic imaging , Radiopharmaceuticals , Aged , Aged, 80 and over , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/metabolism , Autopsy , Brain/pathology , Caudate Nucleus/diagnostic imaging , Cerebral Cortex/diagnostic imaging , Disease Progression , Female , Humans , Male , Middle Aged , Plaque, Amyloid/metabolism , Pons/diagnostic imaging , Pons/metabolism , Predictive Value of Tests
8.
Eur Spine J ; 24 Suppl 4: S472-84, 2015 May.
Article in English | MEDLINE | ID: mdl-25374299

ABSTRACT

Atypical teratoid rhabdoid tumour (ATRT) is a rare and highly aggressive malignant neoplasm of the central nervous system (CNS), which occurs predominantly in children less than 2 years of age. There are less than 50 cases described in adult. We report a case of primary spinal ATRT in a 65-year-old male who presented to us with cauda equina syndrome. To the best of our knowledge, our patient is the (1) second oldest patient to be diagnosed with ATRT and only the third case of adult spinal ATRT report in the literature; (2) first reported case of CNS ATRT occurring in a patient with non-rhabdoid renal cancer; (3) first adult patient of ATRT to present with cauda equina syndrome.


Subject(s)
Polyradiculopathy/etiology , Rhabdoid Tumor/diagnosis , Spinal Cord Neoplasms/diagnosis , Teratoma/diagnosis , Aged , Fatal Outcome , Humans , Male , Rhabdoid Tumor/complications , Spinal Cord Neoplasms/complications , Teratoma/complications , Thoracic Vertebrae
9.
Alzheimers Dement ; 11(8): 975-85, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26141264

ABSTRACT

BACKGROUND: Amyloid positron emission tomography (PET) has become an important tool to identify amyloid-ß (Aß) pathology in Alzheimer's disease (AD) patients. Here, we determined the diagnostic value of the amyloid PET tracer [(18)F]flutemetamol in relation to Aß pathology at autopsy. METHODS: [(18)F]flutemetamol PET was carried out in a cohort of 68 patients included in a [(18)F]flutemetamol amyloid PET imaging end-of-life study (GE067-007). At autopsy, AD pathology was determined and Aß plaque pathology was classified into phases of its regional distribution (0-5). RESULTS: [(18)F]flutemetamol PET was universally positive in cases with advanced stage postmortem Aß pathology (Aß phases 4 and 5). Negative amyloid PET was universally observed in nondemented or non-AD dementia cases with initial Aß phases 1 and 2, whereas 33.3% of the phase 3 cases were positive. CONCLUSIONS: [(18)F]flutemetamol amyloid PET detects primarily advanced stages of Aß pathology in preclinical and symptomatic AD cases.


Subject(s)
Alzheimer Disease/diagnostic imaging , Alzheimer Disease/pathology , Amyloid/metabolism , Aniline Compounds/pharmacokinetics , Benzothiazoles/pharmacokinetics , Positron-Emission Tomography/methods , Aged , Aged, 80 and over , Analysis of Variance , Autopsy , Cohort Studies , Female , Humans , Logistic Models , Magnetic Resonance Imaging , Male , Psychiatric Status Rating Scales , Tomography Scanners, X-Ray Computed
10.
Genome Biol ; 25(1): 45, 2024 02 07.
Article in English | MEDLINE | ID: mdl-38326875

ABSTRACT

BACKGROUND: Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur. RESULTS: Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation. CONCLUSIONS: We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.


Subject(s)
Brain Neoplasms , Glioblastoma , Humans , Glioblastoma/drug therapy , Glioblastoma/genetics , Glioblastoma/pathology , Neoplasm Recurrence, Local/genetics , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Brain/pathology , DNA Methylation , Gene Expression Regulation, Neoplastic , Tumor Microenvironment
11.
J Biol Chem ; 287(29): 24754-64, 2012 Jul 13.
Article in English | MEDLINE | ID: mdl-22593583

ABSTRACT

Tumor cell survival and proliferation is attributable in part to suppression of apoptotic pathways, yet the mechanisms by which cancer cells resist apoptosis are not fully understood. Many cancer cells constitutively express heme oxygenase-1 (HO-1), which catabolizes heme to generate biliverdin, Fe(2+), and carbon monoxide (CO). These breakdown products may play a role in the ability of cancer cells to suppress apoptotic signals. K(+) channels also play a crucial role in apoptosis, permitting K(+) efflux which is required to initiate caspase activation. Here, we demonstrate that HO-1 is constitutively expressed in human medulloblastoma tissue, and can be induced in the medulloblastoma cell line DAOY either chemically or by hypoxia. Induction of HO-1 markedly increases the resistance of DAOY cells to oxidant-induced apoptosis. This effect was mimicked by exogenous application of the heme degradation product CO. Furthermore we demonstrate the presence of the pro-apoptotic K(+) channel, Kv2.1, in both human medulloblastoma tissue and DAOY cells. CO inhibited the voltage-gated K(+) currents in DAOY cells, and largely reversed the oxidant-induced increase in K(+) channel activity. p38 MAPK inhibition prevented the oxidant-induced increase of K(+) channel activity in DAOY cells, and enhanced their resistance to apoptosis. Our findings suggest that CO-mediated inhibition of K(+) channels represents an important mechanism by which HO-1 can increase the resistance to apoptosis of medulloblastoma cells, and support the idea that HO-1 inhibition may enhance the effectiveness of current chemo- and radiotherapies.


Subject(s)
Carbon Monoxide/pharmacology , Heme Oxygenase-1/metabolism , Medulloblastoma/metabolism , Shab Potassium Channels/metabolism , Apoptosis , Blotting, Western , Cell Hypoxia/physiology , Cell Line, Tumor , Cell Survival/genetics , Cell Survival/physiology , Diamide/pharmacology , Electrophysiology , Flow Cytometry , Heme Oxygenase-1/genetics , Humans , Imidazoles/pharmacology , Immunoprecipitation , In Situ Nick-End Labeling , In Vitro Techniques , Phosphorylation/drug effects , Pyridines/pharmacology , Shab Potassium Channels/genetics
12.
Brain ; 135(Pt 9): 2684-98, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22961547

ABSTRACT

The most common progressive myoclonus epilepsies are the late infantile and late infantile-variant neuronal ceroid lipofuscinoses (onset before the age of 6 years), Unverricht-Lundborg disease (onset after the age of 6 years) and Lafora disease. Lafora disease is a distinct disorder with uniform course: onset in teenage years, followed by progressively worsening myoclonus, seizures, visual hallucinations and cognitive decline, leading to a vegetative state in status myoclonicus and death within 10 years. Biopsy reveals Lafora bodies, which are pathognomonic and not seen with any other progressive myoclonus epilepsies. Lafora bodies are aggregates of polyglucosans, poorly constructed glycogen molecules with inordinately long strands that render them insoluble. Lafora disease is caused by mutations in the EPM2A or EPM2B genes, encoding the laforin phosphatase and the malin ubiquitin ligase, respectively, two cytoplasmically active enzymes that regulate glycogen construction, ensuring symmetric expansion into a spherical shape, essential to its solubility. In this work, we report a new progressive myoclonus epilepsy associated with Lafora bodies, early-onset Lafora body disease, map its locus to chromosome 4q21.21, identify its gene and mutation and characterize the relationship of its gene product with laforin and malin. Early-onset Lafora body disease presents early, at 5 years, with dysarthria, myoclonus and ataxia. The combination of early-onset and early dysarthria strongly suggests late infantile-variant neuronal ceroid lipofuscinosis, not Lafora disease. Pathology reveals no ceroid lipofuscinosis, but Lafora bodies. The subsequent course is a typical progressive myoclonus epilepsy, though much more protracted than any infantile neuronal ceroid lipofuscinosis, or Lafora disease, patients living into the fourth decade. The mutation, c.781T>C (Phe261Leu), is in a gene of unknown function, PRDM8. We show that the PRDM8 protein interacts with laforin and malin and causes translocation of the two proteins to the nucleus. We find that Phe261Leu-PRDM8 results in excessive sequestration of laforin and malin in the nucleus and that it therefore likely represents a gain-of-function mutation that leads to an effective deficiency of cytoplasmic laforin and malin. We have identified a new progressive myoclonus epilepsy with Lafora bodies, early-onset Lafora body disease, 101 years after Lafora disease was first described. The results to date suggest that PRDM8, the early-onset Lafora body disease protein, regulates the cytoplasmic quantities of the Lafora disease enzymes.


Subject(s)
Brain/pathology , Carrier Proteins/genetics , Lafora Disease/genetics , Muscle, Skeletal/pathology , Nuclear Proteins/genetics , Adolescent , Adult , Age of Onset , Atrophy , Child , Child, Preschool , Chromosomes, Human, Pair 4 , DNA-Binding Proteins , Disease Progression , Female , Histone Methyltransferases , Humans , Lafora Disease/pathology , Lod Score , Male , Mutation , Skin/pathology
13.
Curr Oncol ; 30(7): 6682-6698, 2023 07 13.
Article in English | MEDLINE | ID: mdl-37504350

ABSTRACT

Glioblastoma (GBM) has the typical radiological appearance (TRA) of a centrally necrotic, peripherally enhancing tumor with surrounding edema. The objective of this study was to determine whether the developing GBM displays a spectrum of imaging changes detectable on routine clinical imaging prior to TRA GBM. Patients with pre-operative imaging diagnosed with GBM (1 January 2014-31 March 2022) were identified from a neuroscience center. The imaging was reviewed by an experienced neuroradiologist. Imaging patterns preceding TRA GBM were analyzed. A total of 76 out of 555 (14%) patients had imaging preceding TRA GBM, 57 had solitary lesions, and 19 had multiple lesions (total = 84 lesions). Here, 83% of the lesions had cortical or cortical/subcortical locations. The earliest imaging features for 84 lesions were T2 hyperintensity/CT low density (n = 18), CT hyperdensity (n = 51), and T2 iso-intensity (n = 15). Lesions initially showing T2 hyperintensity/CT low density later showed T2 iso-intensity. When CT and MRI were available, all CT hyperdense lesions showed T2 iso-intensity, reduced diffusivity, and the following enhancement patterns: nodular 35%, solid 29%, none 26%, and patchy peripheral 10%. The mean time to develop TRA GBM from T2 hyperintensity was 140 days and from CT hyperdensity was 69 days. This research suggests that the developing GBM shows a spectrum of imaging features, progressing through T2 hyperintensity to CT hyperdensity, T2 iso-intensity, reduced diffusivity, and variable enhancement to TRA GBM. Red flags for non-TRA GBM lesions are cortical/subcortical CT hyperdense/T2 iso-intense/low ADC. Future research correlating this imaging spectrum with pathophysiology may provide insight into GBM growth patterns.


Subject(s)
Glioblastoma , Humans , Cross-Sectional Studies , Glioblastoma/diagnostic imaging , Glioblastoma/pathology , Magnetic Resonance Imaging/methods , Tomography, X-Ray Computed
14.
Neuro Oncol ; 25(7): 1236-1248, 2023 07 06.
Article in English | MEDLINE | ID: mdl-36689332

ABSTRACT

BACKGROUND: Characterizing and quantifying cell types within glioblastoma (GBM) tumors at scale will facilitate a better understanding of the association between the cellular landscape and tumor phenotypes or clinical correlates. We aimed to develop a tool that deconvolutes immune and neoplastic cells within the GBM tumor microenvironment from bulk RNA sequencing data. METHODS: We developed an IDH wild-type (IDHwt) GBM-specific single immune cell reference consisting of B cells, T-cells, NK-cells, microglia, tumor associated macrophages, monocytes, mast and DC cells. We used this alongside an existing neoplastic single cell-type reference for astrocyte-like, oligodendrocyte- and neuronal progenitor-like and mesenchymal GBM cancer cells to create both marker and gene signature matrix-based deconvolution tools. We applied single-cell resolution imaging mass cytometry (IMC) to ten IDHwt GBM samples, five paired primary and recurrent tumors, to determine which deconvolution approach performed best. RESULTS: Marker-based deconvolution using GBM-tissue specific markers was most accurate for both immune cells and cancer cells, so we packaged this approach as GBMdeconvoluteR. We applied GBMdeconvoluteR to bulk GBM RNAseq data from The Cancer Genome Atlas and recapitulated recent findings from multi-omics single cell studies with regards associations between mesenchymal GBM cancer cells and both lymphoid and myeloid cells. Furthermore, we expanded upon this to show that these associations are stronger in patients with worse prognosis. CONCLUSIONS: GBMdeconvoluteR accurately quantifies immune and neoplastic cell proportions in IDHwt GBM bulk RNA sequencing data and is accessible here: https://gbmdeconvoluter.leeds.ac.uk.


Subject(s)
Brain Neoplasms , Glioblastoma , Humans , Glioblastoma/pathology , Transcriptome , Brain Neoplasms/pathology , Gene Expression Profiling/methods , Microglia/metabolism , Tumor Microenvironment
15.
Childs Nerv Syst ; 27(5): 811-8, 2011 May.
Article in English | MEDLINE | ID: mdl-21104258

ABSTRACT

PURPOSE: The water channel, aquaporin (AQP)1, is highly specific to the choroid plexus (CP) epithelium within the brain. It is therefore a potential target through which therapeutic agents could be selectively directed to the CP. Here we describe the conjugation of a monoclonal antibody (mAb), raised against an extra-cellular domain of AQP1, to the A chain of ricin (RCA). This reagent should allow study of a highly specific chemical lesion of the CP. METHODS: A published method was used to couple the anti-AQP1 mAb to the A chain of ricin using an SPDP cross-linker. The conjugate was purified by Superdex S-200 chromatography. Column fractions were analysed by SDS-PAGE and Western blotting. Fractions containing conjugate were assayed for cytotoxicity on rat CP cells in culture, using a WST-1 viability assay to assess cell death. RESULTS: SDS-PAGE and Western blotting demonstrated separation of conjugated anti-AQP1 mAb from unconjugated ricin by the Superdex column. Cultured rat CP cells were killed with an IC(50) of 1.81 µg/ml when exposed to the anti-AQP1 mAb-RCA conjugation reaction products. Selectivity of this reagent was demonstrated by the higher IC(50) exhibited by non-AQP1-expressing primary fibroblast cultures and cultures exposed to the reaction products from the non-specific IgG-RCA conjugation attempt. CONCLUSION: We have been able to demonstrate selective cytotoxicity in vitro of an anti-AQP1 mAb-RCA conjugate. We hope that this work will generate further interest in the use of this site-specific conjugate to target the CP in conditions such as hydrocephalus, tumours that arise from here, and other AQP1-expressing tumours.


Subject(s)
Antibodies, Monoclonal/toxicity , Aquaporin 1 , Choroid Plexus/drug effects , Immunotherapy/methods , Immunotoxins/toxicity , Ricin/toxicity , Animals , Aquaporin 1/immunology , Blotting, Western , Cell Death/drug effects , Cells, Cultured , Electrophoresis, Polyacrylamide Gel , Humans , Immunohistochemistry , Neurons/drug effects , Rats
16.
J Plast Reconstr Aesthet Surg ; 74(10): 2776-2820, 2021 Oct.
Article in English | MEDLINE | ID: mdl-34229957

ABSTRACT

Common peroneal nerve (CPN) injury is a recognised complication of traumatic knee dislocation with a direct association between the degree of ligamentous injury and the degree of CPN injury. It is essential explore and repair these injuries in good time to reduce morbidity. Often exploration only involves the portion of this nerve associated with the joint as it courses around the fibular head. However, a recent case highlighted the importance of proximal exploration to its branching point from the sciatic nerve, a known point of fragility, even if other defects have been identified.


Subject(s)
Knee Dislocation/complications , Knee Injuries/complications , Neurosurgical Procedures/methods , Peripheral Nerve Injuries , Peroneal Nerve , Plastic Surgery Procedures/methods , Adult , Athletic Injuries/diagnosis , Bicycling , Humans , Knee Injuries/diagnosis , Knee Injuries/surgery , Male , Patient Care Team , Peripheral Nerve Injuries/etiology , Peripheral Nerve Injuries/physiopathology , Peripheral Nerve Injuries/surgery , Peroneal Nerve/diagnostic imaging , Peroneal Nerve/injuries , Peroneal Nerve/surgery , Time-to-Treatment , Trauma Severity Indices , Treatment Outcome
18.
Lancet Child Adolesc Health ; 4(2): 121-130, 2020 02.
Article in English | MEDLINE | ID: mdl-31786093

ABSTRACT

BACKGROUND: Marked variation exists in the use of genomic data in tumour diagnosis, and optimal integration with conventional diagnostic technology remains uncertain despite several studies reporting improved diagnostic accuracy, selection for targeted treatments, and stratification for trials. Our aim was to assess the added value of molecular profiling in routine clinical practice and the impact on conventional and experimental treatments. METHODS: This population-based study assessed the diagnostic and clinical use of DNA methylation-based profiling in childhood CNS tumours using two large national cohorts in the UK. In the diagnostic cohort-which included routinely diagnosed CNS tumours between Sept 1, 2016, and Sept 1, 2018-we assessed how the methylation profile altered or refined diagnosis in routine clinical practice and estimated how this would affect standard patient management. For the archival cohort of diagnostically difficult cases, we established how many cases could be solved using modern standard pathology, how many could only be solved using the methylation profile, and how many remained unsolvable. FINDINGS: Of 484 patients younger than 20 years with CNS tumours, 306 had DNA methylation arrays requested by the neuropathologist and were included in the diagnostic cohort. Molecular profiling added a unique contribution to clinical diagnosis in 107 (35%; 95% CI 30-40) of 306 cases in routine diagnostic practice-providing additional molecular subtyping data in 99 cases, amended the final diagnosis in five cases, and making potentially significant predictions in three cases. We estimated that it could change conventional management in 11 (4%; 95% CI 2-6) of 306 patients. Among 195 historically difficult-to-diagnose tumours in the archival cohort, 99 (51%) could be diagnosed using standard methods, with the addition of methylation profiling solving a further 34 (17%) cases. The remaining 62 (32%) cases were unresolved despite specialist pathology and methylation profiling. INTERPRETATION: Together, these data provide estimates of the impact that could be expected from routine implementation of genomic profiling into clinical practice, and indicate limitations where additional techniques will be required. We conclude that DNA methylation arrays are a useful diagnostic adjunct for childhood CNS tumours. FUNDING: The Brain Tumour Charity, Children with Cancer UK, Great Ormond Street Hospital Children's Charity, Olivia Hodson Cancer Fund, Cancer Research UK, and the National Institute of Health Research.


Subject(s)
Central Nervous System Neoplasms/diagnosis , DNA Methylation/physiology , Gene Expression Regulation, Neoplastic/physiology , Molecular Targeted Therapy , Biomarkers, Tumor/genetics , Central Nervous System Neoplasms/genetics , Central Nervous System Neoplasms/therapy , Child , Humans , Retrospective Studies , Telomerase
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