Agnihotri S, Suppiah S, Tonge PD, Jalali S, Danesh A, Bruce JP et al (2017) Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas. Nat Comms 8:186. https://doi.org/10.1038/s41467-017-00174-7

Article  ADS  CAS  Google Scholar 

Chen WC, Choudhury A, Youngblood MW, Polley M-YC, Lucas C-HG, Mirchia K et al (2023) Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses. Nat Med. https://doi.org/10.1038/s41591-023-02586-z

Article  PubMed  PubMed Central  Google Scholar 

Choudhury A, Chen WC, Lucas C-HG, Bayley JC, Harmanci AS, Maas SLN et al (2022) Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features. Neuro Oncol. https://doi.org/10.1093/neuonc/noac224

Article  PubMed  PubMed Central  Google Scholar 

Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA et al (2022) Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nat Genet 54:649–659. https://doi.org/10.1038/s41588-022-01061-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635

Article  CAS  PubMed  Google Scholar 

Driver J, Hoffman SE, Tavakol S, Woodward E, Maury EA, Bhave V et al (2021) A Molecularly Integrated Grade for Meningioma. Neuro Oncol. https://doi.org/10.1093/neuonc/noab213

Article  PubMed Central  Google Scholar 

Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA et al (2020) annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinform 21:577. https://doi.org/10.1186/s12859-020-03922-7

Article  CAS  Google Scholar 

Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A (2019) Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol 20:213. https://doi.org/10.1186/s13059-019-1842-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kalamarides M, Stemmer-Rachamimov AO, Niwa-Kawakita M, Chareyre F, Taranchon E, Han Z-Y et al (2011) Identification of a progenitor cell of origin capable of generating diverse meningioma histological subtypes. Oncogene 30:2333–2344. https://doi.org/10.1038/onc.2010.609

Article  CAS  PubMed  Google Scholar 

Khan AB, English CW, Chen WC, Athukuri P, Bayley JC, Brandt VL et al (2023) Even heterozygous loss of CDKN2A/B greatly accelerates recurrence in aggressive meningioma. Acta Neuropathol 145:501–503. https://doi.org/10.1007/s00401-023-02543-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khan AB, Gadot R, Shetty A, Bayley JC, Hadley CC, Cardenas MF et al (2020) Identification of novel fusion transcripts in meningioma. J Neuro-Oncol 149:219–230. https://doi.org/10.1007/s11060-020-03599-1

Article  CAS  Google Scholar 

Latysheva NS, Babu MM (2016) Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res 44:4487–4503. https://doi.org/10.1093/nar/gkw282

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. https://doi.org/10.1093/bioinformatics/btt656

Article  CAS  PubMed  Google Scholar 

Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D et al (2021) The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol 23:1231–1251. https://doi.org/10.1093/neuonc/noab106

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

Maas SLN, Stichel D, Hielscher T, Sievers P, Berghoff AS, Schrimpf D et al (2021) Integrated Molecular-Morphologic Meningioma Classification: A Multicenter Retrospective Analysis. J Clin Oncol, Retrospectively and Prospectively Validated. https://doi.org/10.1200/jco.21.00784

Book  Google Scholar 

Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJ 17:10–12. https://doi.org/10.14806/ej.17.1.200

Article  Google Scholar 

Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R et al (2021) A clinically applicable integrative molecular classification of meningiomas. Nature 597:119–125. https://doi.org/10.1038/s41586-021-03850-3

Article  ADS  CAS  PubMed  Google Scholar 

Olar A, Wani KM, Wilson CD, Zadeh G, DeMonte F, Jones DTW et al (2017) Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma. Acta Neuropathol 133:431–444. https://doi.org/10.1007/s00401-017-1678-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ostrom QT, Price M, Neff C, Cioffi G, Waite KA, Kruchko C et al (2022) CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2015–2019. Neuro Oncol 24:v1–v95. https://doi.org/10.1093/neuonc/noac202

Article  CAS  PubMed  PubMed Central  Google Scholar 

Paramasivam N, Hübschmann D, Toprak UH, Ishaque N, Neidert M, Schrimpf D et al (2019) Mutational patterns and regulatory networks in epigenetic subgroups of meningioma. Acta Neuropathol 208:345–414. https://doi.org/10.1007/s00401-019-02008-w

Article  CAS  Google Scholar 

Patel AJ, Wan Y-W, Al-Ouran R, Revelli J-P, Cardenas MF, Oneissi M et al (2019) Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors. Proc Natl Acad Sci USA 116:21715–21726. https://doi.org/10.1073/pnas.1912858116

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Sadagopan NS, Nandoliya KR, Youngblood MW, Horbinski CM, Ahrendsen JT, Magill ST (2023) A novel BRAF::PTPRN2 fusion in meningioma: a case report. Acta Neuropathol Commun 11:194. https://doi.org/10.1186/s40478-023-01668-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sahm F, Schrimpf D, Olar A, Koelsche C, Reuss D, Bissel J et al (2016) TERT Promoter Mutations and Risk of Recurrence in Meningioma. J Natl Cancer Inst. https://doi.org/10.1093/jnci/djv377

Article  PubMed  Google Scholar 

Sahm F, Schrimpf D, Stichel D, Jones DTW, Hielscher T, Schefzyk S et al (2017) DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis. Lancet Oncol. https://doi.org/10.1016/s1470-2045(17)30155-9

Article  PubMed  Google Scholar 

Sahm F, Toprak UH, Hübschmann D, Kleinheinz K, Buchhalter I, Sill M et al (2017) Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature. Acta Neuropathol 134:155–158. https://doi.org/10.1007/s00401-017-1715-9

Article  CAS  PubMed  Google Scholar 

Shugay M, de Mendíbil IO, Vizmanos JL, Novo FJ (2013) Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions. Bioinformatics 29:2539–2546. https://doi.org/10.1093/bioinformatics/btt445

Article  CAS  PubMed  Google Scholar 

Sievers P, Chiang J, Schrimpf D, Stichel D, Paramasivam N, Sill M et al (2019) YAP1-fusions in pediatric NF2-wildtype meningioma. Acta Neuropathol 91:520–524. https://doi.org/10.1007/s00401-019-02095-9

Article  Google Scholar 

Sievers P, Hielscher T, Schrimpf D, Stichel D, Reuss DE, Berghoff AS et al (2020) CDKN2A/B homozygous deletion is associated with early recurrence in meningiomas. Acta Neuropathol 140:409–413. https://doi.org/10.1007/s00401-020-02188-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Szulzewsky F, Arora S, Arakaki AKS, Sievers P, Bonnin DAA, Paddison PJ et al (2022) Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice. Genes Dev 36:857–870. https://doi.org/10.1101/gad.349876.122

Article  CAS  PubMed  PubMed Central  Google Scholar 

Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B et al (2021) Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Res. https://doi.org/10.1101/gr.257246.119

Article  PubMed  PubMed Central  Google Scholar 

Viaene AN, Zhang B, Martinez-Lage M, Xiang C, Tosi U, Thawani JP et al (2019) Transcriptome signatures associated with meningioma progression. Acta Neuropathol Commun 7:67–13. https://doi.org/10.1186/s40478-019-0690-x

Article  PubMed  PubMed Central  Google Scholar 

Youngblood MW, Duran D, Montejo JD, Li C, Omay SB, Ozduman K et al (2019) Correlations between genomic subgroup and clinical features in a cohort of more than 3000