Publications by authors named "Pim J French"

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma).

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The standard of care for adult patients with gliomas, glioneuronal and neuronal tumors consists of combinations of surgery, radiotherapy, and chemotherapy. For many systemic cancers, targeted treatments are a major part of the standard treatment, however, the predictive significance of most of the targets for treatment in systemic cancer are less well established in central nervous system (CNS) tumors . In 2023 the EANO Guideline Committee presented evidence based recommendations for rational testing of molecular targets for targeted treatments.

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  • Accurate grading of IDH-mutant gliomas is crucial for predicting patient outcomes and selecting treatment strategies, yet histological grading remains difficult, with limited molecular markers available.
  • Researchers performed RNA-sequencing on 138 IDH-mutant astrocytomas from the CATNON trial and analyzed multi-omics data to create a Continuous Grading Coefficient (CGC), which proved to be a better survival predictor than current grading systems.
  • The study identified four distinct transcriptional clusters linked to various gene expression patterns, revealing that higher-grade IDH-mutant astrocytomas exhibit DNA-methylation signatures correlated with increased cell cycling, tumor de-differentiation, and changes in the extracellular matrix.
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Purpose: IDH-mutant glioma is classified as oligodendroglioma or astrocytoma based on 1p19q-codeletion. Whether prognostic factors are similar between these tumor types is not well understood.

Experimental Design: Retrospective cohort study.

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  • The 2016 and 2021 WHO classifications of CNS tumors have improved how we categorize IDH-mutant gliomas, leading to better treatment options and longer survival for patients.
  • Current treatment guidelines are still largely based on older data that mix different tumor types, often focusing on high-risk factors like age and residual tumor post-surgery.
  • New insights from recent studies suggest that postponing aggressive treatments like radiation and chemotherapy may be safe for many patients with lower-grade IDH-mutant gliomas, and that newer medications like vorasidenib could be beneficial before resorting to traditional therapies.
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L-2-hydroxyglutaric aciduria (L-2-HGA) is a rare neurometabolic disorder characterized by accumulation of L2-hydroxyglutarate (L-2-HG) due to mutations in the gene. L-2-HGA patients have a significantly increased lifetime risk of central nervous system (CNS) tumors. Here, we present a 16-year-old girl with L-2-HGA who developed a tumor in the right cerebral hemisphere, which was discovered after left-sided neurological deficits of the patient.

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Accurate grading of IDH-mutant gliomas defines patient prognosis and guides the treatment path. Histological grading is however difficult and, apart from CDKN2A/B homozygous deletions in IDH-mutant astrocytomas, there are no other objective molecular markers used for grading. Experimental Design: RNA-sequencing was conducted on primary IDH-mutant astrocytomas (n=138) included in the prospective CATNON trial, which was performed to assess the prognostic effect of adjuvant and concurrent temozolomide.

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  • The study analyzed the epigenetic changes in gliomas from 132 patients over time, comparing initial and recurrent tumors in both IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) types.
  • IDHwt gliomas remained stable in their epigenetic profile, while IDHmut gliomas showed a notable decrease in DNA methylation, making their profiles more similar to IDHwt tumors.
  • The research identified HOXD13 as crucial for the evolution of IDHmut tumors and found that treatment led to changes in the tumor microenvironment, like increased blood vessel formation and T-cell presence, mimicking the characteristics of IDHwt gliomas.
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  • The T2-FLAIR mismatch sign on MRI indicates a specific feature of IDH-mutant astrocytomas, showing signal loss that may relate to microcystic changes in the tumor, but not all tumors display this sign.
  • A study of patients with lower-grade IDH-mutant astrocytomas aimed to explore the prognostic significance of this sign after surgical resections and its relationship with tumor characteristics.
  • Results revealed that the presence of the T2-FLAIR mismatch is associated with Grade 2 tumors, a better overall survival rate, and expansive tumor growth, suggesting its potential as a positive prognostic marker for these patients.
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The most frequent adult-type primary CNS tumours are diffuse gliomas, but a large variety of rarer CNS tumour types exists. The classification of these tumours is increasingly based on molecular diagnostics, which is reflected in the extensive molecular foundation of the recent WHO 2021 classification of CNS tumours. Resection as extensive as is safely possible is the cornerstone of treatment in most gliomas, and is now also recommended early in the treatment of patients with radiological evidence of histologically low-grade tumours.

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  • Tumor growth models can predict how gliomas develop over time in individual patients, utilizing MRI and DTI to understand cell infiltration patterns along white matter tracts.
  • This research introduces a ranking approach to evaluate tumor growth models using average precision (AP), which simplifies the evaluation of spatial tumor patterns without needing a volume cut-off.
  • The study demonstrates that DTI-informed anisotropic diffusion models significantly enhance the prediction of recurrent tumor shapes post-surgery compared to isotropic models, with all related code and data publicly accessible.
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In the 5th edition of the WHO CNS tumor classification (CNS5, 2021), multiple molecular characteristics became essential diagnostic criteria for many additional CNS tumor types. For those tumors, an integrated, "histomolecular" diagnosis is required. A variety of approaches exists for determining the status of the underlying molecular markers.

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  • Researchers studied glioblastoma, a type of brain cancer, to improve treatments by looking at how these tumors change over time.
  • They used special tests (RNA sequencing) on tumor samples from patients to see how the cells and their environment evolve when the tumors come back after treatment.
  • The study found that instead of changing the main cancer genes, the tumors' surroundings changed a lot, which affected how patients did after their tumors came back.
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The mainstay of treatment for adult patients with gliomas, glioneuronal and neuronal tumors consists of combinations of surgery, radiotherapy, and chemotherapy. For many systemic cancers, targeted treatments are a part of the standard of care, however, the predictive significance of most of these targets in central nervous system (CNS) tumors remains less well-studied. Despite that, there is increasing use of advanced molecular diagnostics that identify potential targets, and tumor-agnostic regulatory approvals on targets also present in CNS tumors have been granted.

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  • Spatial transcriptomics is a new technique that combines RNA expression data with information about tissue context, but there's a lack of quality assessments from users.
  • In this study, the researchers analyzed data from the NanoString GeoMx Digital Spatial Profiling platform across 12 glioma samples, revealing significant variances in signal intensity that could lead to biased results.
  • They found that using quantile normalization effectively addressed data distribution issues and highlighted that NanoString DSP data has a limited dynamic range compared to bulk RNA sequencing, suggesting the need for improved normalization and analysis methods.
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Background: Gliomas with IDH1/2 mutations without 1p19q codeletion have been identified as the distinct diagnostic entity of IDH mutant astrocytoma (IDHmut astrocytoma). Homozygous deletion of Cyclin-dependent kinase 4 inhibitor A/B (CDKN2A/B) has recently been incorporated in the grading of these tumors. The question of whether histologic parameters still contribute to prognostic information on top of the molecular classification, remains unanswered.

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  • Machine learning can work well, but it often struggles to make accurate predictions on new data, which is called out-of-sample generalizability.
  • To solve this problem, researchers are using a method called Federated ML that allows computers to share information about how well they're learning without actually sharing the data itself.
  • In a big study with 71 locations around the world, scientists created a model to help detect brain tumors more accurately, showing a significant improvement compared to older methods and hoping to help with rare illnesses and data sharing in healthcare.
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  • There's a significant challenge in glioma research due to the absence of in vitro models that mimic the characteristics of glioma cells found in live tissues.
  • Researchers have developed a 3D-engineered scaffold using advanced polymerization techniques to create a more accurate cell culture system with patient-derived glioma cells.
  • This 3D model allows for improved observation of cell behavior and structure compared to traditional 2D cultures, making it a valuable tool for studying brain cancer mechanics and testing potential treatments.
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Background: Grading and classification of IDH-mutant astrocytomas has shifted from solely histology towards histology combined with molecular diagnostics. In this systematic review, we give an overview of all currently known clinically relevant molecular markers within IDH-mutant astrocytomas grade 2 to 4.

Methods: A literature search was performed in five electronic databases for English original papers on patient outcome with respect to a molecular marker as determined by DNA/RNA sequencing, micro-arrays, or DNA methylation profiling in IDH-mutant astrocytomas grade 2 to 4.

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  • * Group 4 (G4) MB, the most common subtype, is characterized by somatic mutations affecting the core binding factor alpha (CBFA) complex, including changes to genes like CBFA2T2 and OTX2.
  • * Research indicates that G4 MB cells resemble early progenitor cells in the cerebellar region but are stalled in development; targeting OTX2 may help overcome this block and allow these cells to mature normally.
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  • Dexamethasone, commonly given to glioblastoma patients, may hinder the effectiveness of checkpoint inhibitor immunotherapy by altering the tumor's immune environment.
  • A systematic review of studies revealed that dexamethasone reduces immune cell presence (like microglia and T lymphocytes), which are crucial for fighting tumors.
  • Although direct clinical evidence is limited, existing studies indicate a negative link between dexamethasone use and survival outcomes for glioblastoma patients treated with checkpoint inhibitors.
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  • IDH1/2 wildtype (IDHwt) gliomas classified as lower-grade (WHO grade 2 and 3) with certain genetic mutations exhibit similar survival rates to IDHwt glioblastoma, leading to both being categorized as glioblastoma IDHwt by WHO 2021.
  • A study analyzed epilepsy in these two groups, focusing on the number of patients developing epilepsy, the timing of onset, and the treatment approaches used for managing seizures.
  • Results indicated that while the overall incidence of epilepsy is comparable, IDHwt hLGG patients experience earlier onset and longer diagnosis delays compared to IDHwt glioblastoma patients, suggesting differing clinical pathways for these glioma subtypes.
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