Brain Tumor Classification by Methylation Profile

Article Oncology

Medulloblastoma in adults: evaluation of the Dutch society for neuro-oncology treatment protocol

L. Bleeker et al.

Summary: This study evaluated the toxicity and efficacy of the Dutch treatment protocol for adult medulloblastoma patients. The results showed that combined chemo-radiotherapy can improve the survival of adult medulloblastoma patients.

JOURNAL OF NEURO-ONCOLOGY (2023)

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Article Clinical Neurology

MYCN amplification in spinal ependymoma: A five-year retrospective study

Shilpa Rao et al.

Summary: Spinal ependymoma with MYCN amplification is a newly recognized type of spinal ependymoma associated with poor prognosis. These tumors tend to disseminate along the spinal cord and behave aggressively with worse overall and progression-free survival compared to other types of ependymoma. This study describes the clinical and histopathological features of spinal ependymomas, particularly those with MYCN amplification, in a single institution cohort.

NEUROPATHOLOGY (2023)

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Review Oncology

Early diagnosis of ovarian cancer based on methylation profiles in peripheral blood cell-free DNA: a systematic review

Simone Karlsson Terp et al.

Summary: Liquid biopsy using circulating tumor DNA (ctDNA) shows promise as a minimally invasive approach for early diagnosis of ovarian cancer. DNA methylation biomarkers detected in ctDNA have the potential to distinguish ovarian cancer patients from those with benign conditions or healthy individuals.

CLINICAL EPIGENETICS (2023)

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Editorial Material Pharmacology & Pharmacy

Editorial: Epigenetic drugs and therapeutic resistance for epithelial malignancies

Fangfang Tao et al.

FRONTIERS IN PHARMACOLOGY (2023)

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Review Oncology

2021 updates to the World Health Organization classification of adult-type and pediatric-type diffuse gliomas: a clinical practice review

Diana L. Thomas

Summary: In 2021, the World Health Organization (WHO) made significant changes to the classification of tumors of the central nervous system (CNS), incorporating molecular diagnostics, new tumor types, and grading schemes. The new classification aims to improve diagnostic accuracy and provide better prognostic information and targeted therapies for CNS tumors. Diffuse gliomas are now categorized into pediatric-type and adult-type, highlighting the different molecular drivers and prognostic associations. The classification also introduces new pediatric-type low-grade and high-grade gliomas with distinct clinical and genetic features. This review summarizes the updates in the 2021 CNS WHO classification regarding diffuse gliomas, focusing on histopathology and molecular findings.

CHINESE CLINICAL ONCOLOGY (2023)

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Review Pathology

DNA Methylation Profiling: An Emerging Paradigm for Cancer Diagnosis

Antonios Papanicolau-Sengos et al.

Summary: Histomorphology and DNA methylation profiling are both important diagnostic methods in cancer pathology. While histomorphology is already well-established, DNA methylation profiling serves as an adjunct tool to improve the accuracy of pathological diagnosis. Besides identifying new entities and consolidating morphologically disparate cancers, DNA methylation profiling holds great promise for non-invasive cancer detection and classification.

ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE (2022)

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Article Oncology

Molecular subtyping of ependymoma and prognostic impact of Ki-67

Ka Young Lim et al.

Summary: Ependymomas (EPNs) display diverse characteristics in terms of immunophenotypes, genetics, and clinical behavior depending on their anatomical locations. Ki-67 index serves as a key factor in grading EPNs, while gains of chromosome 1q and CDKN2A/2B deletions are associated with poor prognoses.

BRAIN TUMOR PATHOLOGY (2022)

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Review Oncology

Emerging glioneuronal and neuronal tumors: case-based review

So Dug Lim et al.

Summary: This article provides a thorough analysis of three rare central nervous system tumors, describing their characteristics and diagnostic methods.

BRAIN TUMOR PATHOLOGY (2022)

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Letter Clinical Neurology

ZFTA-YAP1 fusion-positive ependymoma can occur in the spinal cord: Letter to the editor

Ka Young Lim et al.

BRAIN PATHOLOGY (2022)

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Review Biochemistry & Molecular Biology

Histone Modifications and Non-Coding RNAs: Mutual Epigenetic Regulation and Role in Pathogenesis

Irina Bure et al.

Summary: In recent years, scientists have increasingly suggested and confirmed that epigenetic regulators are closely linked and form a comprehensive network of regulatory pathways and feedback loops. This is particularly important for a better understanding of the development and progression of various diseases.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Oncology

Impact of the methylation classifier and ancillary methods on CNS tumor diagnostics

Zhichao Wu et al.

Summary: This study evaluates the use of methylation profiling and additional methods in diagnosing challenging CNS tumors. It finds that methylation profiling can accurately classify cases with high-confidence scores, and other methods can help resolve diagnostic uncertainty in cases with low-confidence scores. Additionally, tumor purity is found to be significantly associated with classifier scores.

NEURO-ONCOLOGY (2022)

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Article Clinical Neurology

Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1

Calixto-Hope G. Lucas et al.

Summary: By analyzing the genetic and epigenetic features of gliomas in NF1 patients, two molecular subgroups were identified. The first subgroup occurs in childhood, has a slower clinical course, and is associated with NF1 inactivation. The second subgroup occurs in adulthood, has a more aggressive clinical course, and harbors additional oncogenic alterations. Treatment with small molecule MEK inhibitors showed effectiveness in some patients.

ACTA NEUROPATHOLOGICA (2022)

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Article Oncology

Sarcoma classification by DNA methylation profiling in clinical everyday life: the Charite experience

Siyer Roohani et al.

Summary: This study describes the clinical course of five sarcoma patients who underwent DNA methylation-based profiling and the impact of the sarcoma classifier on treatment decisions. The results show that the sarcoma classifier can assist in diagnosis and guide treatment decisions in certain cases.

CLINICAL EPIGENETICS (2022)

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Article Pathology

Primary adult sellar SMARCB1/INI1-deficient tumor represents a subtype of atypical teratoid/rhabdoid tumor

Zejun Duan et al.

Summary: Loss of function in SMARCB1/INI1 has been observed in a group of malignancies known as SMARCB1/INI1-deficient neoplasms. In this study, we collected eight rare cases of primary adult sellar SMARCB1/INI1-deficient tumors and found that they resemble a subtype of ATRT with similar epigenetic characteristics. Our findings highlight the importance of utilizing DNA methylation profiling for the differential diagnosis of epithelioid sarcoma and (sellar) rhabdoid tumor.

MODERN PATHOLOGY (2022)

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Article Oncology

Non-invasive diagnosis and surveillance of bladder cancer with driver and passenger DNA methylation in a prospective cohort study

Yu Xiao et al.

Summary: This study found that genome-wide DNAm profile can accurately differentiate between low-grade and high-grade tumors, outperforming genomic mutations or RNA expression profiles. Targeted sequencing can accurately classify non-muscle-invasive bladder cancer tissues from muscle-invasive bladder cancer, and can detect tumors in urine.

CLINICAL AND TRANSLATIONAL MEDICINE (2022)

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Article Oncology

Machine Learning-Based Genome-Wide Salivary DNA Methylation Analysis for Identification of Noninvasive Biomarkers in Oral Cancer Diagnosis

John Adeoye et al.

Summary: This study successfully utilized machine learning techniques to select optimal methylome biomarkers for oral cancer diagnoses. By applying genome-wide methylation analysis to saliva samples, ML-assisted platforms can be useful in stratifying oral squamous cell carcinoma (OSCC) during disease screening and monitoring.

CANCERS (2022)

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Review Cell Biology

The DNA Methylation in Neurological Diseases

Samareh Younesian et al.

Summary: DNA methylation plays a critical role in the development and functioning of the human brain, and is strongly associated with clinical outcomes in neurological diseases, making it a potential novel clinical marker.

CELLS (2022)

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Article Clinical Neurology

Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases

Dorthe Holdhof et al.

Summary: ATRTs are aggressive childhood malignancies of the central nervous system caused by inactivating mutations in SMARCB1 or SMARCA4 genes. SMARCB1 mutated ATRTs can be divided into three molecular subgroups, while ATRT-SMARCA4 represent a distinct molecular subgroup. The distinction is supported by DNA methylation and RNA sequencing analyses.

ACTA NEUROPATHOLOGICA (2021)

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Article Oncology

DNA methylation profiling as a model for discovery and precision diagnostics in neuro-oncology

Drew Pratt et al.

Summary: In recent years, there has been a shift towards more objective and biologically-driven methods for central nervous system (CNS) tumor classification, with the integration of molecular diagnostic criteria. The use of DNA methylation profiling has significantly improved diagnostic precision, reliability, and aided in discovering new tumor types.

NEURO-ONCOLOGY (2021)

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Article Oncology

Clinical Outcomes and Patient-Matched Molecular Composition of Relapsed Medulloblastoma

Rahul Kumar et al.

Summary: The study investigated clinical outcomes of relapsed medulloblastoma and compared molecular features between patient-matched diagnostic and relapsed tumors. Results showed variations in molecular subgroup performance and survival status at relapse.

JOURNAL OF CLINICAL ONCOLOGY (2021)

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Article Oncology

Ultra high-risk PFA ependymoma is characterized by loss of chromosome 6q

Lorena Baroni et al.

Summary: Through genome-wide methylation arrays analysis, a high-risk subgroup with 6q loss has been identified in PF-EPN-A, which can be reliably ascertained in routine clinical use. 6q loss remains the most significant independent predictor of survival in PF-EPN-A after treatment, but not in PF-EPN-B. Distant relapses are more common in 1q gain regardless of 6q loss.

NEURO-ONCOLOGY (2021)

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Article Cell Biology

Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas

Pooja Panwalkar et al.

Summary: Childhood posterior fossa group A ependymomas (PFAs) have limited treatment options and poor prognoses compared to group B ependymomas (PFBs). PFAs exhibit enhanced glycolysis and tricarboxylic acid (TCA) cycle metabolism, with high expression of glycolytic genes associated with a poor outcome. These tumors also show high EZHIP expression linked to a dismal prognosis and elevated activating mark histone H3 lysine 27 acetylation (H3K27ac). Repurposing the antidiabetic drug metformin has shown therapeutic efficacy in vitro and in vivo in patient-derived PFA xenografts by targeting integrated metabolic/epigenetic pathways.

SCIENCE TRANSLATIONAL MEDICINE (2021)

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Article Clinical Neurology

Neurofibromatosis type 2 predisposes to ependymomas of various localization, histology, and molecular subtype

Catena Kresbach et al.

ACTA NEUROPATHOLOGICA (2021)

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Review Oncology

An Epigenetic Perspective on Intra-Tumour Heterogeneity: Novel Insights and New Challenges from Multiple Fields

Sven Beyes et al.

Summary: Research on cancer biology in recent decades has revealed the main genetic perturbations driving tumorigenesis, but treating the disease without drug resistance and metastatic burden remains a challenge. Intra-tumour heterogeneity (ITH) hampers this achievement by increasing cancer cell fitness and plasticity. Epigenetic factors sustain ITH and contribute to cell adaptation to the tumour microenvironment. Improving understanding of the interplay between genetics, epigenetics, and tumour microenvironments is crucial in deciphering the molecular mechanisms governing tumour progression and drug resistance.

CANCERS (2021)

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Article Clinical Neurology

Subgroup and subtype-specific outcomes in adult medulloblastoma

Hallie Coltin et al.

Summary: Medulloblastoma in adults can be classified into WNT, SHH, Group 3, and Group 4 subgroups, with SHH tumors being diagnosed at an older age. The 5-year progression-free survival varies among different subtypes, but clinical variables do not show a significant association with subtype-specific PFS.

ACTA NEUROPATHOLOGICA (2021)

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Review Oncology

The 2021 WHO Classification of Tumors of the Central Nervous System: a summary

David N. Louis et al.

Summary: The fifth edition of the WHO Classification of Tumors of the Central Nervous System integrates molecular diagnostics into CNS tumor classification, introduces different approaches to tumor nomenclature and grading, and emphasizes the importance of integrated diagnoses and layered reports.

NEURO-ONCOLOGY (2021)

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Article Oncology

Spatial concordance of DNA methylation classification in diffuse glioma

Niels Verburg et al.

Summary: This study investigated intratumoral heterogeneity in diffuse gliomas using DNA methylation profiling, demonstrating the infiltrative nature of the tumors and the variability in tumor purity contributing to epigenetic spatial heterogeneity. The results suggest that DNA methylation subtypes in diffuse gliomas are relatively consistent, but some heterogeneity exists.

NEURO-ONCOLOGY (2021)

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Review Oncology

Molecular subgrouping of atypical teratoid/rhabdoid tumors-a reinvestigation and current consensus

Ben Ho et al.

NEURO-ONCOLOGY (2020)

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Article Clinical Neurology

Diffuse glioneuronal tumour with oligodendroglioma-like features and nuclear clusters (DGONC) - a molecularly defined glioneuronal CNS tumour class displaying recurrent monosomy 14

M. Y. Deng et al.

NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY (2020)

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Review Clinical Neurology

Invited Review: DNA methylation-based classification of paediatric brain tumours

E. Perez et al.

NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY (2020)

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Article Neurosciences

High levelMYCNamplification and distinct methylation signature define an aggressive subtype of spinal cord ependymoma

Mark Raffeld et al.

ACTA NEUROPATHOLOGICA COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

Reliable tumor detection by whole-genome methylation sequencing of cell-free DNA in cerebrospinal fluid of pediatric medulloblastoma

Jia Li et al.

SCIENCE ADVANCES (2020)

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Article Genetics & Heredity

Genome-Wide Analysis of Cell-Free DNA Methylation Profiling for the Early Diagnosis of Pancreatic Cancer

Shengyue Li et al.

FRONTIERS IN GENETICS (2020)

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Article Biochemical Research Methods

A transcriptome-based classifier to determine molecular subtypes in medulloblastoma

Komal S. Rathi et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

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Correction Biochemistry & Molecular Biology

A DNA Methylation-Based Panel for the Prognosis and Diagnosis of Patients With Breast Cancer and Its Mechanisms (vol 7, 118, 2020)

X. -P. Liu et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2020)

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Review Oncology

The emerging role of epigenetics in human autoimmune disorders

Roberta Mazzone et al.

CLINICAL EPIGENETICS (2019)

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Article Clinical Neurology

Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes

Tanvi Sharma et al.

ACTA NEUROPATHOLOGICA (2019)

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Review Oncology

Molecular pathology of tumors of the central nervous system

B. W. Kristensen et al.

ANNALS OF ONCOLOGY (2019)

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Article Oncology

Foxr2 promotes formation of CNS-embryonal tumors in a Trp53-deficient background

Boonmin Poh et al.

NEURO-ONCOLOGY (2019)

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Review Genetics & Heredity

Role of DNA Methylation Profile in Diagnosing Astroblastoma: A Case Report and Literature Review

Giuseppe Petruzzellis et al.

FRONTIERS IN GENETICS (2019)

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Article Oncology

Circulating Cell Free Nuclear DNA, Mitochondrial DNA and Global DNA Methylation: Potential Noninvasive Biomarkers for Breast Cancer Diagnosis

Heba A. Pasha et al.

CANCER INVESTIGATION (2019)

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Review Biochemistry & Molecular Biology

DNA methylation at the crossroads of gene and environment interactions

Pui-Pik Law et al.

DNA METHYLATION (2019)

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Article Multidisciplinary Sciences

Alterations in ALK/ROS1/NTRK/MET drive a group of infantile hemispheric gliomas

Ana S. Guerreiro Stucklin et al.

NATURE COMMUNICATIONS (2019)

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Article Neurosciences

Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities

Annekathrin Reinhardt et al.

ACTA NEUROPATHOLOGICA COMMUNICATIONS (2019)

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Article Clinical Neurology

Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas

Kristian W. Pajtler et al.

ACTA NEUROPATHOLOGICA (2018)

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Article Clinical Neurology

Anaplastic astrocytoma with piloid features, a novel molecular class of IDH wildtype glioma with recurrent MAPK pathway, CDKN2A/B and ATRX alterations

Annekathrin Reinhardt et al.

ACTA NEUROPATHOLOGICA (2018)

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Article Pathology

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists

Somak Roy et al.

JOURNAL OF MOLECULAR DIAGNOSTICS (2018)

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Article Multidisciplinary Sciences

DNA methylation-based classification of central nervous system tumours

David Capper et al.

NATURE (2018)

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Review Medicine, Research & Experimental

DNA methylation profiles in cancer diagnosis and therapeutics

Yunbao Pan et al.

CLINICAL AND EXPERIMENTAL MEDICINE (2018)

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Review Clinical Neurology

Medulloblastoma in the Molecular Era

Claudia Miranda Kuzan-Fischer et al.

JOURNAL OF KOREAN NEUROSURGICAL SOCIETY (2018)

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Article Clinical Neurology

Polymorphous low-grade neuroepithelial tumor of the young (PLNTY): an epileptogenic neoplasm with oligodendroglioma-like components, aberrant CD34 expression, and genetic alterations involving the MAP kinase pathway

Jason T. Huse et al.

ACTA NEUROPATHOLOGICA (2017)

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Article Oncology

Novel molecular subgroups for clinical classification and outcome prediction in childhood medulloblastoma: a cohort study

Edward C. Schwalbe et al.

LANCET ONCOLOGY (2017)

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Article Multidisciplinary Sciences

The whole-genome landscape of medulloblastoma subtypes

Paul A. Northcott et al.

NATURE (2017)

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Article Clinical Neurology

H3-/IDH-wild type pediatric glioblastoma is comprised of molecularly and prognostically distinct subtypes with associated oncogenic drivers

Andrey Korshunov et al.

ACTA NEUROPATHOLOGICA (2017)

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Article Biotechnology & Applied Microbiology

CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

Shuli Kang et al.

GENOME BIOLOGY (2017)

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Article Oncology

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

Pascal D. Johann et al.

CANCER CELL (2016)

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Article Biochemistry & Molecular Biology

New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

Dominik Sturm et al.

CELL (2016)

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Article Clinical Neurology

Adult IDH wild type astrocytomas biologically and clinically resolve into other tumor entities

David E. Reuss et al.

ACTA NEUROPATHOLOGICA (2015)

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Article Oncology

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

Kristian W. Pajtler et al.

CANCER CELL (2015)

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Review Pathology

Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer

Diego M. Marzese et al.

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2015)

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Article Cell Biology

DNA Methylation in Mammals

En Li et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)

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Review Biochemistry & Molecular Biology

DNA Methylation and Cancer Diagnosis

Yannick Delpu et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2013)

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Review Neurosciences

DNA Methylation and Its Basic Function

Lisa D. Moore et al.

NEUROPSYCHOPHARMACOLOGY (2013)

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Review Genetics & Heredity

Pediatric high-grade astrocytomas: a distinct neuro-oncological paradigm

Noha Gerges et al.

GENOME MEDICINE (2013)

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Review Biochemistry & Molecular Biology

The DNA methylome

Mattia Pelizzola et al.

FEBS LETTERS (2011)

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Review Genetics & Heredity

DNA methylation in cancer development, diagnosis and therapy-multiple opportunities for genotoxic agents to act as methylome disruptors or remediators

Joanna Lewandowska et al.

MUTAGENESIS (2011)

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Review Pathology

DNA methylation as a universal biomarker

Victor V. Levenson

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2010)

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Article Biochemistry & Molecular Biology

Promoter Hypermethylation-mediated Inactivation of LRRC4 in Gliomas

Zuping Zhang et al.

BMC MOLECULAR BIOLOGY (2008)

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Brain Tumor Classification by Methylation Profile

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