ArticleModern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc2020
PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells.
Article in Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 36 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Transcriptomic Subgroups in Soft Tissue Tumors Correlate with Morphologic Subtype, Genomic Features, and Outcome.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Structural landscape of H3K27me3 recognition by protein domains and their potential for inhibition.The Journal of biological chemistry · 2026Review
- A comprehensive review of ossifying fibromyxoid tumor: insights into its clinical, pathological, and molecular landscape.Journal of pathology and translational medicine · 2026Article
- Resurfacing Threats: Metastatic Ossifying Fibromyxoid Tumor Emerging After Almost Two Decades.Genes, chromosomes & cancer · 2025Article
- Aggressive Malignant Ossifying Fibromyxoid Tumor With a RareInternational journal of surgical pathology · 2025Review
- A potential conundrum in dermatopathology: molecularly confirmed superficial ossifying fibromyxoid tumors with unusual histomorphologic findings and a novel fusion.Virchows Archiv : an international journal of pathology · 2024Article
- MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.Communications biology · 2024Article
- Functional Classification of Fusion Proteins in Sarcoma.Cancers · 2024Review
- Deciphering the dual roles of PHD finger proteins from oncogenic drivers to tumor suppressors.Frontiers in cell and developmental biology · 2024Review
- Molecular pathways and therapeutic strategies in dermatofibrosarcoma protuberans (DFSP): unravelling the tumor's genetic landscape.EXCLI journal · 2024Review
- Expanding the molecular signatures of malignant ossifying fibromyxoid tumours with two novel gene fusions: PHF1::FOXR1 and PHF1::FOXR2.Histopathology · 2023Article
- Review
- Polycomb Repressive Complex 2 in Oncology.Cancer treatment and research · 2023Article
- Critical Roles of Polycomb Repressive Complexes in Transcription and Cancer.International journal of molecular sciences · 2022Review
- Down-regulated m6A reader FTO destabilizes PHF1 that triggers enhanced stemness capacity and tumor progression in lung adenocarcinoma.Cell death discovery · 2022Article
- Mechanisms of Polycomb group protein function in cancer.Cell research · 2022Review
- Absence of TFE3 Immunoexpression in a Spectrum of Cutaneous Mixed Tumors: A Retrospective Pilot Study.Dermatopathology (Basel, Switzerland) · 2022Article
- Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors.The Journal of molecular diagnostics : JMD · 2021Article
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Ossifying fibromyxoid tumor (OFMT) is a soft tissue tumor frequently displaying gene fusions, most of which affect the PHF1 gene. PHF1 encodes plant homeodomain finger protein 1, which is involved in various processes regulating gene transcription, including those orchestrated by the polycomb repressor complex 2. Here, a series of 37 OFMTs, including 18 typical, 9 atypical, and 10 malignant variants, was analyzed with regard to transcriptomic features, gene fusion and copy number status, and/or single-nucleotide variants. The effects on gene expression and chromatin accessibility of three detected fusions (EP400-PHF1, MEAF6-PHF1, and PHF1-TFE3) were further evaluated in fibroblasts. Genomic imbalances showed a progression-related pattern, with more extensive copy number changes among atypical/malignant lesions than among typical OFMTs; loss of the RB1 gene was restricted to atypical/malignant OFMTs, occurring in one-third of the cases. RNA sequencing identified fusion transcripts in >80% of the cases analyzed, including a novel CSMD1-MEAF6. The gene-expression profile of OFMT was distinct from that of other soft tissue tumors, with extensive transcriptional upregulation of genes in OFMT. These findings were largely recapitulated in gene fusion-expressing fibroblast lines, suggesting that genes involved in, e.g., Wnt signaling and/or being regulated through trimethylation of lysine 27 in histone 3 (H3K27me3) are pivotal for OFMT development. The genes showing differentially higher expression in fusion-expressing cells paralleled increased chromatin accessibility, as revealed by ATAC sequencing. Thus, the present study suggests that OFMT develops through gene fusions that have extensive epigenetic consequences.
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Registered trials
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