CNS5:Pleomorphic xanthoastrocytoma: Difference between revisions

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[[CNS5:Table_of_Contents|Central Nervous System Tumours (WHO Classification, 5th ed.)]]
[[CNS5:Table_of_Contents|Central Nervous System Tumours (WHO Classification, 5th ed.)]]


{{Under Construction}}
<span style="color:#0070C0">(''General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type. This is based on up-to-date knowledge from multiple resources such as PubMed and the WHO classification books. The CCGA is meant to be a supplemental resource to the WHO classification books; the CCGA captures in a continually updated wiki-stye manner the current genetics/genomics knowledge of each disease, which evolves more rapidly than books can be revised and published. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page).'' </span>
 
<span style="color:#0070C0">(''General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type. This is based on up-to-date knowledge from multiple resources such as PubMed and the WHO classification books. The CCGA is meant to be a supplemental resource to the WHO classification books; the CCGA captures in a continually updated wiki-stye manner the current genetics/genomics knowledge of each disease, which evolves more rapidly than books can be revised and published. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page). Use [https://www.genenames.org/ <u>HUGO-approved gene names and symbols</u>] (italicized when appropriate), [https://varnomen.hgvs.org/ <u>HGVS-based nomenclature for variants</u>], as well as generic names of drugs and testing platforms or assays if applicable. Please complete tables whenever possible and do not delete them (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column in a table, click nearby within the table and select the > symbol that appears. Please do not delete or alter the section headings. The use of bullet points alongside short blocks of text rather than only large paragraphs is encouraged. Additional instructions below in italicized blue text should not be included in the final page content. Please also see'' </span><u>''[[Author_Instructions]]''</u><span style="color:#0070C0"> ''and [[Frequently Asked Questions (FAQs)|<u>FAQs</u>]] as well as contact your [[Leadership|<u>Associate Editor</u>]] or [mailto:CCGA@cancergenomics.org <u>Technical Support</u>].)''</span>
==Primary Author(s)*==
==Primary Author(s)*==
Wahab A. Khan, PhD, FACMG, Dartmouth Health <span style="color:#0070C0"> </span>
Wahab A. Khan, PhD, FACMG, Dartmouth Health <span style="color:#0070C0"> </span>
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==Related Terminology==
== Related Terminology - Pleomorphic xanthoastrocytoma (PXA) ==


{| class="wikitable"
{| class="wikitable"
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==Gene Rearrangements==
==Gene Rearrangements ==
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Details on clinical significance such as prognosis and other important information can be provided in the notes section. Please include references throughout the table. Do not delete the table.'')</span>
 
{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
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|Telomerase activation (mainly in anaplastic PXA)
|Telomerase activation (mainly in anaplastic PXA)
|TERT promoter mutations/amplifications
|TERT promoter mutations/amplifications
|'''Recurrent (15–47% in anaplastic) PMID: 30051528'''
|Recurrent (15–47% in anaplastic)<ref>{{Cite journal|last=Phillips|first=Joanna J.|last2=Gong|first2=Henry|last3=Chen|first3=Katharine|last4=Joseph|first4=Nancy M.|last5=van Ziffle|first5=Jessica|last6=Bastian|first6=Boris C.|last7=Grenert|first7=James P.|last8=Kline|first8=Cassie N.|last9=Mueller|first9=Sabine|date=2019-01|title=The genetic landscape of anaplastic pleomorphic xanthoastrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/30051528|journal=Brain Pathology (Zurich, Switzerland)|volume=29|issue=1|pages=85–96|doi=10.1111/bpa.12639|issn=1750-3639|pmc=7837273|pmid=30051528}}</ref>
|P (poor; recurrence risk)
|P (poor; recurrence risk)
|Yes (WHO, NCCN-context specefic)
|Yes (WHO, NCCN-context specefic)
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|MAPK pathway activation via kinase fusions
|MAPK pathway activation via kinase fusions
|Variable; not associated with classic chr alterations
|Variable; not associated with classic chr alterations
|'''Rare (<5%) PMID: 37870438'''
|Rare (<5%)<ref>{{Cite journal|last=Galbraith|first=Kristyn|last2=Serrano|first2=Jonathan|last3=Shen|first3=Guomiao|last4=Tran|first4=Ivy|last5=Slocum|first5=Cheyanne C.|last6=Ketchum|first6=Courtney|last7=Abdullaev|first7=Zied|last8=Turakulov|first8=Rust|last9=Bale|first9=Tejus|date=2024-01-02|title=Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors|url=https://pubmed.ncbi.nlm.nih.gov/37870438|journal=Molecular cancer research: MCR|volume=22|issue=1|pages=21–28|doi=10.1158/1541-7786.MCR-23-0627|issn=1557-3125|pmc=10942665|pmid=37870438}}</ref>
|D
|D
|Context-dependent ( e.g. For patients with CNS tumors who harbor NTRK fusions, TRK inhibitors such as larotrectinib or repotrectinib are considered a preferred therapy, regardless of histology, if other options are limited) NCCN CNS Cancer guidelines
|Context-dependent ( e.g. For patients with CNS tumors who harbor NTRK fusions, TRK inhibitors such as larotrectinib or repotrectinib are considered a preferred therapy, regardless of histology, if other options are limited) NCCN CNS Cancer guidelines
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==Individual Region Genomic Gain/Loss/LOH==
==Individual Region Genomic Gain/Loss/LOH==
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Includes aberrations not involving gene rearrangements. Details on clinical significance such as prognosis and other important information can be provided in the notes section. Can refer to CGC workgroup tables as linked on the homepage if applicable. Please include references throughout the table. Do not delete the table.'') </span>
 
{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
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|D, P
|D, P
|Yes (WHO CNS5, NCCN)
|Yes (WHO CNS5, NCCN)
|'''Defining PXA feature; occurs in >85% of cases (PMID: 28181325)'''
|Defining PXA feature; occurs in >85% of cases<ref name=":1" />
|-
|-
|7
|7
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|EGFR not typically amplified)
|EGFR not typically amplified)
|D
|D
|No (however, frequently mentioned in literature as a recurrent copy number change in PXA (PMID:
|No (however, frequently mentioned in literature as a recurrent copy number change in PXA<ref>{{Cite journal|last=Vaubel|first=Rachael|last2=Zschernack|first2=Valentina|last3=Tran|first3=Quynh T.|last4=Jenkins|first4=Sarah|last5=Caron|first5=Alissa|last6=Milosevic|first6=Dragana|last7=Smadbeck|first7=James|last8=Vasmatzis|first8=George|last9=Kandels|first9=Daniela|date=2021-01|title=Biology and grading of pleomorphic xanthoastrocytoma-what have we learned about it?|url=https://pmc.ncbi.nlm.nih.gov/articles/PMC8018001/|journal=Brain Pathology (Zurich, Switzerland)|volume=31|issue=1|pages=20–32|doi=10.1111/bpa.12874|issn=1750-3639|pmc=8018001|pmid=32619305}}</ref>
|Trisomy, supports diagnosis; also seen in other gliomas
|Trisomy, supports diagnosis; also seen in other gliomas
|-
|-
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|P
|P
|No
|No
|Seen in a subset, less common ((PMID: 28181325)
|Seen in a subset, less common
|-
|-
|LOH
|LOH
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==Characteristic Chromosomal or Other Global Mutational Patterns==
==Characteristic Chromosomal or Other Global Mutational Patterns==
Put your text here and fill in the table <span style="color:#0070C0">(I''nstructions: Included in this category are alterations such as hyperdiploid; gain of odd number chromosomes including typically chromosome 1, 3, 5, 7, 11, and 17; co-deletion of 1p and 19q; complex karyotypes without characteristic genetic findings; chromothripsis; microsatellite instability; homologous recombination deficiency; mutational signature pattern; etc. Details on clinical significance such as prognosis and other important information can be provided in the notes section. Please include references throughout the table. Do not delete the table.'')</span>
 
{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
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!Clinical Relevance Details/Other Notes
!Clinical Relevance Details/Other Notes
|-
|-
|<span class="blue-text">EXAMPLE:</span>
|Common chromosome gains: +7, +5, +2, +12, +20, +21, +15
Co-deletion of 1p and 18q
|Variable; chromosomal hyperdiploidy
|<span class="blue-text">EXAMPLE:</span> See chromosomal rearrangements table as this pattern is due to an unbalanced derivative translocation associated with oligodendroglioma (add reference).
|Recurrent (17-20%)
|<span class="blue-text">EXAMPLE:</span> Common (Oligodendroglioma)
|P
|<span class="blue-text">EXAMPLE:</span> D, P
|No
|
|Whole chromosome gains common; gains of +12 and +21 more common in BRAF V600E tumors; may indicate genomic instability<ref name=":1">Vaubel RA, Caron AA, Yamada S, Decker PA, Eckel Passow JE, Rodriguez FJ, Nageswara Rao AA, Lachance D, Parney I, Jenkins R, Giannini C. Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation. Brain Pathol. 2018 Mar;28(2):172-182. doi: 10.1111/bpa.12495. Epub 2017 Apr 2. PMID: 28181325; PMCID: PMC5807227.</ref>
|
|-
|-
|<span class="blue-text">EXAMPLE:</span>
|Whole chromosome loss or cnLOH most commonly involved chromosomes 22, 14, 13, and 10
Microsatellite instability - hypermutated
|Variable gene losses
|
|Recurrent
|<span class="blue-text">EXAMPLE:</span> Common (Endometrial carcinoma)
|P
|<span class="blue-text">EXAMPLE:</span> P, T
|No
|
|Seen in subset; trend toward anaplastic cases<ref name=":1" />
|
|-
|Complex karyotype with multiple CNVs
|Chromosomal instability (CIN)
|Common
|P
|No
|Includes polyploidy, subclones, mosaicism; complexity increases at recurrence/progression<ref name=":1" />
|-
|-
|
|Pleomorphic xanthoastrocytoma (PXA) not identified as a high‑TMB or focal amplifications. No MSI‑driven marker in PXA. Global mutation pattern in PXA dominated by MAPK activation (BRAF or kinase fusions) plus CDKN2A/B loss
|
|CDKN2A/B loss and loss of p16/p14ARF tumor suppressors; cell cycle dysregulation
|
|Common
|
|P,D
|
|Yes
|
|CDKN2A/B loss defining feature of PXA; not associated with grade or BRAF status; central to PXA biology
|}
|}
==Gene Mutations (SNV/INDEL)==
==Gene Mutations (SNV/INDEL)==
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: This table is not meant to be an exhaustive list; please include only genes/alterations that are recurrent or common as well either disease defining and/or clinically significant. If a gene has multiple mechanisms depending on the type or site of the alteration, add multiple entries in the table. For clinical significance, denote associations with FDA-approved therapy (not an extensive list of applicable drugs) and NCCN or other national guidelines if applicable; Can also refer to CGC workgroup tables as linked on the homepage if applicable as well as any high impact papers or reviews of gene mutations in this entity. Details on clinical significance such as prognosis and other important information such as concomitant and mutually exclusive mutations can be provided in the notes section. Please include references throughout the table. Do not delete the table.'') </span>
<span style="color:#0070C0">''This table is not meant to be an exhaustive list''</span>
{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
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|D, P, T
|D, P, T
|Yes (WHO CNS5, NCCN)  
|Yes (WHO CNS5, NCCN)  
|Specific for PXA, actionable with BRAF/MEK inhibitors; rarely found in diffuse astrocytomas. Favorable prognostic marker (PMID: 35545827).
|Specific for PXA, actionable with BRAF/MEK inhibitors; rarely found in diffuse astrocytomas. Favorable prognostic marker<ref name=":2">{{Cite journal|last=Kim|first=Young Zoon|last2=Kim|first2=Chae-Yong|last3=Lim|first3=Do Hoon|date=2022-04|title=The Overview of Practical Guidelines for Gliomas by KSNO, NCCN, and EANO|url=https://pubmed.ncbi.nlm.nih.gov/35545827|journal=Brain Tumor Research and Treatment|volume=10|issue=2|pages=83–93|doi=10.14791/btrt.2022.0001|issn=2288-2405|pmc=9098981|pmid=35545827}}</ref>
|-
|-
|TERT
|TERT
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|P
|P
|Yes (WHO CNS5)
|Yes (WHO CNS5)
|Associated with anaplastic progression, poor recurrence-free survival, and adverse prognosis in high-grade PXA (PMID: 35545827)
|Associated with anaplastic progression, poor recurrence-free survival, and adverse prognosis in high-grade PXA<ref name=":2" />
|-
|-
|IDH1/IDH2
|IDH1/IDH2
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|D
|D
|Yes (WHO CNS5 for differential diagnosis)
|Yes (WHO CNS5 for differential diagnosis)
|Absence confirms classic PXA; if present, suggests diffuse astrocytoma not PXA (PMID: 26414224)
|Absence confirms classic PXA; if present, suggests diffuse astrocytoma not PXA<ref>Yamada S, Kipp BR, Voss JS, Giannini C, Raghunathan A. Combined "Infiltrating Astrocytoma/Pleomorphic Xanthoastrocytoma" Harboring IDH1 R132H and BRAF V600E Mutations. Am J Surg Pathol. 2016 Feb;40(2):279-84. doi: 10.1097/PAS.0000000000000515. PMID: 26414224.</ref>
|-
|-
|NTRK2, ALK
|NTRK2, ALK
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|T
|T
|Yes (FDA/NCCN for fusion-positive CNS tumors, not PXA-specific)
|Yes (FDA/NCCN for fusion-positive CNS tumors, not PXA-specific)
|'''Targetable by TRK/ALK inhibitors (larotrectinib, entrectinib); found chiefly in pediatric BRAF-wildtype PXAs.(PMID: 40568680)'''
|Targetable by TRK/ALK inhibitors (larotrectinib, entrectinib); found chiefly in pediatric BRAF-wildtype PXAs<ref>Fischer JM, Gilbert AR, Galvan EM, Singh AK, Floyd JR, Shah S. Pleomorphic xanthoastrocytoma with anaplasia and BEND5-NTRK2 fusion in a young adult with a history of cranial radiation for childhood rhabdomyosarcoma. Neurooncol Adv. 2025 Mar 8;7(1):vdaf052. doi: 10.1093/noajnl/vdaf052. PMID: 40568680; PMCID: PMC12188291.</ref>
|-
|
|
|
|
|
|
|
|}Note: A more extensive list of mutations can be found in [https://www.cbioportal.org/ <u>cBioportal</u>], [https://cancer.sanger.ac.uk/cosmic <u>COSMIC</u>], and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
|}Note: A more extensive list of mutations can be found in [https://www.cbioportal.org/ <u>cBioportal</u>], [https://cancer.sanger.ac.uk/cosmic <u>COSMIC</u>], and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
==Epigenomic Alterations==
==Epigenomic Alterations==
Put your text here
Dominant epigenomic themes in Pleomorphic xanthoastrocytoma (PXA) are: a distinct methylation class tied to MAPK activation and CDKN2A/B loss, progressive promoter hypermethylation in anaplastic transformation, frequent MGMT promoter methylation, and a relative absence of the H3/ATRX-driven epigenetic programs seen in other glioma subtypes<ref>{{Cite journal|last=Martínez|first=Ramón|last2=Carmona|first2=F. Javier|last3=Vizoso|first3=Miguel|last4=Rohde|first4=Veit|last5=Kirsch|first5=Matthias|last6=Schackert|first6=Gabriele|last7=Ropero|first7=Santiago|last8=Paulus|first8=Werner|last9=Barrantes|first9=Alonso|date=2014-03-20|title=DNA methylation alterations in grade II- and anaplastic pleomorphic xanthoastrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/24650279|journal=BMC cancer|volume=14|pages=213|doi=10.1186/1471-2407-14-213|issn=1471-2407|pmc=4000050|pmid=24650279}}</ref><ref>{{Cite journal|last=Tang|first=Karen|last2=Kurland|first2=David|last3=Vasudevaraja|first3=Varshini|last4=Serrano|first4=Jonathan|last5=Delorenzo|first5=Michael|last6=Radmanesh|first6=Alireza|last7=Thomas|first7=Cheddhi|last8=Spino|first8=Marissa|last9=Gardner|first9=Sharon|date=2020-08-01|title=Exploring DNA Methylation for Prognosis and Analyzing the Tumor Microenvironment in Pleomorphic Xanthoastrocytoma|url=https://pmc.ncbi.nlm.nih.gov/articles/PMC8453609/|journal=Journal of Neuropathology and Experimental Neurology|volume=79|issue=8|pages=880–890|doi=10.1093/jnen/nlaa051|issn=1554-6578|pmc=8453609|pmid=32594172}}</ref>.
 
==Genes and Main Pathways Involved==
==Genes and Main Pathways Involved==
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Please include references throughout the table. Do not delete the table.)''</span>
 
{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
|-
|-
|<span class="blue-text">EXAMPLE:</span> ''BRAF'' and ''MAP2K1''; Activating mutations
|''BRAF'' and ''MAP2K1''; Activating mutations
|<span class="blue-text">EXAMPLE:</span> MAPK signaling
|MAPK signaling
|<span class="blue-text">EXAMPLE:</span> Increased cell growth and proliferation
|Increased cell growth and proliferation
|-
|-
|<span class="blue-text">EXAMPLE:</span> ''CDKN2A''; Inactivating mutations
|''CDKN2A''; Inactivating mutations
|<span class="blue-text">EXAMPLE:</span> Cell cycle regulation
|Cell cycle regulation
|<span class="blue-text">EXAMPLE:</span> Unregulated cell division
|Unregulated cell division
|-
|-
|<span class="blue-text">EXAMPLE:</span> ''KMT2C'' and ''ARID1A''; Inactivating mutations
|TERT promoter mutations or amplification
|<span class="blue-text">EXAMPLE:</span> Histone modification, chromatin remodeling
|TERT – Telomere maintenance pathway
|<span class="blue-text">EXAMPLE:</span> Abnormal gene expression program
|Activate telomerase and support immortalization via the telomere maintenance pathway
|-
|
|
|
|}
|}
==Genetic Diagnostic Testing Methods==
==Genetic Diagnostic Testing Methods==
Put your text here <span style="color:#0070C0">(''Instructions: Include recommended testing type(s) to identify the clinically significant genetic alterations.'')</span>
Diagnostic workup for suspected PXA typically includes BRAF mutation testing, robust assessment of CDKN2A/B deletion (preferably via SNP-microarray or NGS/ddPCR), and DNA methylation profiling, with extended NGS/fusion testing where needed<ref>https://www.frontiersin.org/journals/molecular-neuroscience/articles/10.3389/fnmol.2024.1268038/full</ref>
==Familial Forms==
==Familial Forms==
Put your text here <span style="color:#0070C0">(''Instructions: Include associated hereditary conditions/syndromes that cause this entity or are caused by this entity.'') </span>
For most PXAs, no inherited/familial cause is identified, and they are considered sporadic tumors.  
==Additional Information==
==Additional Information==
Put your text here
PXA belongs to a specific DNA methylation class characterized by BRAF pathway activation (usually BRAF p.V600E) and near‑universal CDKN2A/B homozygous deletion, and is typically IDH1/2‑ and H3‑wildtype; methylation profiling is increasingly used to confirm this integrated molecular diagnosis and to distinguish PXA from pilocytic astrocytoma and epithelioid glioblastoma<ref>{{Cite journal|last=Dampier|first=Christopher H.|last2=Shah|first2=Niharika|last3=Galbraith|first3=Kristyn|last4=Ebrahimi|first4=Azadeh|last5=Neto|first5=Osorio Lopes Abath|last6=Abdullaev|first6=Zied|last7=Alexandrescu|first7=Sanda|last8=Andreiuolo|first8=Felipe|last9=Armstrong|first9=Terri|date=2025|title=Molecular, histologic, and clinical characterization of methylation class pleomorphic xanthoastrocytoma: An analysis of 469 tumors|url=https://pubmed.ncbi.nlm.nih.gov/40735274|journal=Neuro-Oncology Advances|volume=7|issue=1|pages=vdaf089|doi=10.1093/noajnl/vdaf089|issn=2632-2498|pmc=12305539|pmid=40735274}}</ref>.
 
==Links==
==Links==
Put a link here or anywhere appropriate in this page <span style="color:#0070C0">(''Instructions: Highlight the text to which you want to add a link in this section or elsewhere, select the "Link" icon at the top of the wiki page, and search the name of the internal page to which you want to link this text, or enter an external internet address by including the "<nowiki>http://www</nowiki>." portion.'')</span>
[https://www.cancer.gov/rare-brain-spine-tumor/tumors/pleomorphic-xanthroastrocytoma Pleomorphic Xanthoastrocytoma (PXA) and Other BRAF-Altered Tumors: Diagnosis and Treatment - NCI]
==References==
==References==
(use the "Cite" icon at the top of the page) <span style="color:#0070C0">(''Instructions: Add each reference into the text above by clicking where you want to insert the reference, selecting the “Cite” icon at the top of the wiki page, and using the “Automatic” tab option to search by PMID to select the reference to insert. If a PMID is not available, such as for a book, please use the “Cite” icon, select “Manual” and then “Basic Form”, and include the entire reference. To insert the same reference again later in the page, select the “Cite” icon and “Re-use” to find the reference; DO NOT insert the same reference twice using the “Automatic” tab as it will be treated as two separate references. The reference list in this section will be automatically generated and sorted''</span><span style="color:#0070C0">''.''</span><span style="color:#0070C0">)</span>
<references />
 
==Notes==
==Notes==
<nowiki>*</nowiki>Primary authors will typically be those that initially create and complete the content of a page.  If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the [[Leadership|''<u>Associate Editor</u>'']] or other CCGA representative.  When pages have a major update, the new author will be acknowledged at the beginning of the page, and those who contributed previously will be acknowledged below as a prior author.
Khan WA: “Pleomorphic xanthoastrocytoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated {{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}, <nowiki>https://ccga.io/index.php/CNS5:Pleomorphic xanthoastrocytoma</nowiki>.
 
Prior Author(s):
<nowiki>*</nowiki>''Citation of this Page'': “Pleomorphic xanthoastrocytoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated {{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}, <nowiki>https://ccga.io/index.php/CNS5:Pleomorphic xanthoastrocytoma</nowiki>.
[[Category:CNS5]]
[[Category:CNS5]]
[[Category:DISEASE]]
[[Category:DISEASE]]
[[Category:Diseases P]]
[[Category:Diseases P]]
<references />

Latest revision as of 19:51, 25 February 2026


Central Nervous System Tumours (WHO Classification, 5th ed.)

(General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type. This is based on up-to-date knowledge from multiple resources such as PubMed and the WHO classification books. The CCGA is meant to be a supplemental resource to the WHO classification books; the CCGA captures in a continually updated wiki-stye manner the current genetics/genomics knowledge of each disease, which evolves more rapidly than books can be revised and published. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page).

Primary Author(s)*

Wahab A. Khan, PhD, FACMG, Dartmouth Health

WHO Classification of Disease

Structure Disease
Book Central Nervous System Tumours (5th ed.)
Category Gliomas, glioneuronal tumours, and neuronal tumours
Family Gliomas, glioneuronal tumours, and neuronal tumours
Type Circumscribed astrocytic gliomas
Subtype(s) Pleomorphic xanthoastrocytoma

Related Terminology - Pleomorphic xanthoastrocytoma (PXA)

Acceptable N/A
Not Recommended Pleomorphic xanthoastrocytoma with anaplastic features; anaplastic pleomorphic xanthoastrocytoma (for CNS WHO grade 3)

Gene Rearrangements

Driver Gene Fusion(s) and Common Partner Genes Molecular Pathogenesis Typical Chromosomal Alteration(s) Prevalence -Common >20%, Recurrent 5-20% or Rare <5% (Disease) Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
BRAF BRAF-KIAA1549 (rare), RAF1 fusions, NTRK2/ALK/NTRK1 (very rare in PXA) Aberrant MAPK pathway activation (i.e BRAF p.V600E variant) N/A BRAF p.V600E: Common in PXA, Fusions: Rare D, P, T Yes (WHO 2021/2025, NCCN 2023)[1] BRAF p.V600E is diagnostic and predictive; kinase fusions targetable in rare cases[2][3] [4][5]
CDKN2A/B N/A Loss leads to cell cycle dysregulation CDKN2A/B homozygous deletion (9p21); chr7 gain; chr10/22 loss Common D, P Yes (WHO, NCCN—context specific) Co-occurrence with BRAF p.V600E supports PXA diagnosis
TERT N/A Telomerase activation (mainly in anaplastic PXA) TERT promoter mutations/amplifications Recurrent (15–47% in anaplastic)[6] P (poor; recurrence risk) Yes (WHO, NCCN-context specefic) Seen mainly in grade 3/anaplastic; adverse outcome[2]


NTRK2, ALK, RAF1 Fusions: NACC2-NTRK2, BEND5-NTRK2, PPP1CB-ALK, etc. MAPK pathway activation via kinase fusions Variable; not associated with classic chr alterations Rare (<5%)[7] D Context-dependent ( e.g. For patients with CNS tumors who harbor NTRK fusions, TRK inhibitors such as larotrectinib or repotrectinib are considered a preferred therapy, regardless of histology, if other options are limited) NCCN CNS Cancer guidelines Reported in individual cases; more common in glioneuronal/low-grade gliomas

Individual Region Genomic Gain/Loss/LOH

Chr # Gain, Loss, Amp, LOH Minimal Region Cytoband and/or Genomic Coordinates [Genome Build; Size] Relevant Gene(s) Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
9p21 Homozygous loss, LOH 9p21.3; chr9:21,900,000-22,300,000 (GRCh38; ~400Kb) CDKN2A, CDKN2B D, P Yes (WHO CNS5, NCCN) Defining PXA feature; occurs in >85% of cases[8]
7 Gain Chr7 whole arm or segmental (varies) EGFR not typically amplified) D No (however, frequently mentioned in literature as a recurrent copy number change in PXA[9] Trisomy, supports diagnosis; also seen in other gliomas
22 Loss Whole chr22 (varied cytoband, arm) NF2, others D No (not guideline-specific, recurrent in PXA) Frequently reported, may occur with other losses
8p Loss chr 8p (varied region) Varies P No Seen in a subset, less common
LOH Copy-neutral Varies (mainly 9p21) CDKN2A, CDKN2B D, P Yes (NCCN) copy-neutral LOH; supports diagnosis

Characteristic Chromosomal or Other Global Mutational Patterns

Chromosomal Pattern Molecular Pathogenesis Prevalence -

Common >20%, Recurrent 5-20% or Rare <5% (Disease)

Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
Common chromosome gains: +7, +5, +2, +12, +20, +21, +15 Variable; chromosomal hyperdiploidy Recurrent (17-20%) P No Whole chromosome gains common; gains of +12 and +21 more common in BRAF V600E tumors; may indicate genomic instability[8]
Whole chromosome loss or cnLOH most commonly involved chromosomes 22, 14, 13, and 10 Variable gene losses Recurrent P No Seen in subset; trend toward anaplastic cases[8]
Complex karyotype with multiple CNVs Chromosomal instability (CIN) Common P No Includes polyploidy, subclones, mosaicism; complexity increases at recurrence/progression[8]
Pleomorphic xanthoastrocytoma (PXA) not identified as a high‑TMB or focal amplifications. No MSI‑driven marker in PXA. Global mutation pattern in PXA dominated by MAPK activation (BRAF or kinase fusions) plus CDKN2A/B loss CDKN2A/B loss and loss of p16/p14ARF tumor suppressors; cell cycle dysregulation Common P,D Yes CDKN2A/B loss defining feature of PXA; not associated with grade or BRAF status; central to PXA biology

Gene Mutations (SNV/INDEL)

This table is not meant to be an exhaustive list

Gene Genetic Alteration Tumor Suppressor Gene, Oncogene, Other Prevalence -

Common >20%, Recurrent 5-20% or Rare <5% (Disease)

Diagnostic, Prognostic, and Therapeutic Significance - D, P, T   Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
BRAF


p.V600E missense activating mutation Oncogene Common (~60–80%) D, P, T Yes (WHO CNS5, NCCN) Specific for PXA, actionable with BRAF/MEK inhibitors; rarely found in diffuse astrocytomas. Favorable prognostic marker[10]
TERT


Promoter mutation Other Recurrent P Yes (WHO CNS5) Associated with anaplastic progression, poor recurrence-free survival, and adverse prognosis in high-grade PXA[10]
IDH1/IDH2 Missense (R132H, etc) Other Absent in classic PXA D Yes (WHO CNS5 for differential diagnosis) Absence confirms classic PXA; if present, suggests diffuse astrocytoma not PXA[11]
NTRK2, ALK Kinase gene fusions Oncogene Rare T Yes (FDA/NCCN for fusion-positive CNS tumors, not PXA-specific) Targetable by TRK/ALK inhibitors (larotrectinib, entrectinib); found chiefly in pediatric BRAF-wildtype PXAs[12]

Note: A more extensive list of mutations can be found in cBioportal, COSMIC, and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.

Epigenomic Alterations

Dominant epigenomic themes in Pleomorphic xanthoastrocytoma (PXA) are: a distinct methylation class tied to MAPK activation and CDKN2A/B loss, progressive promoter hypermethylation in anaplastic transformation, frequent MGMT promoter methylation, and a relative absence of the H3/ATRX-driven epigenetic programs seen in other glioma subtypes[13][14].

Genes and Main Pathways Involved

Gene; Genetic Alteration Pathway Pathophysiologic Outcome
BRAF and MAP2K1; Activating mutations MAPK signaling Increased cell growth and proliferation
CDKN2A; Inactivating mutations Cell cycle regulation Unregulated cell division
TERT promoter mutations or amplification TERT – Telomere maintenance pathway Activate telomerase and support immortalization via the telomere maintenance pathway

Genetic Diagnostic Testing Methods

Diagnostic workup for suspected PXA typically includes BRAF mutation testing, robust assessment of CDKN2A/B deletion (preferably via SNP-microarray or NGS/ddPCR), and DNA methylation profiling, with extended NGS/fusion testing where needed[15]

Familial Forms

For most PXAs, no inherited/familial cause is identified, and they are considered sporadic tumors.

Additional Information

PXA belongs to a specific DNA methylation class characterized by BRAF pathway activation (usually BRAF p.V600E) and near‑universal CDKN2A/B homozygous deletion, and is typically IDH1/2‑ and H3‑wildtype; methylation profiling is increasingly used to confirm this integrated molecular diagnosis and to distinguish PXA from pilocytic astrocytoma and epithelioid glioblastoma[16].

Links

Pleomorphic Xanthoastrocytoma (PXA) and Other BRAF-Altered Tumors: Diagnosis and Treatment - NCI

References

  1. ↑ d’Amati, Antonio; et al. (2024-03-13). "Pediatric CNS tumors and 2021 WHO classification: what do oncologists need from pathologists?". Frontiers in Molecular Neuroscience. 17. doi:10.3389/fnmol.2024.1268038. ISSN 1662-5099.
  2. ↑ 2.0 2.1 Phillips, Joanna J.; et al. (2019-01). "The genetic landscape of anaplastic pleomorphic xanthoastrocytoma". Brain Pathology (Zurich, Switzerland). 29 (1): 85–96. doi:10.1111/bpa.12639. ISSN 1750-3639. PMC 7837273 Check |pmc= value (help). PMID 30051528. Check date values in: |date= (help)
  3. ↑ Vaubel, Rachael A.; et al. (2018-03). "Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation". Brain Pathology (Zurich, Switzerland). 28 (2): 172–182. doi:10.1111/bpa.12495. ISSN 1750-3639. PMC 5807227. PMID 28181325. Check date values in: |date= (help)
  4. ↑ Tian, Lei; et al. (2025). "Pleomorphic xanthoastrocytoma with multiple recurrences and continuous malignant progression to bone metastasis: a case report". Frontiers in Surgery. 12: 1595199. doi:10.3389/fsurg.2025.1595199. ISSN 2296-875X. PMC 12174448 Check |pmc= value (help). PMID 40535548 Check |pmid= value (help).
  5. ↑ Di Nunno, Vincenzo; et al. (2022). "Implications of BRAF V600E mutation in gliomas: Molecular considerations, prognostic value and treatment evolution". Frontiers in Oncology. 12: 1067252. doi:10.3389/fonc.2022.1067252. ISSN 2234-943X. PMC 9846085 Check |pmc= value (help). PMID 36686797 Check |pmid= value (help).
  6. ↑ Phillips, Joanna J.; et al. (2019-01). "The genetic landscape of anaplastic pleomorphic xanthoastrocytoma". Brain Pathology (Zurich, Switzerland). 29 (1): 85–96. doi:10.1111/bpa.12639. ISSN 1750-3639. PMC 7837273 Check |pmc= value (help). PMID 30051528. Check date values in: |date= (help)
  7. ↑ Galbraith, Kristyn; et al. (2024-01-02). "Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors". Molecular cancer research: MCR. 22 (1): 21–28. doi:10.1158/1541-7786.MCR-23-0627. ISSN 1557-3125. PMC 10942665 Check |pmc= value (help). PMID 37870438 Check |pmid= value (help).
  8. ↑ 8.0 8.1 8.2 8.3 Vaubel RA, Caron AA, Yamada S, Decker PA, Eckel Passow JE, Rodriguez FJ, Nageswara Rao AA, Lachance D, Parney I, Jenkins R, Giannini C. Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation. Brain Pathol. 2018 Mar;28(2):172-182. doi: 10.1111/bpa.12495. Epub 2017 Apr 2. PMID: 28181325; PMCID: PMC5807227.
  9. ↑ Vaubel, Rachael; et al. (2021-01). "Biology and grading of pleomorphic xanthoastrocytoma-what have we learned about it?". Brain Pathology (Zurich, Switzerland). 31 (1): 20–32. doi:10.1111/bpa.12874. ISSN 1750-3639. PMC 8018001 Check |pmc= value (help). PMID 32619305 Check |pmid= value (help). Check date values in: |date= (help)
  10. ↑ 10.0 10.1 Kim, Young Zoon; et al. (2022-04). "The Overview of Practical Guidelines for Gliomas by KSNO, NCCN, and EANO". Brain Tumor Research and Treatment. 10 (2): 83–93. doi:10.14791/btrt.2022.0001. ISSN 2288-2405. PMC 9098981 Check |pmc= value (help). PMID 35545827 Check |pmid= value (help). Check date values in: |date= (help)
  11. ↑ Yamada S, Kipp BR, Voss JS, Giannini C, Raghunathan A. Combined "Infiltrating Astrocytoma/Pleomorphic Xanthoastrocytoma" Harboring IDH1 R132H and BRAF V600E Mutations. Am J Surg Pathol. 2016 Feb;40(2):279-84. doi: 10.1097/PAS.0000000000000515. PMID: 26414224.
  12. ↑ Fischer JM, Gilbert AR, Galvan EM, Singh AK, Floyd JR, Shah S. Pleomorphic xanthoastrocytoma with anaplasia and BEND5-NTRK2 fusion in a young adult with a history of cranial radiation for childhood rhabdomyosarcoma. Neurooncol Adv. 2025 Mar 8;7(1):vdaf052. doi: 10.1093/noajnl/vdaf052. PMID: 40568680; PMCID: PMC12188291.
  13. ↑ Martínez, Ramón; et al. (2014-03-20). "DNA methylation alterations in grade II- and anaplastic pleomorphic xanthoastrocytoma". BMC cancer. 14: 213. doi:10.1186/1471-2407-14-213. ISSN 1471-2407. PMC 4000050. PMID 24650279.
  14. ↑ Tang, Karen; et al. (2020-08-01). "Exploring DNA Methylation for Prognosis and Analyzing the Tumor Microenvironment in Pleomorphic Xanthoastrocytoma". Journal of Neuropathology and Experimental Neurology. 79 (8): 880–890. doi:10.1093/jnen/nlaa051. ISSN 1554-6578. PMC 8453609 Check |pmc= value (help). PMID 32594172 Check |pmid= value (help).
  15. ↑ https://www.frontiersin.org/journals/molecular-neuroscience/articles/10.3389/fnmol.2024.1268038/full
  16. ↑ Dampier, Christopher H.; et al. (2025). "Molecular, histologic, and clinical characterization of methylation class pleomorphic xanthoastrocytoma: An analysis of 469 tumors". Neuro-Oncology Advances. 7 (1): vdaf089. doi:10.1093/noajnl/vdaf089. ISSN 2632-2498. PMC 12305539 Check |pmc= value (help). PMID 40735274 Check |pmid= value (help).

Notes

Khan WA: “Pleomorphic xanthoastrocytoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated 02/25/2026, https://ccga.io/index.php/CNS5:Pleomorphic xanthoastrocytoma.

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