ArticleActa neuropathologica communications2021
Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors.
Article in Acta neuropathologica communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 25 citations in OpenAlex.
- DNA Methylation Profiling in IDH-Mutant Gliomas: Biological Evolution, Molecular Grading and Clinical Implementation.Neuropathology and applied neurobiology · 2026Review
- Identification of a distinct epigenetic subgroup with inferior PFS in intracranial mesenchymal tumors with FET::CREB fusion.Brain pathology (Zurich, Switzerland) · 2026Article
- Comparative cross-methodological analysis of the IDH-wildtype glioblastoma tumor microenvironment.Journal of cancer research and clinical oncology · 2026Article
- Intratumoral preservation of the stem-like malignant cell proportion in glioblastoma, prognostic impact, and its radiomethylomic signatures.Neuro-oncology · 2025Article
- DNA Methylation-Based Classification of Kidney Neoplasms.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2025Article
- Molecularly defined oligodendroglioma evolving to osseous metastases.Journal of neuropathology and experimental neurology · 2025Article
- Peripheral blood-derived immune cell counts as prognostic indicators and their relationship with DNA methylation subclasses in glioblastoma patients.Brain pathology (Zurich, Switzerland) · 2025Article
- Potential use of DNA methylation in cervical swabs for early ovarian cancer diagnosis.Journal of ovarian research · 2025Article
- Longitudinal multimodal profiling of IDH-wildtype glioblastoma reveals the molecular evolution and cellular phenotypes underlying prognostically different treatment responses.Neuro-oncology · 2025Article
- A CDKN2B-Associated Immune Prognostic Model for Predicting Immune Cell Infiltration and Prognosis in Esophageal Carcinoma.Clinical and experimental gastroenterology · 2025Article
- Glioma immune microenvironment composition calculator (GIMiCC): a method of estimating the proportions of eighteen cell types from DNA methylation microarray data.Acta neuropathologica communications · 2024Article
- Microarray-Based DNA Methylation Profiling: Validation Considerations for Clinical Testing.The Journal of molecular diagnostics : JMD · 2024Article
- A prognostic neural epigenetic signature in high-grade glioma.Nature medicine · 2024Article
- Validating reference-based algorithms to determine cell-type heterogeneity in ovarian cancer DNA methylation studies.Scientific reports · 2024Article
- Temporal change of DNA methylation subclasses between matched newly diagnosed and recurrent glioblastoma.Acta neuropathologica · 2024Article
- "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade.Acta neuropathologica · 2023Article
- Host fecal DNA specific methylation signatures mark gut dysbiosis and inflammation in children affected by autism spectrum disorder.Scientific reports · 2023Article
- Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability.bioRxiv : the preprint server for biology · 2023Article
- CLOCK'ing differences in DNA methylation signatures to understand the molecular etiology of lung cancer.Translational lung cancer research · 2023Article
- Immunotherapy for Pediatric Brain and Spine Tumors: Current State and Future Directions.Pediatric neurosurgery · 2023Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of immune cell components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data in a large set of newly profiled samples (n = 741) as well as samples from external data sources (n = 3311) of methylation-defined glial and glioneuronal tumors. Using the cell-type proportion data as input, we used dimensionality reduction to visualize sample-wise patterns that emerge from the cell type proportion estimations. In IDH-wildtype glioblastomas (n = 2,072), we identified distinct tumor clusters based on immune cell proportion and demonstrated an association with oncogenic alterations such as EGFR amplification and CDKN2A/B homozygous deletion. We also investigated the immune cluster-specific distribution of four malignant cellular states (AC-like, OPC-like, MES-like and NPC-like) in the IDH-wildtype cohort. We identified two major immune-based subgroups of IDH-mutant gliomas, which largely aligned with 1p/19q co-deletion status. Non-codeleted gliomas showed distinct proportions of a key genomic aberration (CDKN2A/B loss) among immune cell-based groups. We also observed significant positive correlations between monocyte proportion and expression of PD-L1 and PD-L2 (R = 0.54 and 0.68, respectively). Overall, the findings highlight specific roles of the TME in biology and classification of CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic alterations.
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