{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T18:22:57Z","timestamp":1792174977408,"version":"4.4.0"},"reference-count":64,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Seoul National University Hospital Research Fund","award":["03-20220260"],"award-info":[{"award-number":["03-20220260"]}]},{"name":"SNUH Kun-hee Lee Child Cancer & Rare Disease Project","award":["70-20221202"],"award-info":[{"award-number":["70-20221202"]}]},{"name":"Ulsan 10K Genomes Project","award":["1.180017.01"],"award-info":[{"award-number":["1.180017.01"]}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"crossref","award":["NRF-2021R1A6A3A13045998"],"award-info":[{"award-number":["NRF-2021R1A6A3A13045998"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"crossref","award":["NRF-2018R1A6A1A03025810"],"award-info":[{"award-number":["NRF-2018R1A6A1A03025810"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["acta neuropathol commun"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Choroid plexus tumors (CPTs) are intraventricular tumors derived from the choroid plexus epithelium and occur frequently in children. The aim of this study was to investigate the genomic and epigenomic characteristics of CPT and identify the differences between choroid plexus papilloma (CPP) and choroid plexus carcinoma (CPC). We conducted multiomics analyses of 20 CPT patients including CPP and CPC. Multiomics analysis included whole-genome sequencing, whole-transcriptome sequencing, and methylation sequencing. Mutually exclusive <jats:italic>TP53<\/jats:italic> and <jats:italic>EPHA7<\/jats:italic> point mutations, coupled with the amplification of chromosome 1, were exclusively identified in CPC. In contrast, amplification of chromosome 9 was specific to CPP. Differential gene expression analysis uncovered a significant overexpression of genes related to cell cycle regulation and epithelial-mesenchymal transition pathways in CPC compared to CPP. Overexpression of genes associated with tumor metastasis and progression was observed in the CPC subgroup with leptomeningeal dissemination. Furthermore, methylation profiling unveiled hypomethylation in major repeat regions, including long interspersed nuclear elements, short interspersed nuclear elements, long terminal repeats, and retrotransposons in CPC compared to CPP, implying that the loss of epigenetic silencing of transposable elements may play a role in tumorigenesis of CPC. Finally, the differential expression of <jats:italic>AK1<\/jats:italic>, regulated by both genomic and epigenomic factors, emerged as a potential contributing factor to the histological difference of CPP against CPC. Our results suggest pronounced genomic and epigenomic disparities between CPP and CPC, providing insights into the pathogenesis of CPT at the molecular level.<\/jats:p>","DOI":"10.1186\/s40478-024-01814-y","type":"journal-article","created":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T06:01:47Z","timestamp":1718172107000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Comprehensive multiomics analysis reveals distinct differences between pediatric choroid plexus papilloma and carcinoma"],"prefix":"10.1186","volume":"12","author":[{"given":"Yeonsong","family":"Choi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seung Ah","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eun Jung","family":"Koh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilsun","family":"Yun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suhyun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sungwon","family":"Jeon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeonkyung","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sangbeen","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donggeon","family":"Woo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji Hoon","family":"Phi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sung-Hye","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Seok","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Se Hoon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jung Won","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji Won","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tae-Young","family":"Jung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jong","family":"Bhak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Semin","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seung-Ki","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,12]]},"reference":[{"key":"1814_CR1","doi-asserted-by":"publisher","first-page":"R87","DOI":"10.1186\/gb-2012-13-10-r87","volume":"13","author":"A Akalin","year":"2012","unstructured":"Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13:R87. https:\/\/doi.org\/10.1186\/gb-2012-13-10-r87","journal-title":"Genome Biol"},{"key":"1814_CR2","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. The gene ontology. Consort Nat Genet 25:25\u201329. https:\/\/doi.org\/10.1038\/75556","journal-title":"Consort Nat Genet"},{"key":"1814_CR3","doi-asserted-by":"publisher","first-page":"2345","DOI":"10.1200\/JCO.2014.59.5728","volume":"33","author":"G Bougeard","year":"2015","unstructured":"Bougeard G, Renaux-Petel M, Flaman JM, Charbonnier C, Fermey P, Belotti M, Gauthier-Villars M, Stoppa-Lyonnet D, Consolino E, Brugieres L et al (2015) Revisiting Li-Fraumeni syndrome from TP53 mutation carriers. J Clin Oncol 33:2345\u20132352. https:\/\/doi.org\/10.1200\/JCO.2014.59.5728","journal-title":"J Clin Oncol"},{"key":"1814_CR4","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1186\/s12885-019-5952-2","volume":"19","author":"D Chakroborty","year":"2019","unstructured":"Chakroborty D, Emani MR, Klen R, Bockelman C, Hagstrom J, Haglund C, Ristimaki A, Lahesmaa R, Elo LL (2019) L1TD1\u2014a prognostic marker for colon cancer. BMC Cancer 19:727. https:\/\/doi.org\/10.1186\/s12885-019-5952-2","journal-title":"BMC Cancer"},{"key":"1814_CR5","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-14-128","volume":"14","author":"EY Chen","year":"2013","unstructured":"Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma\u2019ayan A (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform 14:128. https:\/\/doi.org\/10.1186\/1471-2105-14-128","journal-title":"BMC Bioinform"},{"key":"1814_CR6","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1186\/s12935-020-01645-6","volume":"20","author":"SA Choi","year":"2020","unstructured":"Choi SA, Koh EJ, Kim RN, Byun JW, Phi JH, Yang J, Wang KC, Park AK, Hwang DW, Lee JY et al (2020) Extracellular vesicle-associated miR-135b and -135a regulate stemness in Group 4 medulloblastoma cells by targeting angiomotin-like 2. Cancer Cell Int 20:558. https:\/\/doi.org\/10.1186\/s12935-020-01645-6","journal-title":"Cancer Cell Int"},{"key":"1814_CR7","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM et al (2021) Twelve years of SAM tools and BCF tools. Gigascience. https:\/\/doi.org\/10.1093\/gigascience\/giab008","journal-title":"Gigascience"},{"key":"1814_CR8","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1007\/s00262-017-1983-1","volume":"66","author":"MR Dunne","year":"2017","unstructured":"Dunne MR, Michielsen AJ, O\u2019Sullivan KE, Cathcart MC, Feighery R, Doyle B, Watson JA, O\u2019Farrell NJ, Ravi N, Kay E et al (2017) HLA-DR expression in tumor epithelium is an independent prognostic indicator in esophageal adenocarcinoma patients. Cancer Immunol Immunother 66:841\u2013850. https:\/\/doi.org\/10.1007\/s00262-017-1983-1","journal-title":"Cancer Immunol Immunother"},{"key":"1814_CR9","unstructured":"Erickson N, Mueller J, Shirkov A, Zhang H, Larroy P, Li M, Smola A (2020) Autogluon-tabular: robust and accurate automl for structured data. arXiv:200306505"},{"key":"1814_CR10","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1158\/2159-8290.CD-20-1202","volume":"11","author":"E Espinet","year":"2021","unstructured":"Espinet E, Gu Z, Imbusch CD, Giese NA, Buscher M, Safavi M, Weisenburger S, Klein C, Vogel V, Falcone M et al (2021) Aggressive PDACs show hypomethylation of repetitive elements and the execution of an Intrinsic IFN program linked to a ductal cell of origin. Cancer Discov 11:638\u2013659. https:\/\/doi.org\/10.1158\/2159-8290.CD-20-1202","journal-title":"Cancer Discov"},{"key":"1814_CR11","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1002\/humu.24152","volume":"42","author":"C Fortuno","year":"2021","unstructured":"Fortuno C, Lee K, Olivier M, Pesaran T, Mai PL, de Andrade KC, Attardi LD, Crowley S, Evans DG, Feng BJ et al (2021) Specifications of the ACMG\/AMP variant interpretation guidelines for germline TP53 variants. Hum Mutat 42:223\u2013236. https:\/\/doi.org\/10.1002\/humu.24152","journal-title":"Hum Mutat"},{"key":"1814_CR12","doi-asserted-by":"publisher","first-page":"D916","DOI":"10.1093\/nar\/gkaa1087","volume":"49","author":"A Frankish","year":"2021","unstructured":"Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al (2021) Gencode 2021. Nucl Acids Res 49:D916\u2013D923. https:\/\/doi.org\/10.1093\/nar\/gkaa1087","journal-title":"Nucl Acids Res"},{"key":"1814_CR13","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","volume":"49","author":"C Gene Ontology","year":"2021","unstructured":"Gene Ontology C (2021) The gene ontology resource: enriching a GOld mine. Nucleic Acids Res 49:D325\u2013D334. https:\/\/doi.org\/10.1093\/nar\/gkaa1113","journal-title":"Nucleic Acids Res"},{"key":"1814_CR14","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","volume":"526","author":"A Auton","year":"2015","unstructured":"Genomes Project C, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al (2015) A global reference for human genetic variation. Nature 526:68\u201374. https:\/\/doi.org\/10.1038\/nature15393","journal-title":"Nature"},{"key":"1814_CR15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0186649","volume":"12","author":"SL Gonias","year":"2017","unstructured":"Gonias SL, Karimi-Mostowfi N, Murray SS, Mantuano E, Gilder AS (2017) Expression of LDL receptor-related proteins (LRPs) in common solid malignancies correlates with patient survival. PLoS ONE 12:e0186649. https:\/\/doi.org\/10.1371\/journal.pone.0186649","journal-title":"PLoS ONE"},{"key":"1814_CR16","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a026187","author":"T Guha","year":"2017","unstructured":"Guha T, Malkin D (2017) Inherited TP53 mutations and the Li-Fraumeni syndrome. Cold Spring Harb Perspect Med. https:\/\/doi.org\/10.1101\/cshperspect.a026187","journal-title":"Cold Spring Harb Perspect Med"},{"key":"1814_CR17","doi-asserted-by":"publisher","DOI":"10.3892\/mmr.2020.11717","author":"Y Guo","year":"2021","unstructured":"Guo Y, Shi W, Fang R (2021) miR-18a-5p promotes melanoma cell proliferation and inhibits apoptosis and autophagy by targeting EPHA7 signaling. Mol Med Rep. https:\/\/doi.org\/10.3892\/mmr.2020.11717","journal-title":"Mol Med Rep"},{"key":"1814_CR18","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/j.tcb.2022.08.004","volume":"33","author":"D Huang","year":"2023","unstructured":"Huang D, Alexander PB, Li QJ, Wang XF (2023) GABAergic signaling beyond synapses: an emerging target for cancer therapy. Trends Cell Biol 33:403\u2013412. https:\/\/doi.org\/10.1016\/j.tcb.2022.08.004","journal-title":"Trends Cell Biol"},{"key":"1814_CR19","doi-asserted-by":"publisher","first-page":"12329","DOI":"10.1038\/s41598-019-48243-9","volume":"9","author":"YH Jan","year":"2019","unstructured":"Jan YH, Lai TC, Yang CJ, Huang MS, Hsiao M (2019) A co-expressed gene status of adenylate kinase 1\/4 reveals prognostic gene signature associated with prognosis and sensitivity to EGFR targeted therapy in lung adenocarcinoma. Sci Rep 9:12329. https:\/\/doi.org\/10.1038\/s41598-019-48243-9","journal-title":"Sci Rep"},{"key":"1814_CR20","doi-asserted-by":"publisher","first-page":"eaaz7835","DOI":"10.1126\/sciadv.aaz7835","volume":"6","author":"S Jeon","year":"2020","unstructured":"Jeon S, Bhak Y, Choi Y, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y et al (2020) Korean Genome Project: 1094 Korean personal genomes with clinical information. Sci Adv 6:eaaz7835. https:\/\/doi.org\/10.1126\/sciadv.aaz7835","journal-title":"Sci Adv"},{"key":"1814_CR21","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1186\/s12885-018-4149-4","volume":"18","author":"K Kanbara","year":"2018","unstructured":"Kanbara K, Otsuki Y, Watanabe M, Yokoe S, Mori Y, Asahi M, Neo M (2018) GABA(B) receptor regulates proliferation in the high-grade chondrosarcoma cell line OUMS-27 via apoptotic pathways. BMC Cancer 18:263. https:\/\/doi.org\/10.1186\/s12885-018-4149-4","journal-title":"BMC Cancer"},{"key":"1814_CR22","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","volume":"581","author":"KJ Karczewski","year":"2020","unstructured":"Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al (2020) The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581:434\u2013443. https:\/\/doi.org\/10.1038\/s41586-020-2308-7","journal-title":"Nature"},{"key":"1814_CR23","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","volume":"27","author":"F Krueger","year":"2011","unstructured":"Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571\u20131572. https:\/\/doi.org\/10.1093\/bioinformatics\/btr167","journal-title":"Bioinformatics"},{"key":"1814_CR24","doi-asserted-by":"publisher","first-page":"W90","DOI":"10.1093\/nar\/gkw377","volume":"44","author":"MV Kuleshov","year":"2016","unstructured":"Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A et al (2016) Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucl Acids Res 44:W90-97. https:\/\/doi.org\/10.1093\/nar\/gkw377","journal-title":"Nucl Acids Res"},{"key":"1814_CR25","doi-asserted-by":"publisher","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","volume":"46","author":"MJ Landrum","year":"2018","unstructured":"Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Jang W et al (2018) ClinVar: improving access to variant interpretations and supporting evidence. Nucl Acids Res 46:D1062\u2013D1067. https:\/\/doi.org\/10.1093\/nar\/gkx1153","journal-title":"Nucl Acids Res"},{"key":"1814_CR26","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:323. https:\/\/doi.org\/10.1186\/1471-2105-12-323","journal-title":"BMC Bioinform"},{"key":"1814_CR27","first-page":"575","volume":"23","author":"D Li","year":"2014","unstructured":"Li D, Xiang B, Ying XX, Ying XX, Dong H (2014) Correlation analysis of EphA7 expression with clinico-pathological parameters and prognosis in tongue squamous cell carcinoma. Shanghai Kou Qiang Yi Xue 23:575\u2013579","journal-title":"Shanghai Kou Qiang Yi Xue"},{"key":"1814_CR28","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25:1754\u20131760. https:\/\/doi.org\/10.1093\/bioinformatics\/btp324","journal-title":"Bioinformatics"},{"key":"1814_CR29","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.jmoldx.2016.10.002","volume":"19","author":"MM Li","year":"2017","unstructured":"Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A et al (2017) Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the association for molecular pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn 19:4\u201323. https:\/\/doi.org\/10.1016\/j.jmoldx.2016.10.002","journal-title":"J Mol Diagn"},{"key":"1814_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/cddis.2017.507","volume":"8","author":"S Li","year":"2017","unstructured":"Li S, Wu Z, Ma P, Xu Y, Chen Y, Wang H, He P, Kang Z, Yin L, Zhao Y et al (2017) Ligand-dependent EphA7 signaling inhibits prostate tumor growth and progression. Cell Death Dis 8:e3122. https:\/\/doi.org\/10.1038\/cddis.2017.507","journal-title":"Cell Death Dis"},{"key":"1814_CR31","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.751784","volume":"11","author":"Y Li","year":"2021","unstructured":"Li Y, Liu H, Li T, Feng J, He Y, Chen L, Li C, Qiu X (2021) Choroid plexus carcinomas with TP53 germline mutations: management and outcome. Front Oncol 11:751784. https:\/\/doi.org\/10.3389\/fonc.2021.751784","journal-title":"Front Oncol"},{"key":"1814_CR32","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1093\/neuonc\/noab106","volume":"23","author":"DN Louis","year":"2021","unstructured":"Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, Hawkins C, Ng HK, Pfister SM, Reifenberger G et al (2021) The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro Oncol 23:1231\u20131251. https:\/\/doi.org\/10.1093\/neuonc\/noab106","journal-title":"Neuro Oncol"},{"key":"1814_CR33","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8","journal-title":"Genome Biol"},{"key":"1814_CR34","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297\u20131303. https:\/\/doi.org\/10.1101\/gr.107524.110","journal-title":"Genome Res"},{"key":"1814_CR35","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","volume":"17","author":"W McLaren","year":"2016","unstructured":"McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F (2016) The Ensembl variant effect predictor. Genome Biol 17:122. https:\/\/doi.org\/10.1186\/s13059-016-0974-4","journal-title":"Genome Biol"},{"key":"1814_CR36","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1158\/1078-0432.CCR-14-1324","volume":"21","author":"DM Merino","year":"2015","unstructured":"Merino DM, Shlien A, Villani A, Pienkowska M, Mack S, Ramaswamy V, Shih D, Tatevossian R, Novokmet A, Choufani S et al (2015) Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups. Clin Cancer Res 21:184\u2013192. https:\/\/doi.org\/10.1158\/1078-0432.CCR-14-1324","journal-title":"Clin Cancer Res"},{"key":"1814_CR37","doi-asserted-by":"publisher","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","volume":"12","author":"CH Mermel","year":"2011","unstructured":"Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G (2011) GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 12:R41. https:\/\/doi.org\/10.1186\/gb-2011-12-4-r41","journal-title":"Genome Biol"},{"key":"1814_CR38","doi-asserted-by":"publisher","first-page":"32","DOI":"10.2214\/ajr.08.1128","volume":"192","author":"RM Naeini","year":"2009","unstructured":"Naeini RM, Yoo JH, Hunter JV (2009) Spectrum of choroid plexus lesions in children. AJR Am J Roentgenol 192:32\u201340. https:\/\/doi.org\/10.2214\/ajr.08.1128","journal-title":"AJR Am J Roentgenol"},{"key":"1814_CR39","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1002\/stem.1013","volume":"30","author":"E Narva","year":"2012","unstructured":"Narva E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP, Nasti J, Autio R, Rasool O, Denessiouk K, Lahdesmaki H et al (2012) RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells 30:452\u2013460. https:\/\/doi.org\/10.1002\/stem.1013","journal-title":"Stem Cells"},{"key":"1814_CR40","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1016\/j.cell.2011.09.035","volume":"147","author":"E Oricchio","year":"2011","unstructured":"Oricchio E, Nanjangud G, Wolfe AL, Schatz JH, Mavrakis KJ, Jiang M, Liu X, Bruno J, Heguy A, Olshen AB et al (2011) The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma. Cell 147:554\u2013564. https:\/\/doi.org\/10.1016\/j.cell.2011.09.035","journal-title":"Cell"},{"key":"1814_CR41","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1016\/j.tranon.2015.08.001","volume":"8","author":"JH Phi","year":"2015","unstructured":"Phi JH, Choi SA, Kim SK, Wang KC, Lee JY, Kim DG (2015) Overcoming chemoresistance of pediatric ependymoma by inhibition of STAT3 signaling. Transl Oncol 8:376\u2013386. https:\/\/doi.org\/10.1016\/j.tranon.2015.08.001","journal-title":"Transl Oncol"},{"key":"1814_CR42","doi-asserted-by":"publisher","first-page":"237.e21","DOI":"10.1016\/j.urolonc.2020.11.017","volume":"39","author":"XM Piao","year":"2021","unstructured":"Piao XM, Kang HW, Jeong P, Byun YJ, Lee HY, Kim K, Seo SP, Kim WT, Lee JY, Ha YS et al (2021) A prognostic immune predictor, HLA-DRA, plays diverse roles in non-muscle invasive and muscle invasive bladder cancer. Urol Oncol 39:237.e21-237.e29. https:\/\/doi.org\/10.1016\/j.urolonc.2020.11.017","journal-title":"Urol Oncol"},{"key":"1814_CR43","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1186\/s13148-019-0708-z","volume":"11","author":"M Pienkowska","year":"2019","unstructured":"Pienkowska M, Choufani S, Turinsky AL, Guha T, Merino DM, Novokmet A, Brudno M, Weksberg R, Shlien A, Hawkins C et al (2019) DNA methylation signature is prognostic of choroid plexus tumor aggressiveness. Clin Epigenet 11:117. https:\/\/doi.org\/10.1186\/s13148-019-0708-z","journal-title":"Clin Epigenet"},{"key":"1814_CR44","doi-asserted-by":"publisher","first-page":"1171887","DOI":"10.3389\/fonc.2023.1171887","volume":"13","author":"E Rebane-Klemm","year":"2023","unstructured":"Rebane-Klemm E, Reinsalu L, Puurand M, Shevchuk I, Bogovskaja J, Suurmaa K, Valvere V, Moreno-Sanchez R, Kaambre T (2023) Colorectal polyps increase the glycolytic activity. Front Oncol 13:1171887. https:\/\/doi.org\/10.3389\/fonc.2023.1171887","journal-title":"Front Oncol"},{"key":"1814_CR45","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1016\/S0002-9440(10)64931-0","volume":"160","author":"CH Rickert","year":"2002","unstructured":"Rickert CH, Wiestler OD, Paulus W (2002) Chromosomal imbalances in choroid plexus tumors. Am J Pathol 160:1105\u20131113. https:\/\/doi.org\/10.1016\/S0002-9440(10)64931-0","journal-title":"Am J Pathol"},{"key":"1814_CR46","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1002\/gcc.22148","volume":"53","author":"V Ruland","year":"2014","unstructured":"Ruland V, Hartung S, Kordes U, Wolff JE, Paulus W, Hasselblatt M (2014) Choroid plexus carcinomas are characterized by complex chromosomal alterations related to patient age and prognosis. Genes Chromosomes Cancer 53:373\u2013380. https:\/\/doi.org\/10.1002\/gcc.22148","journal-title":"Genes Chromosomes Cancer"},{"key":"1814_CR47","doi-asserted-by":"publisher","first-page":"2700","DOI":"10.1089\/scd.2015.0052","volume":"24","author":"MC Santos","year":"2015","unstructured":"Santos MC, Silva PB, Rodini CO, Furukawa G, Marco Antonio DS, Zanotto-Filho A, Moreira JC, Okamoto OK (2015) Embryonic stem cell-related protein L1TD1 is required for cell viability, neurosphere formation, and chemoresistance in medulloblastoma. Stem Cells Dev 24:2700\u20132708. https:\/\/doi.org\/10.1089\/scd.2015.0052","journal-title":"Stem Cells Dev"},{"key":"1814_CR48","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1093\/neuonc\/noab246","volume":"24","author":"K Satomi","year":"2022","unstructured":"Satomi K, Takami H, Fukushima S, Yamashita S, Matsushita Y, Nakazato Y, Suzuki T, Tanaka S, Mukasa A, Saito N et al (2022) 12p gain is predominantly observed in non-germinomatous germ cell tumors and identifies an unfavorable subgroup of central nervous system germ cell tumors. Neuro Oncol 24:834\u2013846. https:\/\/doi.org\/10.1093\/neuonc\/noab246","journal-title":"Neuro Oncol"},{"key":"1814_CR49","doi-asserted-by":"publisher","DOI":"10.1016\/j.genrep.2019.100430","volume":"16","author":"J-w Shi","year":"2019","unstructured":"Shi J-w, Huang Y (2019) Screen and classify genes on bladder cancer associated with metastasis. Gene Reports 16:100430","journal-title":"Gene Reports"},{"key":"1814_CR50","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1038\/s41568-018-0060-1","volume":"18","author":"Z Sondka","year":"2018","unstructured":"Sondka Z, Bamford S, Cole CG, Ward SA, Dunham I, Forbes SA (2018) The COSMIC cancer gene census: describing genetic dysfunction across all human cancers. Nat Rev Cancer 18:696\u2013705. https:\/\/doi.org\/10.1038\/s41568-018-0060-1","journal-title":"Nat Rev Cancer"},{"key":"1814_CR51","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545\u201315550. https:\/\/doi.org\/10.1073\/pnas.0506580102","journal-title":"Proc Natl Acad Sci USA"},{"key":"1814_CR52","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.1200\/JCO.2009.26.8169","volume":"28","author":"U Tabori","year":"2010","unstructured":"Tabori U, Shlien A, Baskin B, Levitt S, Ray P, Alon N, Hawkins C, Bouffet E, Pienkowska M, Lafay-Cousin L et al (2010) TP53 alterations determine clinical subgroups and survival of patients with choroid plexus tumors. J Clin Oncol 28:1995\u20132001. https:\/\/doi.org\/10.1200\/JCO.2009.26.8169","journal-title":"J Clin Oncol"},{"key":"1814_CR53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004873","volume":"12","author":"E Talevich","year":"2016","unstructured":"Talevich E, Shain AH, Botton T, Bastian BC (2016) CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput Biol 12:e1004873. https:\/\/doi.org\/10.1371\/journal.pcbi.1004873","journal-title":"PLoS Comput Biol"},{"key":"1814_CR54","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/s12253-013-9692-3","volume":"20","author":"S Theocharis","year":"2014","unstructured":"Theocharis S, Klijanienko J, Giaginis C, Alexandrou P, Patsouris E, Sastre-Garau X (2014) Ephrin receptor (Eph) -A1, -A2, -A4 and -A7 expression in mobile tongue squamous cell carcinoma: associations with clinicopathological parameters and patients survival. Pathol Oncol Res 20:277\u2013284. https:\/\/doi.org\/10.1007\/s12253-013-9692-3","journal-title":"Pathol Oncol Res"},{"key":"1814_CR55","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1093\/neuonc\/nov322","volume":"18","author":"C Thomas","year":"2016","unstructured":"Thomas C, Sill M, Ruland V, Witten A, Hartung S, Kordes U, Jeibmann A, Beschorner R, Keyvani K, Bergmann M et al (2016) Methylation profiling of choroid plexus tumors reveals 3 clinically distinct subgroups. Neuro Oncol 18:790\u2013796. https:\/\/doi.org\/10.1093\/neuonc\/nov322","journal-title":"Neuro Oncol"},{"key":"1814_CR56","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1093\/neuonc\/noaa267","volume":"23","author":"C Thomas","year":"2021","unstructured":"Thomas C, Soschinski P, Zwaig M, Oikonomopoulos S, Okonechnikov K, Pajtler KW, Sill M, Schweizer L, Koch A, Neumann J et al (2021) The genetic landscape of choroid plexus tumors in children and adults. Neuro Oncol 23:650\u2013660. https:\/\/doi.org\/10.1093\/neuonc\/noaa267","journal-title":"Neuro Oncol"},{"key":"1814_CR57","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1016\/j.ccell.2015.04.005","volume":"27","author":"Y Tong","year":"2015","unstructured":"Tong Y, Merino D, Nimmervoll B, Gupta K, Wang YD, Finkelstein D, Dalton J, Ellison DW, Ma X, Zhang J et al (2015) Cross-species genomics identifies TAF12, NFYC, and RAD54L as choroid plexus carcinoma oncogenes. Cancer Cell 27:712\u2013727. https:\/\/doi.org\/10.1016\/j.ccell.2015.04.005","journal-title":"Cancer Cell"},{"key":"1814_CR58","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1476-4598-4-4","volume":"4","author":"S Vasseur","year":"2005","unstructured":"Vasseur S, Malicet C, Calvo EL, Dagorn JC, Iovanna JL (2005) Gene expression profiling of tumours derived from rasV12\/E1A-transformed mouse embryonic fibroblasts to identify genes required for tumour development. Mol Cancer 4:4. https:\/\/doi.org\/10.1186\/1476-4598-4-4","journal-title":"Mol Cancer"},{"key":"1814_CR59","doi-asserted-by":"publisher","first-page":"103311","DOI":"10.1016\/j.isci.2021.103311","volume":"24","author":"B Wei","year":"2021","unstructured":"Wei B, Zhu Y, Yang P, Han Y, Wang S, Wang X, Xia S, Song X, Zhang Z, Wang S et al (2021) GABA(B1e) promotes the malignancy of human cancer cells by targeting the tyrosine phosphatase PTPN12. iScience 24:103311. https:\/\/doi.org\/10.1016\/j.isci.2021.103311","journal-title":"iScience"},{"key":"1814_CR60","doi-asserted-by":"crossref","unstructured":"Wu W, Chang F, Zhang J, Tang S, Chen F (2022) GABBR1 as a predictor of prognosis and its correlation with immune infiltration and dysfunction in clear cell renal cell carcinoma","DOI":"10.21203\/rs.3.rs-2291503\/v1"},{"key":"1814_CR61","doi-asserted-by":"publisher","first-page":"4469","DOI":"10.1038\/s41467-020-18169-2","volume":"11","author":"Y Xiao","year":"2020","unstructured":"Xiao Y, Wang X, Zhang H, Ulintz PJ, Li H, Guan Y (2020) FastClone is a probabilistic tool for deconvoluting tumor heterogeneity in bulk-sequencing samples. Nat Commun 11:4469. https:\/\/doi.org\/10.1038\/s41467-020-18169-2","journal-title":"Nat Commun"},{"key":"1814_CR62","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.90","volume":"1","author":"Z Xie","year":"2021","unstructured":"Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM et al (2021) Gene set knowledge discovery with Enrichr. Curr Protoc 1:e90. https:\/\/doi.org\/10.1002\/cpz1.90","journal-title":"Curr Protoc"},{"key":"1814_CR63","doi-asserted-by":"publisher","first-page":"1132","DOI":"10.1093\/neuonc\/noac274","volume":"25","author":"M Zaytseva","year":"2023","unstructured":"Zaytseva M, Valiakhmetova A, Yasko L, Samarin A, Papusha L, Shekhtman A, Usman N, Voronin K, Karachunskiy A, Novichkova G et al (2023) Molecular heterogeneity of pediatric choroid plexus carcinomas determines the distinctions in clinical course and prognosis. Neuro Oncol 25:1132\u20131145. https:\/\/doi.org\/10.1093\/neuonc\/noac274","journal-title":"Neuro Oncol"},{"key":"1814_CR64","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.709931","volume":"11","author":"S Zhao","year":"2021","unstructured":"Zhao S, Dong X, Ni X, Li L, Lu X, Zhang K, Gao Y (2021) Exploration of a novel prognostic risk signature and its effect on the immune response in nasopharyngeal carcinoma. Front Oncol 11:709931. https:\/\/doi.org\/10.3389\/fonc.2021.709931","journal-title":"Front Oncol"}],"container-title":["Acta Neuropathologica Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40478-024-01814-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40478-024-01814-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40478-024-01814-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T06:06:13Z","timestamp":1718172373000},"score":1,"resource":{"primary":{"URL":"https:\/\/actaneurocomms.biomedcentral.com\/articles\/10.1186\/s40478-024-01814-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,12]]},"references-count":64,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1814"],"URL":"https:\/\/doi.org\/10.1186\/s40478-024-01814-y","relation":{},"ISSN":["2051-5960"],"issn-type":[{"value":"2051-5960","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,12]]},"assertion":[{"value":"8 February 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no potential conflicts of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"93"}}