A case of BRAF-mutant High-Grade Glioma with Pleomorphic and Pseudopapillary Features (HPAP) mimicking PLNTY but Exhibiting Aggressive Clinical Behavior

A case of BRAF-mutant High-Grade Glioma with Pleomorphic and Pseudopapillary Features (HPAP) mimicking PLNTY but Exhibiting Aggressive Clinical Behavior | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Case Report A case of BRAF-mutant High-Grade Glioma with Pleomorphic and Pseudopapillary Features (HPAP) mimicking PLNTY but Exhibiting Aggressive Clinical Behavior Yutaro Takayama, Mariko Yaegashi, Kaishi Satomi, Takahiro Ishiyama, and 16 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7429677/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background High-grade glioma with pleomorphic and pseudopapillary features (HPAP) is a recently recognized glioma subtype defined by DNA methylation profiling. While it exhibits overlapping histological features with various CNS tumors, such as polymorphous low-grade neuroepithelial tumor of the young (PLNTY) and pleomorphic xanthoastrocytoma, its molecular pathogenesis and clinical behavior remain incompletely understood. Case Presentation: We report a rare case of HPAP with BRAF p.V600E mutation and PLNTY-like histological features that showed rapid tumor progression during long-term follow-up. A 47-year-old woman harbored a lesion that remained asymptomatic and slow-growing for over 20 years, but later exhibited contrast enhancement and rapid expansion. Partial tumor resection was performed with hippocampal preservation based on intraoperative genetic testing and functional considerations. No regrowth of the residual hippocampal lesion was observed at 12 months postoperatively. Histologically, the tumor showed oligodendroglioma-like morphology, strong CD34 immunopositivity, consistent with PLNTY-like features, but indicated a high proliferative index. Molecular analysis revealed co-occurring BRAF p.V600E and TERT promoter ( pTERT , c.-124C > T) mutations, with a lower variant allele frequency for the pTERT mutation. This disparity, confirmed by droplet digital PCR, suggests that the BRAF p.V600E mutation was an early, clonal event, whereas the pTERT mutation likely arose later in a subclonal population. DNA methylation profiling classified the tumor as HPAP with high confidence (NCI-Bethesda score: 0.969), and uniform manifold approximation and projection showed clustering within HPAP reference cases. Conclusion This case represents a rare example of BRAF p.V600E -mutant HPAP with PLNTY-like features in which a subclonal pTERT mutation likely emerged during tumor evolution, contributing to rapid tumor progression. The combination of a prolonged indolent phase followed by rapid growth, along with the intratumoral genetic heterogeneity observed, provides novel insights into the biological diversity and evolutionary dynamics of HPAP. HPAP DNA methylation classifier PLNTY BRAF TERT Figures Figure 1 Figure 2 Introduction In the 2021 World Health Organization (WHO) Classification of Tumors of the Central Nervous System (WHO CNS 5), a group of circumscribed astrocytic gliomas was formally defined. This category includes pilocytic astrocytoma, high-grade glioma with piloid features, pleomorphic xanthoastrocytoma (PXA), subependymal giant cell astrocytoma, chordoid glioma, and astroblastoma, MN1 -altered [ 6 ]. Following this framework, high-grade glioma with pleomorphic and pseudopapillary features (HPAP) has been recognized as a novel methylation-defined class of relatively circumscribed gliomas [ 8 ]. Currently, HPAP can only be reliably identified using the NCI-Bethesda CNS tumor classifier (v2) (Laboratory of Pathology, NCI, accessed via Methylscape https://methylscape.ccr.cancer.gov/ , accessed [Aug. 20th, 2025]). To date, 34 cases have been reported across three publications [ 3 , 8 , 9 ]. Histologically, HPAP demonstrates heterogenous features, overlapping with both low- and high-grade gliomas, including polymorphous low-grade neuroepithelial tumor of the young (PLNTY), astroblastoma, glioblastoma, anaplastic ependymoma, and anaplastic pleomorphic xanthoastrocytoma (PXA), as well as glioneuronal tumors [ 8 ]. Among these, PLNTY is a low-grade epilepsy-associated tumor (LEAT) that predominantly affects young adults and usually follows an indolent clinical course. Histopathologically, PLNTY is characterized by oligoastrocytoma-like morphology with diffuse strong CD34 immunoreactivity. Genomic studies have revealed mutually exclusive BRAF p.V600E mutations or FGFR gene fusions, both activating the mitogen-activated protein kinase (MAPK) signaling pathway [ 5 , 12 ]. Importantly, malignant progression of PLNTY is rarely observed [ 1 ]. Here, we report a unique case of BRAF p.V600E -mutant HPAP that exhibited PLNTY-like features. Longitudinal follow-up revealed aggressive clinical behavior, and molecular analysis identified a TERT promoter ( pTERT ) mutation, whose variant allele frequency (VAF) was lower than that of the BRAFV600E mutation. These findings suggest that malignant progression in HPAP may be driven by the acquisition of a pTERT mutation. Case presentation A 26-year-old right-handed woman (YMG316) previously underwent stereotactic radiotherapy for a right parietal arteriovenous malformation. During MRI for radiosurgical planning, an incidental abnormal signal was detected in the left hippocampus ( Fig. 1 A ) . As the lesion was asymptomatic, she was placed under regular imaging surveillance. At age 45, the patient experienced an incidental hemorrhage in the left medial temporal lobe. Serial imaging demonstrated that the hemorrhage remained stable without expansion. At age 46, she developed transient aphasia, and MRI revealed enlargement of the previously identified abnormal signal, now extending into the temporal stem. By age 47, further progression was noted, although the original hippocampal component remained unchanged. Gadolinium-enhanced MRI demonstrated irregular contrast enhancement ( Fig. 1 B and S1A ) , and volumetric analysis showed a marked acceleration in tumor growth compared with the preceding indolent phase ( Fig. 1 C ) . These findings suggested partial malignant transformation of a long-standing low-grade lesion. Remarkably, the patient remained seizure-free throughout the 21-year observation period. Preoperative imaging demonstrated tumor infiltration extending from the hippocampus into the adjacent temporal white matter. CT imaging revealed no calcification ( Fig. 1 D ) . Functional assessments showed left hemisphere language dominance on Wada testing, and the Wechsler Memory Scale-Revised (WMS-R) indicated mildly reduced verbal memory relative to visual memory. Given the patient’s strong desire to preserve memory function, particularly verbal memory, we planned hippocampal preservation contingent upon intraoperative findings. Craniotomy and tumor resection were subsequently performed ( Fig. 1 E and S1B ) . Photodynamic diagnosis using 5-aminolevulinic acid was strongly positive. Intraoperative frozen sections suggested a low-grade neoplasm. Using our original intraoperative genetic assay system, a BRAF p.V600E mutation was identified [ 4 ] ( Fig. 1 F ) . Considering the potential for targeted therapy with dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor), as well as the need to preserve hippocampal memory function, we elected to perform a partial resection sparing the hippocampal-involved portion ( Fig. 1 G and S1C ) . Postoperatively, the patient experienced no neurological complications, and follow-up neuropsychological testing demonstrated preserved memory function, including verbal memory. At 16 months postoperatively, volumetric analysis revealed no progression of the contrast-enhancing lesion despite the absence of adjuvant therapy. This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of Yokohama City University (approval number: A171130006). All mouse experiments were approved by the Institutional Animal Care and Use Committee at YCU (IRB no. FA25-007). Written informed consent for publication was obtained from the patient and her family. Histopathological and Molecular Characterization Histopathological analysis revealed a low-grade oligodendroglioma-like tumor with strong CD34 immunopositivity and no evidence of calcification. Immunohistochemistry showed positive reactivity for GFAP, Oligo2, S100, Nestin, and BRAF V600E . The Ki-67 labeling index was approximately 20%, suggesting a relatively high proliferative potential. Histological features indicative of PXA, astroblastoma, or other neuroglial tumors were absent ( Fig. 1 H ) . Molecular genetic analysis demonstrated the absence of IDH1/2 mutations and 1p/19q co-deletion (Fig. S1 D and S1E) , while identifying BRAF p.V600E and TERT c.-124C > T (C228T) mutations ( Fig. 1 I ) . Functional evaluation in our translational research platform[ 11 ], demonstrated that dabrafenib, but not trametinib, significantly suppressed cell viability in patient-derived primary tumor cultures at day 3 ( Fig. 1 J ) . Further analysis using a Comprehensive Genomic Profiling (GeneMineTOP) identified additional alterations in KEL (p.P669H, VAF 10.8%) and STIM1 (p.E434*, VAF 13.7%), in addition to BRAF p.V600E (VAF 56.9%) and TERT c.-124C > T (VAF 31.8%). The tumor mutation burden was low, calculated at 1.6 mutations per megabase. To validate the apparent disparity in VAFs between BRAF and TERT mutations, droplet digital PCR was performed for distinct tumor specimens ( Fig. 2 A ) . This confirmed BRAFV600E VAF of approximately 40–60% and a pTERT VAF of 20–30%, supporting the presence of a clonally ubiquitous BRAF mutation and a subclonal acquisition of pTERT mutation. Based on the integrated histopathological and molecular features, we initially considered this tumor to represent a malignant transformation of PLNTY; however, its clinical characteristics were atypical for this tumor type. DNA methylation profiling using the Heidelberg Brain Tumor Classifier (v12.8) did not yield a confident match to any established WHO-defined tumor class (Fig. S2 A) . Copy number analysis revealed multiple chromosomal losses, including chromosomes 13–15, 17–18, and 22 ( Fig. 2 B ) . MGMT promoter methylation was predicted with high confidence (estimated score: 0.94) (Fig. S2 B) . Notably, classification using the NCI-Bethesda DNA methylation classifier (v2) yielded a high-confidence match HPAP, with a calibrated score of 0.969 ( Fig. S2 C ). The uniform manifold approximation and projection (UMAP) confirmed the present case clusters within the HPAP group (Fig. 2 C). To validate these findings, we performed t-distributed stochastic neighbor embedding (t-SNE) analysis incorporating 2801 reference samples [ 2 ] and 23 HPAP cases [GSE195567]. The present case was clustered within the HPAP reference group (Fig. S2 D) . Finally, to assess xenograft forming-potential, we attempted to establish orthotopic patient-derived xenograft models. Whereas YMG89 ( BRAF p.V600E -mutant high-grade glioma) readily formed stable xenografts [ 10 ], YMG316-implanted mice failed to develop tumors. Discussion Pratt et al. first proposed the descriptive yet representative term “HPAP” for a distinct DNA methylation class encompassing 31 cases identified from approximately 14,000 CNS tumor samples through unsupervised clustering via the NCI-Bethesda classifier. This methylation class is closely related to, but distinct from PXA and PLNTY [ 8 ]. In the present case, t-SNE analysis using the Heidelberg Brain Tumor Classifier incorporating with 23 HPAP cases revealed that the HPAP cluster, including the present case, was located near PXA cases, while phenotypic features of the tumor aligned more closely with PLNTY. These features included the presence of a BRAFV600E mutation, oligodendroglioma-like cellular morphology, strong CD34 immunopositivity, and the absence of IDH1/2 mutation and 1p/19q co-deletions. However, the tumor exhibited atypical biological behavior not characteristic of classic PLNTY: a high Ki-67 labeling index (20%), lack of calcification, emergence of contrast enhancement, and rapid progression on serial imaging. These features are inconsistent with the typical indolent nature of PLNTY [ 3 ], suggesting that the tumor may harbor biological characteristics distinct from conventional PLNTY. Furthermore, the absence of epilepsy throughout the long-term clinical course, unusual for classic PLNTY, adds to the evidence that this tumor may arise from a different cell of origin. Taken together, these histological, molecular, and clinical findings raise the possibility that this case represents a distinct tumor entity, recently recognized under the designation HPAP, rather than conventional PLNTY. To further characterize the genetic features of HPAP, we reviewed 35 cases, including the present case ( Supplementary Tables 1 ). The most frequent mutation was TP53 (15/27, 55.6%), followed by RB1 (7/27, 25.9%) and NF1 (6/24, 25.0%). The BRAF p.V600E E mutation was detected in 3/29 (10.3%) cases. Among the 35 HPAP cases, PLNTY-like morphology was observed in 3 cases (8.6%), which was less common than glioblastoma-like (8/35, 22.9%) or astroblastoma-like features (6/35, 17.1%). Notably, PLNTY-like pathological features were seen in two NF1 -mutant cases and one BRAF p.V600E-mutant case. We and others have shown that CIC , a downstream effector of the MAPK pathway, is linked to oligodendroglioma-like morphology [ 7 , 13 ]. By analogy with PLNTY [ 12 ], MAPK-pathway alterations may underlie the development of oligodendroglioma-like morphologies in HPAP, a hypothesis that warrants further investigation. Importantly, the present tumor harbored a pTERT mutation, although its VAF was lower than that of BRAFV600E . This finding suggests that the BRAF -mutant tumor population may have contained a pTERT -mutant subclone. Clinically, the tumor exhibited a prolonged indolent phase, followed by rapid growth outside the hippocampus. The co-occurrence of BRAF p.V600E and pTERT mutations may synergistically enhance tumor aggressiveness via MAPK-pathway activation and telomerase regulation, likely contributing to the abrupt tumor progression observed in this case. Nevertheless, unlike BRAF p.V600E mutant high-grade glioma, including epithelioid glioblastoma, the prognosis in BRAF -mutant HPAP may be relatively favorable. These features paralleled the tumor’s capacity for xenograft formation [ 10 ]. Interestingly, after resection of the progressed pTERT -mutant tumor, the residual hippocampal lesion has remained stable for 12 months, further supporting the presence of intra-tumoral genomic heterogeneity. Moreover, primary cultured cell exhibited sensitivity to BRAF inhibition, highlighting the potential utility of molecular targeted therapy in BRAF -mutant HPAP. Conclusion We report a unique case of BRAF -mutant HPAP harboring a pTERT mutation that demonstrated tumor progression during long-term follow-up. Although the histopathological and genomic features partially resembled PLNTY, the clinical course reflected a distinctly more aggressive behavior. Declarations Ethic approval and consent to participate: This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of Yokohama City University (approval number: A171130006). All mouse experiments were approved by the Institutional Animal Care and Use Committee at YCU (IRB no. FA25-007). Written informed consent for publication was obtained from the patient and her family. Availability of data and material: The data that support the findings of this study are available from the corresponding author upon reasonable request. Competing interests: The authors declare no conflicts of interest in this study. Funding: This study was supported by Grant-Aid for Scientific Research (22K09210 to KT), Strategic Research Promotion of Yokohama City University Research, and Yokohama Foundation for Advancement of Medical Science (to KT). Authors’ contribution : Y.T., and M.Y. collected samples, designed and performed experiments, and wrote the manuscript. They contributed equally to this work. K.S., T.I., K.I., S.Y., and S.F. performed histological and molecular assessment. M.S. and M.S collected clinical data. O.Y., W.Y., H.O., S.S., K.S., M.O., and A.K performed experiments. M.N., and T.Y. supervised the study. K.T. led the study, collected samples, designed experiments, interpreted data, and wrote the manuscript. Acknowledgments: The authors thank Mrs. Emi Hirata and Nami Wakai (YCU) for technical assistance and Dr. Takashi Shuto (Yokohama Rosai Hospital) for providing data. References Bale TA, Sait SF, Benhamida J, Ptashkin R, Haque S, Villafania L, Sill M, Sadowska J, Akhtar RB, Liechty Bet al (2021) Malignant transformation of a polymorphous low grade neuroepithelial tumor of the young (PLNTY). Acta Neuropathol 141: 123-125 Doi 10.1007/s00401-020-02245-4 Capper D, Jones DTW, Sill M, Hovestadt V, Schrimpf D, Sturm D, Koelsche C, Sahm F, Chavez L, Reuss DEet al (2018) DNA methylation-based classification of central nervous system tumours. Nature 555: 469-474 Doi 10.1038/nature26000 Gubbiotti MA, Weinberg JS, Weathers SP, Dasgupta P, Tom MC, Aldape K, Quezado M, Abdullaev Z, Huse JT, Ballester LY (2024) An incidental finding of a high-grade glioma with pleomorphic and pseudopapillary features (HPAP) with PBRM1 mutation. J Neuropathol Exp Neurol 83: 139-141 Doi 10.1093/jnen/nlad114 Hayashi T, Tateishi K, Matsuyama S, Iwashita H, Miyake Y, Oshima A, Honma H, Sasame J, Takabayashi K, Sugino Ket al (2024) Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors. Clin Cancer Res 30: 116-126 Doi 10.1158/1078-0432.CCR-23-1660 Huse JT, Snuderl M, Jones DT, Brathwaite CD, Altman N, Lavi E, Saffery R, Sexton-Oates A, Blumcke I, Capper Det al (2017) 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. Acta Neuropathol 133: 417-429 Doi 10.1007/s00401-016-1639-9 Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, Hawkins C, Ng HK, Pfister SM, Reifenberger Get al (2021) The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol 23: 1231-1251 Doi 10.1093/neuonc/noab106 Miyake Y, Fujii K, Nakamaura T, Ikegaya N, Matsushita Y, Gobayashi Y, Iwashita H, Udaka N, Kumagai J, Murata Het al (2021) IDH-Mutant Astrocytoma With Chromosome 19q13 Deletion Manifesting as an Oligodendroglioma-Like Morphology. J Neuropathol Exp Neurol 80: 247-253 Doi 10.1093/jnen/nlaa161 Pratt D, Abdullaev Z, Papanicolau-Sengos A, Ketchum C, Panneer Selvam P, Chung HJ, Lee I, Raffeld M, Gilbert MR, Armstrong TSet al (2022) High-grade glioma with pleomorphic and pseudopapillary features (HPAP): a proposed type of circumscribed glioma in adults harboring frequent TP53 mutations and recurrent monosomy 13. Acta Neuropathol 143: 403-414 Doi 10.1007/s00401-022-02404-9 Rossi S, Giovannoni I, Patrizi S, Mafficcini A, Piccirilli E, Ricciardi GK, Megaro G, Arienzo F, Tancredi C, Agolini Eet al (2025) Expanding clinicopathologic knowledge in high-grade glioma with pleomorphic and pseudopapillary features (HPAP): a report of two cases. Acta Neuropathol Commun 13: 97 Doi 10.1186/s40478-025-02017-9 Sasame J, Ikegaya N, Kawazu M, Natsumeda M, Hayashi T, Isoda M, Satomi K, Tomiyama A, Oshima A, Honma Het al (2022) HSP90 Inhibition Overcomes Resistance to Molecular Targeted Therapy in BRAFV600E-mutant High-grade Glioma. Clin Cancer Res 28: 2425-2439 Doi 10.1158/1078-0432.CCR-21-3622 Tateishi K (2024) Translational Research Platform for Malignant Central Nervous System Tumors. Neurol Med Chir (Tokyo) 64: 323-329 Doi 10.2176/jns-nmc.2024-0078 Tateishi K, Ikegaya N, Udaka N, Sasame J, Hayashi T, Miyake Y, Okabe T, Minamimoto R, Murata H, Utsunomiya Det al (2020) BRAF V600E mutation mediates FDG-methionine uptake mismatch in polymorphous low-grade neuroepithelial tumor of the young. Acta Neuropathol Commun 8: 139 Doi 10.1186/s40478-020-01023-3 Yang R, Chen LH, Hansen LJ, Carpenter AB, Moure CJ, Liu H, Pirozzi CJ, Diplas BH, Waitkus MS, Greer PKet al (2017) Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation. Cancer Res 77: 6097-6108 Doi 10.1158/0008-5472.CAN-17-1018 Additional Declarations No competing interests reported. Supplementary Files PLNTYSupplementaryFigure.pdf SupplementaryTable080825.xlsx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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00:53:15","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7429677/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7429677/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":89995720,"identity":"594e8f31-24f3-47c4-8318-82fcc0a01582","added_by":"auto","created_at":"2025-08-27 07:58:32","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":23321923,"visible":true,"origin":"","legend":"\u003cp\u003eSee image above for figure legend\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-7429677/v1/955af2a4720e77c7e49f567b.png"},{"id":89994311,"identity":"8d24fc8f-3fea-4def-87ce-4e92a2c67f00","added_by":"auto","created_at":"2025-08-27 07:50:32","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":16377217,"visible":true,"origin":"","legend":"\u003cp\u003eSee image above for figure legend\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-7429677/v1/0530a8ba7888cf2fde2c08da.png"},{"id":92505679,"identity":"302c7ac9-5416-41f0-8ffe-0996198db6b9","added_by":"auto","created_at":"2025-09-30 12:32:41","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":68111386,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7429677/v1/dec4a052-83f6-43e1-b2e5-b6776c4e7224.pdf"},{"id":89994302,"identity":"7c80c798-6b1a-4486-8893-e1abac9dc6c2","added_by":"auto","created_at":"2025-08-27 07:50:32","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":1440205,"visible":true,"origin":"","legend":"","description":"","filename":"PLNTYSupplementaryFigure.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7429677/v1/a1a5b1b3fed09e5097953abb.pdf"},{"id":89994301,"identity":"f4075b7c-6f86-4160-a6ad-914b97cbefb5","added_by":"auto","created_at":"2025-08-27 07:50:32","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":17503,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryTable080825.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7429677/v1/f5b949f0b80ad411c90f1b02.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"A case of BRAF-mutant High-Grade Glioma with Pleomorphic and Pseudopapillary Features (HPAP) mimicking PLNTY but Exhibiting Aggressive Clinical Behavior","fulltext":[{"header":"Introduction","content":"\u003cp\u003eIn the 2021 World Health Organization (WHO) Classification of Tumors of the Central Nervous System (WHO CNS 5), a group of circumscribed astrocytic gliomas was formally defined. This category includes pilocytic astrocytoma, high-grade glioma with piloid features, pleomorphic xanthoastrocytoma (PXA), subependymal giant cell astrocytoma, chordoid glioma, and astroblastoma, \u003cem\u003eMN1\u003c/em\u003e-altered [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Following this framework, high-grade glioma with pleomorphic and pseudopapillary features (HPAP) has been recognized as a novel methylation-defined class of relatively circumscribed gliomas [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eCurrently, HPAP can only be reliably identified using the NCI-Bethesda CNS tumor classifier (v2) (Laboratory of Pathology, NCI, accessed via Methylscape \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://methylscape.ccr.cancer.gov/\u003c/span\u003e\u003cspan address=\"https://methylscape.ccr.cancer.gov/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, accessed [Aug. 20th, 2025]). To date, 34 cases have been reported across three publications [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e, \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Histologically, HPAP demonstrates heterogenous features, overlapping with both low- and high-grade gliomas, including polymorphous low-grade neuroepithelial tumor of the young (PLNTY), astroblastoma, glioblastoma, anaplastic ependymoma, and anaplastic pleomorphic xanthoastrocytoma (PXA), as well as glioneuronal tumors [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. Among these, PLNTY is a low-grade epilepsy-associated tumor (LEAT) that predominantly affects young adults and usually follows an indolent clinical course. Histopathologically, PLNTY is characterized by oligoastrocytoma-like morphology with diffuse strong CD34 immunoreactivity. Genomic studies have revealed mutually exclusive \u003cem\u003eBRAF\u003c/em\u003e p.V600E mutations or \u003cem\u003eFGFR\u003c/em\u003e gene fusions, both activating the mitogen-activated protein kinase (MAPK) signaling pathway [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Importantly, malignant progression of PLNTY is rarely observed [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eHere, we report a unique case of \u003cem\u003eBRAF\u003c/em\u003e p.V600E -mutant HPAP that exhibited PLNTY-like features. Longitudinal follow-up revealed aggressive clinical behavior, and molecular analysis identified a \u003cem\u003eTERT\u003c/em\u003e promoter (\u003cem\u003epTERT\u003c/em\u003e) mutation, whose variant allele frequency (VAF) was lower than that of the \u003cem\u003eBRAFV600E\u003c/em\u003e mutation. These findings suggest that malignant progression in HPAP may be driven by the acquisition of a \u003cem\u003epTERT\u003c/em\u003e mutation.\u003c/p\u003e"},{"header":"Case presentation","content":"\u003cp\u003eA 26-year-old right-handed woman (YMG316) previously underwent stereotactic radiotherapy for a right parietal arteriovenous malformation. During MRI for radiosurgical planning, an incidental abnormal signal was detected in the left hippocampus \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA\u003cb\u003e)\u003c/b\u003e. As the lesion was asymptomatic, she was placed under regular imaging surveillance. At age 45, the patient experienced an incidental hemorrhage in the left medial temporal lobe. Serial imaging demonstrated that the hemorrhage remained stable without expansion. At age 46, she developed transient aphasia, and MRI revealed enlargement of the previously identified abnormal signal, now extending into the temporal stem. By age 47, further progression was noted, although the original hippocampal component remained unchanged. Gadolinium-enhanced MRI demonstrated irregular contrast enhancement \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB and S1A\u003cb\u003e)\u003c/b\u003e, and volumetric analysis showed a marked acceleration in tumor growth compared with the preceding indolent phase \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eC\u003cb\u003e)\u003c/b\u003e. These findings suggested partial malignant transformation of a long-standing low-grade lesion. Remarkably, the patient remained seizure-free throughout the 21-year observation period.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003ePreoperative imaging demonstrated tumor infiltration extending from the hippocampus into the adjacent temporal white matter. CT imaging revealed no calcification \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eD\u003cb\u003e)\u003c/b\u003e. Functional assessments showed left hemisphere language dominance on Wada testing, and the Wechsler Memory Scale-Revised (WMS-R) indicated mildly reduced verbal memory relative to visual memory. Given the patient\u0026rsquo;s strong desire to preserve memory function, particularly verbal memory, we planned hippocampal preservation contingent upon intraoperative findings. Craniotomy and tumor resection were subsequently performed \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eE and S1B\u003cb\u003e)\u003c/b\u003e. Photodynamic diagnosis using 5-aminolevulinic acid was strongly positive. Intraoperative frozen sections suggested a low-grade neoplasm. Using our original intraoperative genetic assay system, a \u003cem\u003eBRAF\u003c/em\u003e p.V600E mutation was identified [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e] \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eF\u003cb\u003e)\u003c/b\u003e. Considering the potential for targeted therapy with dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor), as well as the need to preserve hippocampal memory function, we elected to perform a partial resection sparing the hippocampal-involved portion \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eG and S1C\u003cb\u003e)\u003c/b\u003e. Postoperatively, the patient experienced no neurological complications, and follow-up neuropsychological testing demonstrated preserved memory function, including verbal memory. At 16 months postoperatively, volumetric analysis revealed no progression of the contrast-enhancing lesion despite the absence of adjuvant therapy. This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of Yokohama City University (approval number: A171130006). All mouse experiments were approved by the Institutional Animal Care and Use Committee at YCU (IRB no. FA25-007). Written informed consent for publication was obtained from the patient and her family.\u003c/p\u003e\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003eHistopathological and Molecular Characterization\u003c/h2\u003e\u003cp\u003eHistopathological analysis revealed a low-grade oligodendroglioma-like tumor with strong CD34 immunopositivity and no evidence of calcification. Immunohistochemistry showed positive reactivity for GFAP, Oligo2, S100, Nestin, and BRAF\u003csup\u003eV600E\u003c/sup\u003e. The Ki-67 labeling index was approximately 20%, suggesting a relatively high proliferative potential. Histological features indicative of PXA, astroblastoma, or other neuroglial tumors were absent \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eH\u003cb\u003e)\u003c/b\u003e.\u003c/p\u003e\u003cp\u003eMolecular genetic analysis demonstrated the absence of \u003cem\u003eIDH1/2\u003c/em\u003e mutations and 1p/19q co-deletion \u003cb\u003e(Fig. \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eD and S1E)\u003c/b\u003e, while identifying \u003cem\u003eBRAF\u003c/em\u003e p.V600E and \u003cem\u003eTERT\u003c/em\u003e c.-124C\u0026thinsp;\u0026gt;\u0026thinsp;T (C228T) mutations \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eI\u003cb\u003e)\u003c/b\u003e. Functional evaluation in our translational research platform[\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e], demonstrated that dabrafenib, but not trametinib, significantly suppressed cell viability in patient-derived primary tumor cultures at day 3 \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eJ\u003cb\u003e)\u003c/b\u003e.\u003c/p\u003e\u003cp\u003eFurther analysis using a Comprehensive Genomic Profiling (GeneMineTOP) identified additional alterations in \u003cem\u003eKEL\u003c/em\u003e (p.P669H, VAF 10.8%) and \u003cem\u003eSTIM1\u003c/em\u003e (p.E434*, VAF 13.7%), in addition to \u003cem\u003eBRAF\u003c/em\u003e p.V600E (VAF 56.9%) and \u003cem\u003eTERT\u003c/em\u003e c.-124C\u0026thinsp;\u0026gt;\u0026thinsp;T (VAF 31.8%). The tumor mutation burden was low, calculated at 1.6 mutations per megabase. To validate the apparent disparity in VAFs between \u003cem\u003eBRAF\u003c/em\u003e and \u003cem\u003eTERT\u003c/em\u003e mutations, droplet digital PCR was performed for distinct tumor specimens \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA\u003cb\u003e)\u003c/b\u003e. This confirmed \u003cem\u003eBRAFV600E\u003c/em\u003e VAF of approximately 40\u0026ndash;60% and a \u003cem\u003epTERT\u003c/em\u003e VAF of 20\u0026ndash;30%, supporting the presence of a clonally ubiquitous \u003cem\u003eBRAF\u003c/em\u003e mutation and a subclonal acquisition of \u003cem\u003epTERT\u003c/em\u003e mutation. Based on the integrated histopathological and molecular features, we initially considered this tumor to represent a malignant transformation of PLNTY; however, its clinical characteristics were atypical for this tumor type.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003eDNA methylation profiling using the Heidelberg Brain Tumor Classifier (v12.8) did not yield a confident match to any established WHO-defined tumor class \u003cb\u003e(Fig. \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003eA)\u003c/b\u003e. Copy number analysis revealed multiple chromosomal losses, including chromosomes 13\u0026ndash;15, 17\u0026ndash;18, and 22 \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB\u003cb\u003e)\u003c/b\u003e. \u003cem\u003eMGMT\u003c/em\u003e promoter methylation was predicted with high confidence (estimated score: 0.94) \u003cb\u003e(Fig. \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003eB)\u003c/b\u003e. Notably, classification using the NCI-Bethesda DNA methylation classifier (v2) yielded a high-confidence match HPAP, with a calibrated score of 0.969 (\u003cb\u003eFig. \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003eC\u003c/b\u003e). The uniform manifold approximation and projection (UMAP) confirmed the present case clusters within the HPAP group (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC). To validate these findings, we performed t-distributed stochastic neighbor embedding (t-SNE) analysis incorporating 2801 reference samples [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e] and 23 HPAP cases [GSE195567]. The present case was clustered within the HPAP reference group \u003cb\u003e(Fig. \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003eD)\u003c/b\u003e. Finally, to assess xenograft forming-potential, we attempted to establish orthotopic patient-derived xenograft models. Whereas YMG89 (\u003cem\u003eBRAF\u003c/em\u003e p.V600E -mutant high-grade glioma) readily formed stable xenografts [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e], YMG316-implanted mice failed to develop tumors.\u003c/p\u003e\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003ePratt et al. first proposed the descriptive yet representative term \u0026ldquo;HPAP\u0026rdquo; for a distinct DNA methylation class encompassing 31 cases identified from approximately 14,000 CNS tumor samples through unsupervised clustering via the NCI-Bethesda classifier. This methylation class is closely related to, but distinct from PXA and PLNTY [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. In the present case, t-SNE analysis using the Heidelberg Brain Tumor Classifier incorporating with 23 HPAP cases revealed that the HPAP cluster, including the present case, was located near PXA cases, while phenotypic features of the tumor aligned more closely with PLNTY. These features included the presence of a \u003cem\u003eBRAFV600E\u003c/em\u003e mutation, oligodendroglioma-like cellular morphology, strong CD34 immunopositivity, and the absence of \u003cem\u003eIDH1/2\u003c/em\u003e mutation and 1p/19q co-deletions. However, the tumor exhibited atypical biological behavior not characteristic of classic PLNTY: a high Ki-67 labeling index (20%), lack of calcification, emergence of contrast enhancement, and rapid progression on serial imaging. These features are inconsistent with the typical indolent nature of PLNTY [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e], suggesting that the tumor may harbor biological characteristics distinct from conventional PLNTY. Furthermore, the absence of epilepsy throughout the long-term clinical course, unusual for classic PLNTY, adds to the evidence that this tumor may arise from a different cell of origin. Taken together, these histological, molecular, and clinical findings raise the possibility that this case represents a distinct tumor entity, recently recognized under the designation HPAP, rather than conventional PLNTY.\u003c/p\u003e\u003cp\u003eTo further characterize the genetic features of HPAP, we reviewed 35 cases, including the present case (\u003cb\u003eSupplementary Tables\u0026nbsp;1\u003c/b\u003e). The most frequent mutation was \u003cem\u003eTP53\u003c/em\u003e (15/27, 55.6%), followed by \u003cem\u003eRB1\u003c/em\u003e (7/27, 25.9%) and \u003cem\u003eNF1\u003c/em\u003e (6/24, 25.0%). The \u003cem\u003eBRAF\u003c/em\u003e p.V600E \u003cem\u003eE\u003c/em\u003e mutation was detected in 3/29 (10.3%) cases. Among the 35 HPAP cases, PLNTY-like morphology was observed in 3 cases (8.6%), which was less common than glioblastoma-like (8/35, 22.9%) or astroblastoma-like features (6/35, 17.1%). Notably, PLNTY-like pathological features were seen in two \u003cem\u003eNF1\u003c/em\u003e-mutant cases and one \u003cem\u003eBRAF\u003c/em\u003e p.V600E-mutant case. We and others have shown that \u003cem\u003eCIC\u003c/em\u003e, a downstream effector of the MAPK pathway, is linked to oligodendroglioma-like morphology [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. By analogy with PLNTY [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e], MAPK-pathway alterations may underlie the development of oligodendroglioma-like morphologies in HPAP, a hypothesis that warrants further investigation.\u003c/p\u003e\u003cp\u003eImportantly, the present tumor harbored a \u003cem\u003epTERT\u003c/em\u003e mutation, although its VAF was lower than that of \u003cem\u003eBRAFV600E\u003c/em\u003e. This finding suggests that the \u003cem\u003eBRAF\u003c/em\u003e-mutant tumor population may have contained a \u003cem\u003epTERT\u003c/em\u003e-mutant subclone. Clinically, the tumor exhibited a prolonged indolent phase, followed by rapid growth outside the hippocampus. The co-occurrence of \u003cem\u003eBRAF\u003c/em\u003e p.V600E and \u003cem\u003epTERT\u003c/em\u003e mutations may synergistically enhance tumor aggressiveness via MAPK-pathway activation and telomerase regulation, likely contributing to the abrupt tumor progression observed in this case. Nevertheless, unlike \u003cem\u003eBRAF\u003c/em\u003e p.V600E mutant high-grade glioma, including epithelioid glioblastoma, the prognosis in \u003cem\u003eBRAF\u003c/em\u003e-mutant HPAP may be relatively favorable. These features paralleled the tumor\u0026rsquo;s capacity for xenograft formation [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Interestingly, after resection of the progressed \u003cem\u003epTERT\u003c/em\u003e-mutant tumor, the residual hippocampal lesion has remained stable for 12 months, further supporting the presence of intra-tumoral genomic heterogeneity. Moreover, primary cultured cell exhibited sensitivity to BRAF inhibition, highlighting the potential utility of molecular targeted therapy in \u003cem\u003eBRAF\u003c/em\u003e-mutant HPAP.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eWe report a unique case of \u003cem\u003eBRAF\u003c/em\u003e-mutant HPAP harboring a \u003cem\u003epTERT\u003c/em\u003e mutation that demonstrated tumor progression during long-term follow-up. Although the histopathological and genomic features partially resembled PLNTY, the clinical course reflected a distinctly more aggressive behavior.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthic approval and consent to participate:\u0026nbsp;\u003c/strong\u003eThis study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of Yokohama City University (approval number: A171130006).\u0026nbsp;All mouse experiments were approved by the Institutional Animal Care and Use Committee at YCU (IRB no. FA25-007).\u0026nbsp;Written informed consent for publication was obtained from the patient and her family.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and material:\u003c/strong\u003e The data that support the findings of this study are available from the corresponding author upon reasonable request.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests:\u003c/strong\u003e The authors declare no conflicts of interest in this study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eFunding:\u003c/strong\u003e This study was supported by Grant-Aid for Scientific Research (22K09210 to KT), Strategic Research Promotion of Yokohama City University Research, and Yokohama Foundation for Advancement of Medical Science (to KT).\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eAuthors\u0026rsquo; contribution\u003c/strong\u003e: Y.T., and M.Y. collected samples, designed and performed experiments, and wrote the manuscript. They contributed equally to this work. K.S., T.I., K.I., S.Y., and S.F. performed histological and molecular assessment. M.S. and M.S collected clinical data. O.Y., W.Y., H.O., S.S., K.S., M.O., and A.K performed experiments. M.N., and T.Y. supervised the study. K.T. led the study, collected samples, designed experiments, interpreted data, and wrote the manuscript. \u003cstrong\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgments:\u0026nbsp;\u003c/strong\u003eThe authors thank Mrs. Emi Hirata and Nami Wakai (YCU) for technical assistance and Dr. Takashi Shuto (Yokohama Rosai Hospital) for providing data.\u0026nbsp;\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eBale TA, Sait SF, Benhamida J, Ptashkin R, Haque S, Villafania L, Sill M, Sadowska J, Akhtar RB, Liechty Bet al (2021) Malignant transformation of a polymorphous low grade neuroepithelial tumor of the young (PLNTY). Acta Neuropathol 141: 123-125 Doi 10.1007/s00401-020-02245-4\u003c/li\u003e\n\u003cli\u003eCapper D, Jones DTW, Sill M, Hovestadt V, Schrimpf D, Sturm D, Koelsche C, Sahm F, Chavez L, Reuss DEet al (2018) DNA methylation-based classification of central nervous system tumours. Nature 555: 469-474 Doi 10.1038/nature26000\u003c/li\u003e\n\u003cli\u003eGubbiotti MA, Weinberg JS, Weathers SP, Dasgupta P, Tom MC, Aldape K, Quezado M, Abdullaev Z, Huse JT, Ballester LY (2024) An incidental finding of a high-grade glioma with pleomorphic and pseudopapillary features (HPAP) with PBRM1 mutation. J Neuropathol Exp Neurol 83: 139-141 Doi 10.1093/jnen/nlad114\u003c/li\u003e\n\u003cli\u003eHayashi T, Tateishi K, Matsuyama S, Iwashita H, Miyake Y, Oshima A, Honma H, Sasame J, Takabayashi K, Sugino Ket al (2024) Intraoperative Integrated Diagnostic System for Malignant Central Nervous System Tumors. Clin Cancer Res 30: 116-126 Doi 10.1158/1078-0432.CCR-23-1660\u003c/li\u003e\n\u003cli\u003eHuse JT, Snuderl M, Jones DT, Brathwaite CD, Altman N, Lavi E, Saffery R, Sexton-Oates A, Blumcke I, Capper Det al (2017) 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. Acta Neuropathol 133: 417-429 Doi 10.1007/s00401-016-1639-9\u003c/li\u003e\n\u003cli\u003eLouis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, Hawkins C, Ng HK, Pfister SM, Reifenberger Get al (2021) The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol 23: 1231-1251 Doi 10.1093/neuonc/noab106\u003c/li\u003e\n\u003cli\u003eMiyake Y, Fujii K, Nakamaura T, Ikegaya N, Matsushita Y, Gobayashi Y, Iwashita H, Udaka N, Kumagai J, Murata Het al (2021) IDH-Mutant Astrocytoma With Chromosome 19q13 Deletion Manifesting as an Oligodendroglioma-Like Morphology. J Neuropathol Exp Neurol 80: 247-253 Doi 10.1093/jnen/nlaa161\u003c/li\u003e\n\u003cli\u003ePratt D, Abdullaev Z, Papanicolau-Sengos A, Ketchum C, Panneer Selvam P, Chung HJ, Lee I, Raffeld M, Gilbert MR, Armstrong TSet al (2022) High-grade glioma with pleomorphic and pseudopapillary features (HPAP): a proposed type of circumscribed glioma in adults harboring frequent TP53 mutations and recurrent monosomy 13. Acta Neuropathol 143: 403-414 Doi 10.1007/s00401-022-02404-9\u003c/li\u003e\n\u003cli\u003eRossi S, Giovannoni I, Patrizi S, Mafficcini A, Piccirilli E, Ricciardi GK, Megaro G, Arienzo F, Tancredi C, Agolini Eet al (2025) Expanding clinicopathologic knowledge in high-grade glioma with pleomorphic and pseudopapillary features (HPAP): a report of two cases. Acta Neuropathol Commun 13: 97 Doi 10.1186/s40478-025-02017-9\u003c/li\u003e\n\u003cli\u003eSasame J, Ikegaya N, Kawazu M, Natsumeda M, Hayashi T, Isoda M, Satomi K, Tomiyama A, Oshima A, Honma Het al (2022) HSP90 Inhibition Overcomes Resistance to Molecular Targeted Therapy in BRAFV600E-mutant High-grade Glioma. Clin Cancer Res 28: 2425-2439 Doi 10.1158/1078-0432.CCR-21-3622\u003c/li\u003e\n\u003cli\u003eTateishi K (2024) Translational Research Platform for Malignant Central Nervous System Tumors. Neurol Med Chir (Tokyo) 64: 323-329 Doi 10.2176/jns-nmc.2024-0078\u003c/li\u003e\n\u003cli\u003eTateishi K, Ikegaya N, Udaka N, Sasame J, Hayashi T, Miyake Y, Okabe T, Minamimoto R, Murata H, Utsunomiya Det al (2020) BRAF V600E mutation mediates FDG-methionine uptake mismatch in polymorphous low-grade neuroepithelial tumor of the young. Acta Neuropathol Commun 8: 139 Doi 10.1186/s40478-020-01023-3\u003c/li\u003e\n\u003cli\u003eYang R, Chen LH, Hansen LJ, Carpenter AB, Moure CJ, Liu H, Pirozzi CJ, Diplas BH, Waitkus MS, Greer PKet al (2017) Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation. Cancer Res 77: 6097-6108 Doi 10.1158/0008-5472.CAN-17-1018\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"HPAP, DNA methylation classifier, PLNTY, BRAF, TERT","lastPublishedDoi":"10.21203/rs.3.rs-7429677/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7429677/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eHigh-grade glioma with pleomorphic and pseudopapillary features (HPAP) is a recently recognized glioma subtype defined by DNA methylation profiling. While it exhibits overlapping histological features with various CNS tumors, such as polymorphous low-grade neuroepithelial tumor of the young (PLNTY) and pleomorphic xanthoastrocytoma, its molecular pathogenesis and clinical behavior remain incompletely understood.\u003c/p\u003e\u003ch2\u003eCase Presentation:\u003c/h2\u003e\u003cp\u003eWe report a rare case of HPAP with \u003cem\u003eBRAF\u003c/em\u003e p.V600E mutation and PLNTY-like histological features that showed rapid tumor progression during long-term follow-up. A 47-year-old woman harbored a lesion that remained asymptomatic and slow-growing for over 20 years, but later exhibited contrast enhancement and rapid expansion. Partial tumor resection was performed with hippocampal preservation based on intraoperative genetic testing and functional considerations. No regrowth of the residual hippocampal lesion was observed at 12 months postoperatively. Histologically, the tumor showed oligodendroglioma-like morphology, strong CD34 immunopositivity, consistent with PLNTY-like features, but indicated a high proliferative index. Molecular analysis revealed co-occurring \u003cem\u003eBRAF\u003c/em\u003e p.V600E and \u003cem\u003eTERT\u003c/em\u003e promoter (\u003cem\u003epTERT\u003c/em\u003e, c.-124C\u0026thinsp;\u0026gt;\u0026thinsp;T) mutations, with a lower variant allele frequency for the \u003cem\u003epTERT\u003c/em\u003e mutation. This disparity, confirmed by droplet digital PCR, suggests that the \u003cem\u003eBRAF\u003c/em\u003e p.V600E mutation was an early, clonal event, whereas the \u003cem\u003epTERT\u003c/em\u003e mutation likely arose later in a subclonal population. DNA methylation profiling classified the tumor as HPAP with high confidence (NCI-Bethesda score: 0.969), and uniform manifold approximation and projection showed clustering within HPAP reference cases.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e\u003cp\u003eThis case represents a rare example of \u003cem\u003eBRAF\u003c/em\u003e p.V600E -mutant HPAP with PLNTY-like features in which a subclonal \u003cem\u003epTERT\u003c/em\u003e mutation likely emerged during tumor evolution, contributing to rapid tumor progression. The combination of a prolonged indolent phase followed by rapid growth, along with the intratumoral genetic heterogeneity observed, provides novel insights into the biological diversity and evolutionary dynamics of HPAP.\u003c/p\u003e","manuscriptTitle":"A case of BRAF-mutant High-Grade Glioma with Pleomorphic and Pseudopapillary Features (HPAP) mimicking PLNTY but Exhibiting Aggressive Clinical Behavior","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-27 07:50:27","doi":"10.21203/rs.3.rs-7429677/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"66dcd018-ad13-44aa-82da-5dd9696d06fd","owner":[],"postedDate":"August 27th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-09-30T12:23:58+00:00","versionOfRecord":[],"versionCreatedAt":"2025-08-27 07:50:27","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7429677","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7429677","identity":"rs-7429677","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}