Skip to main content

Advertisement

SpringerLink
Log in

Genomic landscape of glioblastoma without IDH somatic mutation in 42 cases: a comprehensive analysis using RNA sequencing data

  • Research
  • Published:
Journal of Neuro-Oncology Aims and scope Submit manuscript

Abstract

Purpose

Glioblastoma is a malignant brain tumor with a poor prognosis. Genetic mutations associated with this disease are complex are not fully understood and require further elucidation for the development of new treatments. The purpose of this study was to comprehensively analyze genetic mutations in glioblastomas and evaluate the usefulness of RNA sequencing.

Patients and methods

We analyzed 42 glioblastoma specimens that were resected in routine clinical practice and found wild-type variants of the IDH1 and IDH2 genes. RNA was extracted from frozen specimens and sequenced, and genetic analyses were performed using the CLC Genomics Workbench.

Results

The most common genetic alterations in the 42 glioblastoma specimens were TP53 mutation (28.6%), EGFR splicing variant (16.7%), EGFR mutation (9.5%), and FGFR3 fusion (9.5%). Novel genetic mutations were detected in 8 patients (19%). In 12 cases (28.6%), driver gene mutations were not detected, suggesting an association with PPP1R14A overexpression. Our findings suggest the transcription factors SOX10 and NKX6-2 are potential markers in glioblastoma.

Conclusion

RNA sequencing is a promising approach for genotyping glioblastomas because it provides comprehensive information on gene expression and is relatively cost-effective.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Data availability

No datasets were generated or analysed during the current study.

References

  1. Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, Hawkins C, Ng HK, Pfister SM, Reifenberger G, Soffietti R, von Deimling A, Ellison DW (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 

  2. Network CGAR (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455:1061–1068. https://doi.org/10.1038/nature07385

    Article  CAS  Google Scholar 

  3. Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A (2012) Transforming fusions of FGFR and TACC genes in human glioblastoma. Science (New York, NY) 337:1231–1235. https://doi.org/10.1126/science.1220834

    Article  CAS  Google Scholar 

  4. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O’Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN (2010) Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17:98–110. https://doi.org/10.1016/j.ccr.2009.12.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O’Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L (2013) The somatic genomic landscape of glioblastoma. Cell 155:462–477. https://doi.org/10.1016/j.cell.2013.09.034

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nishikawa R, Furnari FB, Lin H, Arap W, Berger MS, Cavenee WK, Su Huang HJ (1995) Loss of P16INK4 expression is frequent in high grade gliomas. Can Res 55:1941–1945

    CAS  Google Scholar 

  7. Reifenberger G, Reifenberger J, Ichimura K, Collins VP (1995) Amplification at 12q13-14 in human malignant gliomas is frequently accompanied by loss of heterozygosity at loci proximal and distal to the amplification site. Can Res 55:731–734

    CAS  Google Scholar 

  8. Yin J, Yin W, Zheng L, Li Y, Luo C, Zhang S, Duan L, Zhou H, Cheng K, Lang J, Xu K (2023) Anlotinib as monotherapy or combination therapy for recurrent high-grade glioma: a retrospective study. Clin Med Insights Oncol 17:11795549231175714. https://doi.org/10.1177/11795549231175714

    Article  PubMed  PubMed Central  Google Scholar 

  9. Davidson NM, Majewski IJ, Oshlack A (2015) JAFFA: High sensitivity transcriptome-focused fusion gene detection. Genome Med 7:43. https://doi.org/10.1186/s13073-015-0167-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 29:15–21. https://doi.org/10.1093/bioinformatics/bts635

    Article  CAS  PubMed  Google Scholar 

  11. Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, Brown MA, Naqvi AS, Zhang B, Storm PB, Maris JM, Raman P, Resnick AC, Strauch K, Taroni JN, Rokita JL (2020) annoFuse: an R package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinformatics 21:577. https://doi.org/10.1186/s12859-020-03922-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Flensburg C, Oshlack A, Majewski IJ (2021) Detecting copy number alterations in RNA-Seq using SuperFreq. Bioinformatics (Oxford, England) 37:4023–4032. https://doi.org/10.1093/bioinformatics/btab440

    Article  CAS  PubMed  Google Scholar 

  13. Yasumizu Y, Hara A, Sakaguchi S, Ohkura N (2021) VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data. Bioinformatics (Oxford, England) 37:1465–1467. https://doi.org/10.1093/bioinformatics/btaa859

    Article  CAS  PubMed  Google Scholar 

  14. Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M (2022) Metagenome analysis using the Kraken software suite. Nat Protoc 17:2815–2839. https://doi.org/10.1038/s41596-022-00738-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Frappaz D, Ricci AC, Kohler R, Bret P, Mottolese C (1999) Diffuse brain stem tumor in an adolescent with multiple enchondromatosis (Ollier’s disease). Child’s Nervous Syst: ChNS: Off J Int Soc Pediatric Neurosurg 15:222–225. https://doi.org/10.1007/s003810050377

    Article  CAS  Google Scholar 

  16. Ozawa T, Brennan CW, Wang L, Squatrito M, Sasayama T, Nakada M, Huse JT, Pedraza A, Utsuki S, Yasui Y, Tandon A, Fomchenko EI, Oka H, Levine RL, Fujii K, Ladanyi M, Holland EC (2010) PDGFRA gene rearrangements are frequent genetic events in PDGFRA-amplified glioblastomas. Genes Dev 24:2205–2218. https://doi.org/10.1101/gad.1972310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Tian L, Li Y, Edmonson MN, Zhou X, Newman S, McLeod C, Thrasher A, Liu Y, Tang B, Rusch MC, Easton J, Ma J, Davis E, Trull A, Michael JR, Szlachta K, Mullighan C, Baker SJ, Downing JR, Ellison DW, Zhang J (2020) CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data. Genome Biol 21:126. https://doi.org/10.1186/s13059-020-02043-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Pedersen MW, Meltorn M, Damstrup L, Poulsen HS (2001) The type III epidermal growth factor receptor mutation. Biological significance and potential target for anti-cancer therapy. Ann Oncol: Off J Eur Soc Med Oncol 12:745–760. https://doi.org/10.1023/a:1011177318162

    Article  CAS  Google Scholar 

  19. Sugawa N, Ekstrand AJ, James CD, Collins VP (1990) Identical splicing of aberrant epidermal growth factor receptor transcripts from amplified rearranged genes in human glioblastomas. Proc Natl Acad Sci U S A 87:8602-8606.https://doi.org/10.1073/pnas.87.21.8602

  20. Varghese RT, Liang Y, Guan T, Franck CT, Kelly DF, Sheng Z (2016) Survival kinase genes present prognostic significance in glioblastoma. Oncotarget 7:20140–20151. https://doi.org/10.18632/oncotarget.7917

    Article  PubMed  PubMed Central  Google Scholar 

  21. Makino Y, Arakawa Y, Yoshioka E, Shofuda T, Minamiguchi S, Kawauchi T, Tanji M, Kanematsu D, Nonaka M, Okita Y, Kodama Y, Mano M, Hirose T, Mineharu Y, Miyamoto S, Kanemura Y (2021) Infrequent RAS mutation is not associated with specific histological phenotype in gliomas. BMC Cancer 21:1025. https://doi.org/10.1186/s12885-021-08733-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Maleszewska M, Kaminska B (2013) Is glioblastoma an epigenetic malignancy? Cancers 5:1120–1139. https://doi.org/10.3390/cancers5031120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Stichel D, Ebrahimi A, Reuss D, Schrimpf D, Ono T, Shirahata M, Reifenberger G, Weller M, Hänggi D, Wick W, Herold-Mende C, Westphal M, Brandner S, Pfister SM, Capper D, Sahm F, von Deimling A (2018) Distribution of EGFR amplification, combined chromosome 7 gain and chromosome 10 loss, and TERT promoter mutation in brain tumors and their potential for the reclassification of IDHwt astrocytoma to glioblastoma. Acta Neuropathol 136:793–803. https://doi.org/10.1007/s00401-018-1905-0

    Article  PubMed  Google Scholar 

  24. Boisselier B, Dugay F, Belaud-Rotureau MA, Coutolleau A, Garcion E, Menei P, Guardiola P, Rousseau A (2018) Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma. Oncotarget 9:36017–36028. https://doi.org/10.18632/oncotarget.26330

    Article  PubMed  PubMed Central  Google Scholar 

  25. Guo X, Gu L, Li Y, Zheng Z, Chen W, Wang Y, Wang Y, Xing H, Shi Y, Liu D, Yang T, Xia Y, Li J, Wu J, Zhang K, Liang T, Wang H, Liu Q, Jin S, Qu T, Guo S, Li H, Wang Y, Ma W (2023) Histological and molecular glioblastoma, IDH-wildtype: a real-world landscape using the 2021 WHO classification of central nervous system tumors. Front Oncol 13:1200815. https://doi.org/10.3389/fonc.2023.1200815

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Farsi Z, AllahyariFard N (2023) The identification of key genes and pathways in glioblastoma by bioinformatics analysis. Mol Cell Oncol 10:2246657. https://doi.org/10.1080/23723556.2023.2246657

    Article  PubMed  PubMed Central  Google Scholar 

  27. Wu Y, Fletcher M, Gu Z, Wang Q, Costa B, Bertoni A, Man KH, Schlotter M, Felsberg J, Mangei J, Barbus M, Gaupel AC, Wang W, Weiss T, Eils R, Weller M, Liu H, Reifenberger G, Korshunov A, Angel P, Lichter P, Herrmann C, Radlwimmer B (2020) Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype. Nat Commun 11:6434. https://doi.org/10.1038/s41467-020-20225-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW (2008) An integrated genomic analysis of human glioblastoma multiforme. Science (New York, NY) 321:1807–1812. https://doi.org/10.1126/science.1164382

    Article  CAS  Google Scholar 

  29. Virshup DM, Shenolikar S (2009) From promiscuity to precision: protein phosphatases get a makeover. Mol Cell 33:537–545. https://doi.org/10.1016/j.molcel.2009.02.015

    Article  CAS  PubMed  Google Scholar 

  30. Wang Z, Huang R, Wang H, Peng Y, Fan Y, Feng Z, Zeng Z, Ji Y, Wang Y, Lu J (2022) Prognostic and immunological role of PPP1R14A as a pan-cancer analysis candidate. Front Genet 13:842975. https://doi.org/10.3389/fgene.2022.842975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Zavala-Vega S, Palma-Lara I, Ortega-Soto E, Trejo-Solis C, de Arellano IT, Ucharima-Corona LE, Garcia-Chacón G, Ochoa SA, Xicohtencatl-Cortes J, Cruz-Córdova A, Luna-Pineda VM, Jiménez-Hernández E, Vázquez-Meraz E, Mejía-Aranguré JM, Guzmán-Bucio S, Rembao-Bojorquez D, Sánchez-Gómez C, Salazar-Garcia M, Arellano-Galindo J (2019) Role of Epstein-Barr virus in glioblastoma. Crit Rev Oncog 24:307–338. https://doi.org/10.1615/CritRevOncog.2019032655

    Article  PubMed  Google Scholar 

  32. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM (2013) The cancer genome atlas pan-cancer analysis project. Nat Genet 45:1113–1120. https://doi.org/10.1038/ng.2764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Tomczak K, Czerwińska P, Wiznerowicz M (2015) The cancer genome atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Poznan, Poland) 19:A68-77. https://doi.org/10.5114/wo.2014.47136

    Article  Google Scholar 

Download references

Acknowledgements

We are grateful to the patients who participated in this study. We would like to acknowledge the excellent technical assistance of Ms. Reina Nishida and Ms. Seiko Shibata for the preparation of tumor tissue specimens or RNA extraction.

Funding

This work was supported in part by the Aichi Cancer Center Joint Research Project on Priority Areas (Hirokazu Matsushita).

Author information

Authors and Affiliations

  1. Department of Neurosurgery, Kyoto Prefectural University of Medicine, Kyoto, Japan

    Takanari Okamoto, Yoshinobu Takahashi & Naoya Hashimoto

  2. Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan

    Ryo Mizuta, Yoshihiro Otani & Isao Date

  3. Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan

    Eiichi Sasaki & Katsuhiro Masago

  4. Department of Thoracic oncology, Aichi Cancer Center Hospital, Aichi, Japan

    Yoshitsugu Horio

  5. Department of Thoracic Surgery, Teikyo University Mizonokuchi Hospital, Kanagawa, Japan

    Hiroaki Kuroda

  6. Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Aichi, Japan

    Takanari Okamoto, Ryo Mizuta, Eiichi Sasaki, Yoshitsugu Horio, Hiroaki Kuroda, Hirokazu Matsushita & Katsuhiro Masago

Authors
  1. Takanari Okamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ryo Mizuta
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yoshinobu Takahashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yoshihiro Otani
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Eiichi Sasaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yoshitsugu Horio
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hiroaki Kuroda
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hirokazu Matsushita
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Isao Date
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Naoya Hashimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Katsuhiro Masago
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization, Methodology, Software, Investigation, T.O., R.M., K.M., H.K., H.M.; Methodology, T.O., R.M., K.M., E.S., Y.H.; Project administration, T.O., H.M., K.M.; Resources, Data curation, T.O., R.M., T.Y., Y.O., I.D., N.H.; Supervision, H.M., I.D., N.H.; Writing—original draft, T.O., K.M.; Writing—review & editing, All authors. English editting, Brian Quinn: Japan Medical Communication: www.japan-mc.co.jp. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Katsuhiro Masago.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Takanari Okamoto and Ryo Mizuta are joint first authors.

Importance of the study

In IDH wild-type glioblastoma, pre-treatment molecular pathological classification holds paramount importance for both tumor diagnosis and therapeutic guidance using targeted agents like FGFR3 inhibitors. However, comprehensive genetic analysis remains laborious in current clinical settings, hindering widespread adoption. This study explores the utility of RNA sequencing as a diagnostic tool and assesses its potential for integration into routine clinical practice.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PPTX 16402 KB)

Supplementary file2 (DOCX 46 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Okamoto, T., Mizuta, R., Takahashi, Y. et al. Genomic landscape of glioblastoma without IDH somatic mutation in 42 cases: a comprehensive analysis using RNA sequencing data. J Neurooncol 167, 489–499 (2024). https://doi.org/10.1007/s11060-024-04628-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11060-024-04628-z

Keywords

Search

Navigation