Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort
Abstract Detecting homozygous deletion (HD) of CDKN2A is critical in BRAF-altered gliomas, as this molecular alteration has both diagnostic and prognostic significance. It is predominantly associated with BRAF-altered high-grade gliomas and has been associated with poorer prognosis in certain BRAF-a...
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BMC
2025-08-01
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| Series: | Acta Neuropathologica Communications |
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| Online Access: | https://doi.org/10.1186/s40478-025-02089-7 |
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| author | Thibaut Wolf Damien Reita Marlène Deschuyter Chinar Salmanli Julie Buffa Erwan Pencreach Eric Guérin Eric Jeandidier Marguerite Miguet Marie-Pierre Chenard Lucas Geyer Georges Noel Julien Todeschi Guillaume Gauchotte Sophie Martin Natacha Entz-Werlé Benoît Lhermitte |
| author_facet | Thibaut Wolf Damien Reita Marlène Deschuyter Chinar Salmanli Julie Buffa Erwan Pencreach Eric Guérin Eric Jeandidier Marguerite Miguet Marie-Pierre Chenard Lucas Geyer Georges Noel Julien Todeschi Guillaume Gauchotte Sophie Martin Natacha Entz-Werlé Benoît Lhermitte |
| author_sort | Thibaut Wolf |
| collection | DOAJ |
| description | Abstract Detecting homozygous deletion (HD) of CDKN2A is critical in BRAF-altered gliomas, as this molecular alteration has both diagnostic and prognostic significance. It is predominantly associated with BRAF-altered high-grade gliomas and has been associated with poorer prognosis in certain BRAF-altered low-grade glioma tumor types. The 2021 WHO classification of central nervous system tumors therefore recommends screening for this alteration in most BRAF-altered gliomas, but it does not recommend one specific technique over another. Here, we compare the performance of several detection methods, including p16 immunohistochemistry, fluorescence in situ hybridization (FISH), droplet digital PCR, next-generation sequencing and DNA methylation profiling-derived copy-number variation (CNV) analysis, in a retrospective cohort of 25 BRAF-altered gliomas. Ten cases showed diffuse p16 immunohistochemical expression (10/25) with no associated CDKN2A HD, whereas 15 cases had complete absence of p16 expression (15/25). In the latter group, a high level of discrepancy in CDKN2A HD detection when considering FISH versus other techniques was observed, suggesting a high false-negative rate with FISH. Using an original bioinformatic pipeline leveraging genome alignment of routinely available CNV raw data, we identified among most false-negative cases (4/5) a large and undeleted region encompassing MTAP, which is targeted by most commercial CDKN2A FISH probes. This is likely due to non-specific probe hybridization. Our finding suggests that FISH probes targeting the entire 9p21 locus may have lower sensitivity than anticipated among BRAF-altered gliomas and emphasizes the critical need for appropriate probe selection. |
| format | Article |
| id | doaj-art-b6497efe0b664ca78c6067f91c8dc877 |
| institution | DOAJ |
| issn | 2051-5960 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Acta Neuropathologica Communications |
| spelling | doaj-art-b6497efe0b664ca78c6067f91c8dc8772025-08-20T03:06:27ZengBMCActa Neuropathologica Communications2051-59602025-08-011311910.1186/s40478-025-02089-7Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohortThibaut Wolf0Damien Reita1Marlène Deschuyter2Chinar Salmanli3Julie Buffa4Erwan Pencreach5Eric Guérin6Eric Jeandidier7Marguerite Miguet8Marie-Pierre Chenard9Lucas Geyer10Georges Noel11Julien Todeschi12Guillaume Gauchotte13Sophie Martin14Natacha Entz-Werlé15Benoît Lhermitte16Pathology Department, University Hospitals of StrasbourgLaboratory of Biochemistry and Molecular Biology, Department of Cancer Molecular Genetics, University Hospitals of StrasbourgLaboratory Bioimaging and Pathologies, UMR CNRS 7021, OnKO3T Team, Faculty of PharmacyLaboratory Bioimaging and Pathologies, UMR CNRS 7021, OnKO3T Team, Faculty of PharmacyLaboratory of Biochemistry and Molecular Biology, Department of Cancer Molecular Genetics, University Hospitals of StrasbourgLaboratory of Biochemistry and Molecular Biology, Department of Cancer Molecular Genetics, University Hospitals of StrasbourgLaboratory of Biochemistry and Molecular Biology, Department of Cancer Molecular Genetics, University Hospitals of StrasbourgCytogenetic Department, Hospital of MulhouseCytogenetic Department, Hospital of MulhousePathology Department, University Hospitals of StrasbourgPathology Department, University Hospitals of StrasbourgRadiotherapy Department, Institut de Cancérologie Strasbourg EuropeNeurosurgery Department, University Hospitals of StrasbourgDepartment of Biopathology, University Hospitals of NancyLaboratory Bioimaging and Pathologies, UMR CNRS 7021, OnKO3T Team, Faculty of PharmacyLaboratory Bioimaging and Pathologies, UMR CNRS 7021, OnKO3T Team, Faculty of PharmacyPathology Department, University Hospitals of StrasbourgAbstract Detecting homozygous deletion (HD) of CDKN2A is critical in BRAF-altered gliomas, as this molecular alteration has both diagnostic and prognostic significance. It is predominantly associated with BRAF-altered high-grade gliomas and has been associated with poorer prognosis in certain BRAF-altered low-grade glioma tumor types. The 2021 WHO classification of central nervous system tumors therefore recommends screening for this alteration in most BRAF-altered gliomas, but it does not recommend one specific technique over another. Here, we compare the performance of several detection methods, including p16 immunohistochemistry, fluorescence in situ hybridization (FISH), droplet digital PCR, next-generation sequencing and DNA methylation profiling-derived copy-number variation (CNV) analysis, in a retrospective cohort of 25 BRAF-altered gliomas. Ten cases showed diffuse p16 immunohistochemical expression (10/25) with no associated CDKN2A HD, whereas 15 cases had complete absence of p16 expression (15/25). In the latter group, a high level of discrepancy in CDKN2A HD detection when considering FISH versus other techniques was observed, suggesting a high false-negative rate with FISH. Using an original bioinformatic pipeline leveraging genome alignment of routinely available CNV raw data, we identified among most false-negative cases (4/5) a large and undeleted region encompassing MTAP, which is targeted by most commercial CDKN2A FISH probes. This is likely due to non-specific probe hybridization. Our finding suggests that FISH probes targeting the entire 9p21 locus may have lower sensitivity than anticipated among BRAF-altered gliomas and emphasizes the critical need for appropriate probe selection.https://doi.org/10.1186/s40478-025-02089-7p16CDKN2A homozygous deletionFISHDNA methylationBRAF-altered gliomas |
| spellingShingle | Thibaut Wolf Damien Reita Marlène Deschuyter Chinar Salmanli Julie Buffa Erwan Pencreach Eric Guérin Eric Jeandidier Marguerite Miguet Marie-Pierre Chenard Lucas Geyer Georges Noel Julien Todeschi Guillaume Gauchotte Sophie Martin Natacha Entz-Werlé Benoît Lhermitte Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort Acta Neuropathologica Communications p16 CDKN2A homozygous deletion FISH DNA methylation BRAF-altered gliomas |
| title | Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort |
| title_full | Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort |
| title_fullStr | Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort |
| title_full_unstemmed | Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort |
| title_short | Challenging CDKN2A assessment in BRAF-altered gliomas: lessons from a pleomorphic xanthoastrocytoma-enriched cohort |
| title_sort | challenging cdkn2a assessment in braf altered gliomas lessons from a pleomorphic xanthoastrocytoma enriched cohort |
| topic | p16 CDKN2A homozygous deletion FISH DNA methylation BRAF-altered gliomas |
| url | https://doi.org/10.1186/s40478-025-02089-7 |
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