IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.

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.

GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data.

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.

Glioma progression is shaped by genetic evolution and microenvironment interactions.

The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status and attributable to changes in histological feature composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A deletions were associated with an increase in proliferating neoplastic cells at recurrence in both glioma subtypes, reflecting active tumor growth. IDH-wild-type tumors were more invasive at recurrence, and their neoplastic cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a myeloid cell state defined by specific ligand-receptor interactions with neoplastic cells. Collectively, these recurrence-associated phenotypes represent potential targets to alter disease progression.

Incidence of systemic autoimmune myopathies and their risk of cancer in Leeds, UK: an 11-year epidemiological study.

Objectives: The aims were to identify all incident adult cases of systemic autoimmune myopathies (SAMs) in the city of Leeds, UK, and to estimate the risk of cancer in SAMs as compared with the general population. Methods: Cases of SAMs were ascertained by review of all muscle biopsy reports from the Neuropathology Laboratory. A review of medical records was undertaken for each case to review the clinical diagnosis and collect epidemiological data such as age, ethnicity, sex and comorbidities, including cancer. Leeds denominator population numbers were publicly obtainable. Results: A total of 206 biopsy reports were identified and, after review, 50 incident cases were included in the study between June 2010 and January 2021. Of the 50 cases, 27 were male and 23 were female. The mean incidence rate of SAMs in Leeds throughout the study period was 7.42/1 000 000 person-years. The proportion of SAMs cases with a confirmed malignancy was 22%. Compared with the general population, the relative risk of cancer was significantly greater in the SAMs population (31.56; P < 0.01). Conclusions: The incidence rate of SAMs in Leeds was consistent with data from previous literature; however, disagreement exists between different methods of SAMs case inclusion due to varying clinical criteria and definitions. SAMs are associated with an increased risk of cancer, but the pathogenesis of this relationship still requires investigating. This study supports the practice of malignancy screening and long-term surveillance in patients with SAMs.

Adalimumab-induced sensory vasculitic neuropathy.

Vasculitis and other autoimmune conditions are known complications of tumour necrosis factor alpha (TNF-α) inhibitor use. By definition, TNF-α inhibitor induced vasculitis is a secondary systemic vasculitis. However, its phenotype is varied and can present as an isolated vasculitic neuropathy. This presents a diagnostic challenge as the gold standard for diagnosis of a vasculitic neuropathy is a peripheral nerve biopsy that meets predefined histopathological criteria. Given the poor sensitivity of the peripheral nerve biopsy, it is important that clinicians take a good history and maintain a high index of suspicion, as this is a treatable iatrogenic condition. Here we present a case of adalimumab-induced sensory vasculitic neuropathy, treated according to the Peripheral Nerve Society guideline for non-systemic vasculitic neuropathy, given her disease phenotype.

Homozygous intronic variants in TPM2 cause recessively inherited Escobar variant of multiple pterygium syndrome and congenital myopathy.

Pathogenic variants in TPM2 have been associated with a variable clinical spectrum, including congenital myopathies and distal arthrogryposis, all but one with dominant inheritance. We report the second case of recessively inherited TPM2-related Escobar variant of multiple pterygium syndrome and congenital myopathy in a patient from a consanguineous family. Ultra-structural examination of the biopsy revealed few cores/mini-cores and sparse nemaline rods. We found a novel homozygous intronic sequence variant, c.564-2A>C in TPM2. This variant is predicted to abolish the consensus acceptor splice site for exon 6b of TPM2 gene. Parents of the proband, both healthy adults with no clinical features, were heterozygous for the variant. Here we establish a homozygous intronic variant in TPM2 as the likely cause of Escobar variant of multiple pterygium syndrome and congenital myopathy, with sparse nemaline rods.

Cerebral protothecosis mimicking high-grade glioma.

Prototheca wickerhamii is a common, indolent alga that seldom causes central nervous system infections in humans. We report the first UK case of cerebral protothecosis in an immunocompetent 56-year-old woman who presented with a 5-month history of intermittent fatigue followed by a 2-week history of symptoms, including right arm and leg weakness, a loss of fine motor coordination, worsening gait, right facial tingling, diplopia and a metallic oral taste. MRI scans revealed a multifocal abnormality suggestive of high-grade glioma. Given the clinical presentation, absence of immunodeficiency and characteristic MRI features, a diagnosis of high-grade glioma was deemed most likely by the multidisciplinary team. Surgical biopsy provided material for histopathological and microbiological diagnosis. She underwent a 2-year course of antimicrobials with surveillance MRI scans. The patient made a good functional recovery but still retains mild neurological sequelae.

Clinical digital neuropathology: experience and observations from a departmental digital pathology training programme, validation and deployment.

AIM: To train and individually validate the neuropathologists in digital primary diagnosis and frozen section reporting using a novel protocol endorsed by the Royal College of Pathologists. The protocol allows early exposure to live digital reporting in a risk mitigated environment. METHODS: Two specialist neuropathologists completed training in the use of a digital microscopy system for primary neuropathological diagnosis and frozen section assessment. Participants were exposed to training sets of 20 histology cases and 10 frozen sections designed to help them identify their personal digital diagnostic pitfalls. Following this, the pathologists viewed 340 live, complete neuropathology cases. All primary diagnoses were made on digital slides with immediate glass slide reconciliation before final case sign-out. RESULTS: There was 100% clinical concordance between the digital slide and glass slide assessment of frozen section cases for each pathologist, and these assessments corresponded with the ground truth diagnoses obtained from examination of definitive histology. For primary diagnosis, there was complete clinical concordance between digital slide and glass slide diagnosis in 98.1% of cases. The majority of discordances were related to grading differences attributable to mitotic count differences. CONCLUSION: Neuropathologists can develop the ability to make primary digital diagnosis competently and confidently following a course of individual training and validation.

Rapid Growth of a Facet Joint Cyst Mimicking an Aggressive Tumor in the Lumbar Spine.

A 67-year-old patient with a history of fully treated bowel carcinoma presented with a short history of unilateral lumbosacral radiculopathy. No neurological deficit was found on examination. Magnetic resonance imaging (MRI) demonstrated initially L4/5 foraminal narrowing that was believed to be the cause for the patient's symptoms; however, a nerve root block led to no improvement in symptoms. MRI was repeated at 5 months and demonstrated a mass causing compression of the S1 nerve. However, the patient declined surgical decompression. MRI at 14 months subsequently showed rapid growth of the lesion suggestive of an aggressive process such as a metastatic lesion or even a nerve sheath tumor such as a Schwannoma. Open biopsy and decompression revealed the lesion to be a facet joint cyst and the patient recovered well and had satisfactory postoperative imaging at 3 months follow-up. There are no reports in the literature of facet joint cysts growing this quickly and thus mimicking other forms of lesion.

Correction to: Different aspects of Alzheimer's disease-related amyloid ß-peptide pathology and their relationship to amyloid positron emission tomography imaging and dementia.

An amendment to this paper has been published and can be accessed via the original article.

DNA methylation-based profiling for paediatric CNS tumour diagnosis and treatment: a population-based study.

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.

Longitudinal molecular trajectories of diffuse glioma in adults.

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.

Different aspects of Alzheimer's disease-related amyloid ß-peptide pathology and their relationship to amyloid positron emission tomography imaging and dementia.

Alzheimer's disease (AD)-related amyloid ß-peptide (Aß) pathology in the form of amyloid plaques and cerebral amyloid angiopathy (CAA) spreads in its topographical distribution, increases in quantity, and undergoes qualitative changes in its composition of modified Aß species throughout the pathogenesis of AD. It is not clear which of these aspects of Aß pathology contribute to AD progression and to what extent amyloid positron emission tomography (PET) reflects each of these aspects. To address these questions three cohorts of human autopsy cases (in total n = 271) were neuropathologically and biochemically examined for the topographical distribution of Aß pathology (plaques and CAA), its quantity and its composition. These parameters were compared with neurofibrillary tangle (NFT) and neuritic plaque pathology, the degree of dementia and the results from [18F]flutemetamol amyloid PET imaging in cohort 3. All three aspects of Aß pathology correlated with one another, the estimation of Aß pathology by [18F]flutemetamol PET, AD-related NFT pathology, neuritic plaques, and with the degree of dementia. These results show that one aspect of Aß pathology can be used to predict the other two, and correlates well with the development of dementia, advancing NFT and neuritic plaque pathology. Moreover, amyloid PET estimates all three aspects of Aß pathology in-vivo. Accordingly, amyloid PET-based estimates for staging of amyloid pathology indicate the progression status of amyloid pathology in general and, in doing so, also of AD pathology. Only 7.75% of our cases deviated from this general association.

FGFR1 Expression and Role in Migration in Low and High Grade Pediatric Gliomas.

The heterogeneous and invasive nature of pediatric gliomas poses significant treatment challenges, highlighting the importance of identifying novel chemotherapeutic targets. Recently, recurrent Fibroblast growth factor receptor 1 (FGFR1) mutations in pediatric gliomas have been reported. Here, we explored the clinical relevance of FGFR1 expression, cell migration in low and high grade pediatric gliomas and the role of FGFR1 in cell migration/invasion as a potential chemotherapeutic target. A high density tissue microarray (TMA) was used to investigate associations between FGFR1 and activated phosphorylated FGFR1 (pFGFR1) expression and various clinicopathologic parameters. Expression of FGFR1 and pFGFR1 were measured by immunofluorescence and by immunohistochemistry (IHC) in 3D spheroids in five rare patient-derived pediatric low-grade glioma (pLGG) and two established high-grade glioma (pHGG) cell lines. Two-dimensional (2D) and three-dimensional (3D) migration assays were performed for migration and inhibitor studies with three FGFR1 inhibitors. High FGFR1 expression was associated with age, malignancy, tumor location and tumor grade among astrocytomas. Membranous pFGFR1 was associated with malignancy and tumor grade. All glioma cell lines exhibited varying levels of FGFR1 and pFGFR1 expression and migratory phenotypes. There were significant anti-migratory effects on the pHGG cell lines with inhibitor treatment and anti-migratory or pro-migratory responses to FGFR1 inhibition in the pLGGs. Our findings support further research to target FGFR1 signaling in pediatric gliomas.

Clinicopathological case: rapid cognitive decline and myoclonus associated with fever, arthropathy and scleritis.

A 65-year-old man presented with transient neurological symptoms, followed by rapid cognitive decline, myoclonus and fevers. He had evidence of scleritis and an arthropathy. This paper reports the clinicopathological conference discussed at the Association of British Neurologists Annual Meeting 2017.

Estimation of amyloid distribution by [18F]flutemetamol PET predicts the neuropathological phase of amyloid ß-protein deposition.

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.

Primary orbital melanoma: a case series and literature review.

Primary orbital melanoma (POM) is a very rare condition. We report further four cases and review all previously reported cases. We present a multicentre retrospective review of patients with POM. Clinical, radiological, surgical, histological, and follow-up data is presented. Four patients with POM were identified between 2000 and 2013. All presented with proptosis and diplopia without reduced vision. Two had known pre-existing blue cell naevi. All were stage T1N0M0. All underwent exenteration with adjuvant radiotherapy. All are disease free at follow-up durations of 24-151 months. The present three cases and review of all cases in the literature suggest a higher likelihood of disease-free survival from primary exenteration (7/8 disease-free survival, 1/8 death from metastatic disease) than wide local excision (7/16 disease-free survival, 9 recurrence or metastasis of whom 4 died). Adjuvant radiotherapy may additionally improve outcomes.

How to analyse the spatiotemporal tumour samples needed to investigate cancer evolution: A case study using paired primary and recurrent glioblastoma.

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.