Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas
Abstract Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylat...
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| Veröffentlicht in: | Journal of neuropathology and experimental neurology 2021-07, Vol.80 (7), p.663-673 |
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| container_title | Journal of neuropathology and experimental neurology |
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| creator | Lebrun, Laetitia Bizet, Martin Melendez, Barbara Alexiou, Barbara Absil, Lara Van Campenhout, Claude D’Haene, Nicky Rorive, Sandrine Fuks, François Decaestecker, Christine Salmon, Isabelle |
| description | Abstract
Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylation-related studies specifically addressing to IMAs have been performed yet. In the present study, we analyzed 16 IMA samples subjected to morphological and molecular analyses, including DNA methylation profiling. Among the 16 samples, only 3 cases were classified in a reference methylation class (MC) with the recommended calibrated score (≥0.9). The remaining cases were either considered “no-match” cases (calibrated score |
| doi_str_mv | 10.1093/jnen/nlab052 |
| format | Article |
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Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylation-related studies specifically addressing to IMAs have been performed yet. In the present study, we analyzed 16 IMA samples subjected to morphological and molecular analyses, including DNA methylation profiling. Among the 16 samples, only 3 cases were classified in a reference methylation class (MC) with the recommended calibrated score (≥0.9). The remaining cases were either considered “no-match” cases (calibrated score <0.3, n = 7) or were classified with low calibrated scores (ranging from 0.32 to 0.53, n = 6), including inconsistent classification. To obtain a more comprehensive tool for pathologists, we used different unsupervised analyses of DNA methylation profiles, including our data and those from the Heidelberg reference cohort. Even though our cohort included only 16 cases, hypotheses regarding IMA-specific classification were underlined; a potential specific MC of PA_SPINE was identified and high-grade IMAs, probably consisting of H3K27M wild-type IMAs, were mainly associated with ANA_PA MC. These hypotheses strongly suggest that a specific classification for IMAs has to be investigated.</description><identifier>ISSN: 0022-3069</identifier><identifier>EISSN: 1554-6578</identifier><identifier>DOI: 10.1093/jnen/nlab052</identifier><identifier>PMID: 34363673</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Adolescent ; Adult ; Aged ; Analysis ; Astrocytoma ; Astrocytoma - diagnosis ; Astrocytoma - genetics ; Brain tumors ; Child ; Classification ; Diagnosis ; DNA ; DNA Methylation ; DNA sequencing ; Female ; Health aspects ; Humans ; Hypotheses ; Male ; Methods ; Methylation ; Middle Aged ; Neurological research ; Nucleotide sequencing ; Original ; Spinal Cord Neoplasms - diagnosis ; Spinal Cord Neoplasms - genetics</subject><ispartof>Journal of neuropathology and experimental neurology, 2021-07, Vol.80 (7), p.663-673</ispartof><rights>2021 American Association of Neuropathologists, Inc. 2021</rights><rights>2021 American Association of Neuropathologists, Inc.</rights><rights>COPYRIGHT 2021 Oxford University Press</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4262-9399706e84b81d8d225fddeccc53df2b48422e376006f8dbea06d8bf8225a7a73</citedby><cites>FETCH-LOGICAL-c4262-9399706e84b81d8d225fddeccc53df2b48422e376006f8dbea06d8bf8225a7a73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,1583,27922,27923</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34363673$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lebrun, Laetitia</creatorcontrib><creatorcontrib>Bizet, Martin</creatorcontrib><creatorcontrib>Melendez, Barbara</creatorcontrib><creatorcontrib>Alexiou, Barbara</creatorcontrib><creatorcontrib>Absil, Lara</creatorcontrib><creatorcontrib>Van Campenhout, Claude</creatorcontrib><creatorcontrib>D’Haene, Nicky</creatorcontrib><creatorcontrib>Rorive, Sandrine</creatorcontrib><creatorcontrib>Fuks, François</creatorcontrib><creatorcontrib>Decaestecker, Christine</creatorcontrib><creatorcontrib>Salmon, Isabelle</creatorcontrib><title>Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas</title><title>Journal of neuropathology and experimental neurology</title><addtitle>J Neuropathol Exp Neurol</addtitle><description>Abstract
Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylation-related studies specifically addressing to IMAs have been performed yet. In the present study, we analyzed 16 IMA samples subjected to morphological and molecular analyses, including DNA methylation profiling. Among the 16 samples, only 3 cases were classified in a reference methylation class (MC) with the recommended calibrated score (≥0.9). The remaining cases were either considered “no-match” cases (calibrated score <0.3, n = 7) or were classified with low calibrated scores (ranging from 0.32 to 0.53, n = 6), including inconsistent classification. To obtain a more comprehensive tool for pathologists, we used different unsupervised analyses of DNA methylation profiles, including our data and those from the Heidelberg reference cohort. Even though our cohort included only 16 cases, hypotheses regarding IMA-specific classification were underlined; a potential specific MC of PA_SPINE was identified and high-grade IMAs, probably consisting of H3K27M wild-type IMAs, were mainly associated with ANA_PA MC. These hypotheses strongly suggest that a specific classification for IMAs has to be investigated.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Analysis</subject><subject>Astrocytoma</subject><subject>Astrocytoma - diagnosis</subject><subject>Astrocytoma - genetics</subject><subject>Brain tumors</subject><subject>Child</subject><subject>Classification</subject><subject>Diagnosis</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA sequencing</subject><subject>Female</subject><subject>Health aspects</subject><subject>Humans</subject><subject>Hypotheses</subject><subject>Male</subject><subject>Methods</subject><subject>Methylation</subject><subject>Middle Aged</subject><subject>Neurological research</subject><subject>Nucleotide sequencing</subject><subject>Original</subject><subject>Spinal Cord Neoplasms - diagnosis</subject><subject>Spinal Cord Neoplasms - genetics</subject><issn>0022-3069</issn><issn>1554-6578</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kktv1DAUhS0EokNhxxpFYgEL0jp2_NogRS2PSuWxoGvLcW5mPErsqZ0gzb_HYYZCEUJeeOHvHp977kXoeYXPKqzo-daDP_eDaTEjD9CqYqwuORPyIVphTEhJMVcn6ElKW4yxwqp-jE5oTTnlgq7QTePNsE-QitAXl5-b4hNMm_1gJhd88TWG3g3Orwvni2kDxaUzax-S-0lf-SmaEbp5GEzcF02aYrD7KYwmPUWPejMkeHa8T9HN-3ffLj6W118-XF0016WtCSelokoJzEHWraw62RHC-q4Day2jXU_aWtaEABUcY97LrgWDeSfbXmbQCCPoKXp70N3NbXZiYbE06F10Y7akg3H6_ot3G70O37WkTNAaZ4HXR4EYbmdIkx5dspA78hDmpAljKlvN0Wb05V_oNswxp5cpXgmlZM2r39TaDKCd70P-1y6iuhFcMoIlXqizf1D5dDA6Gzzk2OF-wZtDgY0hpQj9XY8V1ssa6GUN9HENMv7iz1zu4F9zz8CrAxDm3f-lfgCYg7wK</recordid><startdate>20210701</startdate><enddate>20210701</enddate><creator>Lebrun, Laetitia</creator><creator>Bizet, Martin</creator><creator>Melendez, Barbara</creator><creator>Alexiou, Barbara</creator><creator>Absil, Lara</creator><creator>Van Campenhout, Claude</creator><creator>D’Haene, Nicky</creator><creator>Rorive, Sandrine</creator><creator>Fuks, François</creator><creator>Decaestecker, Christine</creator><creator>Salmon, Isabelle</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88G</scope><scope>88I</scope><scope>8AF</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>S0X</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20210701</creationdate><title>Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas</title><author>Lebrun, Laetitia ; Bizet, Martin ; Melendez, Barbara ; Alexiou, Barbara ; Absil, Lara ; Van Campenhout, Claude ; D’Haene, Nicky ; Rorive, Sandrine ; Fuks, François ; Decaestecker, Christine ; Salmon, Isabelle</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4262-9399706e84b81d8d225fddeccc53df2b48422e376006f8dbea06d8bf8225a7a73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Aged</topic><topic>Analysis</topic><topic>Astrocytoma</topic><topic>Astrocytoma - diagnosis</topic><topic>Astrocytoma - genetics</topic><topic>Brain tumors</topic><topic>Child</topic><topic>Classification</topic><topic>Diagnosis</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA sequencing</topic><topic>Female</topic><topic>Health aspects</topic><topic>Humans</topic><topic>Hypotheses</topic><topic>Male</topic><topic>Methods</topic><topic>Methylation</topic><topic>Middle Aged</topic><topic>Neurological research</topic><topic>Nucleotide sequencing</topic><topic>Original</topic><topic>Spinal Cord Neoplasms - diagnosis</topic><topic>Spinal Cord Neoplasms - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lebrun, Laetitia</creatorcontrib><creatorcontrib>Bizet, Martin</creatorcontrib><creatorcontrib>Melendez, Barbara</creatorcontrib><creatorcontrib>Alexiou, Barbara</creatorcontrib><creatorcontrib>Absil, Lara</creatorcontrib><creatorcontrib>Van Campenhout, Claude</creatorcontrib><creatorcontrib>D’Haene, Nicky</creatorcontrib><creatorcontrib>Rorive, Sandrine</creatorcontrib><creatorcontrib>Fuks, François</creatorcontrib><creatorcontrib>Decaestecker, Christine</creatorcontrib><creatorcontrib>Salmon, Isabelle</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Psychology Database (Alumni)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of neuropathology and experimental neurology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lebrun, Laetitia</au><au>Bizet, Martin</au><au>Melendez, Barbara</au><au>Alexiou, Barbara</au><au>Absil, Lara</au><au>Van Campenhout, Claude</au><au>D’Haene, Nicky</au><au>Rorive, Sandrine</au><au>Fuks, François</au><au>Decaestecker, Christine</au><au>Salmon, Isabelle</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas</atitle><jtitle>Journal of neuropathology and experimental neurology</jtitle><addtitle>J Neuropathol Exp Neurol</addtitle><date>2021-07-01</date><risdate>2021</risdate><volume>80</volume><issue>7</issue><spage>663</spage><epage>673</epage><pages>663-673</pages><issn>0022-3069</issn><eissn>1554-6578</eissn><abstract>Abstract
Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylation-related studies specifically addressing to IMAs have been performed yet. In the present study, we analyzed 16 IMA samples subjected to morphological and molecular analyses, including DNA methylation profiling. Among the 16 samples, only 3 cases were classified in a reference methylation class (MC) with the recommended calibrated score (≥0.9). The remaining cases were either considered “no-match” cases (calibrated score <0.3, n = 7) or were classified with low calibrated scores (ranging from 0.32 to 0.53, n = 6), including inconsistent classification. To obtain a more comprehensive tool for pathologists, we used different unsupervised analyses of DNA methylation profiles, including our data and those from the Heidelberg reference cohort. Even though our cohort included only 16 cases, hypotheses regarding IMA-specific classification were underlined; a potential specific MC of PA_SPINE was identified and high-grade IMAs, probably consisting of H3K27M wild-type IMAs, were mainly associated with ANA_PA MC. These hypotheses strongly suggest that a specific classification for IMAs has to be investigated.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34363673</pmid><doi>10.1093/jnen/nlab052</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adolescent Adult Aged Analysis Astrocytoma Astrocytoma - diagnosis Astrocytoma - genetics Brain tumors Child Classification Diagnosis DNA DNA Methylation DNA sequencing Female Health aspects Humans Hypotheses Male Methods Methylation Middle Aged Neurological research Nucleotide sequencing Original Spinal Cord Neoplasms - diagnosis Spinal Cord Neoplasms - genetics |
| title | Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas |
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