A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy

References

• Perkins A, G Liu. Primary brain tumors in adults: diagnosis and treatment. Am Fam Physician [Internet]. 2016;93:211–217B. [cited 2023 Jun 30]. Available from: https://www.aafp.org/pubs/afp/issues/2016/0201/p211.html
   PubMed Web of Science ®Google Scholar
• McFaline-Figueroa JR, Lee EQ. Brain tumors. Am J Med. 2018;131(8):874–882. doi: 10.1016/j.amjmed.2017.12.039
   PubMed Web of Science ®Google Scholar
• Strowd RE, Blakeley JO. Common histologically benign tumors of the brain. Continuum (Minneap Minn) [Internet]. 2017;23(6):1680–1708. [cited 2023 Jun 30]. doi: 10.1212/CON.0000000000000541.
   PubMedGoogle Scholar
• Aghi M, Barker FG. Benign adult brain tumors: an evidence-based medicine review. Prog Neurol Surg [Internet]. 2006;19:80–96. [cited 2023 Jul 2]. Available from: https://pubmed.ncbi.nlm.nih.gov/17033148/
   PubMedGoogle Scholar
• Quail DF, Joyce JA. The microenvironmental landscape of brain tumors. Cancer Cell. 2017;31(3):326–341. doi: 10.1016/j.ccell.2017.02.009
   PubMed Web of Science ®Google Scholar
• Lah TT, Novak M, Breznik B. Brain malignancies: Glioblastoma and brain metastases. Semin Cancer Biol [Internet]. 2020;60:262–273. [cited 2023 Jun 30]. doi: 10.1016/j.semcancer.2019.10.010.
   PubMed Web of Science ®Google Scholar
• Arvanitis CD, Ferraro GB, Jain RK. The blood–brain barrier and blood–tumour barrier in brain tumours and metastases. Nat Rev Cancer [Internet]. 2020;20(1):26–41. [cited 2023 Jun 30]. Available from: https://pubmed.ncbi.nlm.nih.gov/31601988/.
   PubMed Web of Science ®Google Scholar
• Boire A, Brastianos PK, Garzia L, et al. Brain metastasis. Nat Rev Cancer [Internet]. 2020;20(1):4–11. [cited 2023 Jun 30]. doi: 10.1038/s41568-019-0220-y
   PubMed Web of Science ®Google Scholar
• Amoo M, Henry J, Farrell M, et al. Meningioma in the elderly. Neurooncol Adv [Internet]. 2023;5(Supplement_1):I13–I25. [cited 2023 Oct 27]. doi: 10.1093/noajnl/vdac107
   PubMedGoogle Scholar
• Ostrom QT, Gittleman H, Truitt G, et al. CBTRUS statistical report: primary brain and other central nervous system tumors diagnosed in the United States in 2011–2015. Neuro Oncol. 2018;20(suppl_4):iv1–iv86. doi: 10.1093/neuonc/noy131
   PubMed Web of Science ®Google Scholar
• McNeill KA. Epidemiology of brain tumors. Neurol Clin [Internet]. 2016;34(4):981–998. [cited 2023 Jun 30]. doi: 10.1016/j.ncl.2016.06.014.
   PubMed Web of Science ®Google Scholar
• Kwon YW, Jo HS, Bae S, et al. Application of proteomics in Cancer: recent trends and approaches for biomarkers discovery. Front Med [Internet]. 2021;8. [cited 2023 Jul 1]. doi: 10.3389/fmed.2021.747333
   Web of Science ®Google Scholar
• Srivastava S. From proteins to proteomics: basic concepts, techniques, and applications. From proteins to proteomics: basic concepts. Tech Appl [Internet]. 2022;1–261. [cited 2023 Jul 1]. Available from: https://www.taylorfrancis.com/books/mono/10.1201/9781003098645/proteins-proteomics-sanjeeva-srivastava.
   Google Scholar
• Khalil AA, James P. Biomarker discovery: a proteomic approach for brain cancer profiling. Cancer Sci [Internet]. 2007;98(2):201–213. [cited 2023 Jul 1]. Available from: https://pubmed.ncbi.nlm.nih.gov/17233837/.
   PubMed Web of Science ®Google Scholar
• Wang LB, Karpova A, Gritsenko MA, et al. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell. 2021;39(4):509–528.e20. doi: 10.1016/j.ccell.2021.01.006
   PubMed Web of Science ®Google Scholar
• Davalieva K, Rusevski A, Velkov M, et al. Comparative proteomics analysis of human FFPE testicular tissues reveals new candidate biomarkers for distinction among azoospermia types and subtypes. J Proteomics [Internet]. 2022;267:104686. [cited 2023 Sep 22]. Available from: doi: 10.1016/j.jprot.2022.104686
   PubMed Web of Science ®Google Scholar
• Pujari GP, Mangalaparthi KK, Madden BJ, et al. A high-throughput workflow for FFPE tissue proteomics. J Am Soc Mass Spectrom [Internet]. 2023;34(7):1225–1229. [cited 2023 Sep 22]. doi: 10.1021/jasms.3c00099
   PubMed Web of Science ®Google Scholar
• Zhu Y, Weiss T, Zhang Q, et al. High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification. Mol Oncol [Internet]. 2019;13(11):2305–2328. [cited 2023 Sep 22]. doi: 10.1002/1878-0261.12570
   PubMed Web of Science ®Google Scholar
• Coscia F, Doll S, Bech JM, et al. A streamlined mass spectrometry–based proteomics workflow for large-scale FFPE tissue analysis. The Journal Of Pathology. 2020;251(1):100–112. [cited 2023 Sep 22]. Available from: https://pubmed.ncbi.nlm.nih.gov/32154592/
   PubMed Web of Science ®Google Scholar
• Nissa MU, Pinto N, Varshnay A, et al. Ecological monitoring and omics: a comprehensive comparison of workflows for mass spectrometry-based Quantitative proteomics of fish (labeo rohita) liver tissue. OMICS [Internet]. 2022;26(9):489–503. [cited 2023 Sep 22]. Available from: doi: 10.1089/omi.2022.0086
   PubMed Web of Science ®Google Scholar
• Bang G, Lee H, Kim H, et al. Comparison of protein characterization using in solution and S-Trap digestion methods for proteomics. Biochem Biophys Res Commun [Internet]. 2022;589:197–203 [cited 2023 Sep 22]. Available from: doi: 10.1016/j.bbrc.2021.12.026
   PubMed Web of Science ®Google Scholar
• Zheng W, Yang P, Sun C, et al. Comprehensive comparison of sample preparation workflows for proteomics. Mol Omics [Internet]. 2022;18(6):555–567. [cited 2023 Sep 22]. doi: 10.1039/D2MO00076H
   PubMed Web of Science ®Google Scholar
• Wiśniewski JR, Zougman A, Nagaraj N, et al. Universal sample preparation method for proteome analysis. Nat Methods [Internet]. 2009;6(5):359–362. [cited 2023 Oct 22]. doi: 10.1038/nmeth.1322
   PubMed Web of Science ®Google Scholar
• Wiśniewski JR, Nagaraj N, Zougman A, et al. Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology. J Proteome Res [Internet]. 2010;9(6):3280–3289. [cited 2023 Oct 22]. doi: 10.1021/pr1002214
   PubMed Web of Science ®Google Scholar
• Ghantasala S, Pai MGJ, Srivastava S. Quantitative proteomics workflow using multiple Reaction monitoring based detection of proteins from human brain tissue. J Vis Exp [Internet]. 2021;2021(174):e61833. [[cited 2022 Mar 5]]. doi: 10.3791/61833.
   Google Scholar
• Pagel O, Kollipara L, Sickmann A. Tandem mass tags for comparative and discovery proteomics. Methods Mol Biol [Internet]. 2021;2228:117–131. [cited 2023 Oct 22]. Available from: https://pubmed.ncbi.nlm.nih.gov/33950487/
   PubMedGoogle Scholar
• Evans C, Noirel J, Ow SY, et al. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem [Internet]. 2012;404(4):1011–1027. [cited 2023 Oct 22]. doi: 10.1007/s00216-012-5918-6
   PubMed Web of Science ®Google Scholar
• Chen X, Wei S, Ji Y, et al. Quantitative proteomics using SILAC: principles, applications, and developments. Proteomics [Internet]. 2015;15(18):3175–3192. [cited 2023 Oct 22]. doi: 10.1002/pmic.201500108
   PubMed Web of Science ®Google Scholar
• Verma A, Kumar V, Ghantasala S, et al. Comprehensive workflow of mass spectrometry-based shotgun proteomics of tissue samples. J Visual Exp [Internet]. 2021 (177):e61786. [cited 2022 Mar 5]. Available from: https://www.jove.com/v/61786/comprehensive-workflow-mass-spectrometry-based-shotgun-proteomics.
   Google Scholar
• Rozanova S, Barkovits K, Nikolov M, et al. Quantitative mass spectrometry-based proteomics: an overview. Methods Mol Biol [Internet]. 2021;2228:85–116 [cited 2023 Oct 22]. Available from: https://pubmed.ncbi.nlm.nih.gov/33950486/
   PubMedGoogle Scholar
• Bantscheff M, Schirle M, Sweetman G, et al. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem [Internet]. 2007;389(4):1017–1031. [cited 2023 Oct 22]. doi: 10.1007/s00216-007-1486-6
   PubMed Web of Science ®Google Scholar
• Mendes ML, Dittmar G. Targeted proteomics on its way to discovery. Proteomics [Internet]. 2022;22(15–16). [cited 2023 Jul 1]. doi: 10.1002/pmic.202100330.
   PubMed Web of Science ®Google Scholar
• Biswas D, Shenoy SV, Chetanya C, et al. Deciphering the interregional and interhemisphere proteome of the human brain in the context of the human proteome project. J Proteome Res. 2021;20(12):5280–5293. doi: 10.1021/acs.jproteome.1c00511
   PubMed Web of Science ®Google Scholar
• Ghantasala S, Pai MGJ, Biswas D, et al. Multiple Reaction monitoring-based targeted assays for the validation of protein biomarkers in brain tumors. Front Oncol [Internet]. 2021;11:1623 [cited 2021 Jul 13]. doi: 10.3389/fonc.2021.548243
   Web of Science ®Google Scholar
• Schaff LR, Yan D, Thyparambil S, et al. Characterization of MGMT and EGFR protein expression in glioblastoma and association with survival. J Neurooncol [Internet]. 2020;146(1):163–170. [cited 2023 Jul 2]. doi: 10.1007/s11060-019-03358-x
   PubMed Web of Science ®Google Scholar
• Archer TC, Ehrenberger T, Mundt F, et al. Proteomics, post-translational modifications, and integrative analyses reveal molecular heterogeneity within medulloblastoma subgroups. Cancer Cell [Internet]. 2018;34(3):396–410.e8. doi: 10.1016/j.ccell.2018.08.004
   PubMed Web of Science ®Google Scholar
• Leutert M, Entwisle SW, Villén J. Decoding post-translational modification crosstalk with proteomics. Mol & Cell Proteomics [Internet]. 2021;20:100129. [cited 2023 Jul 1]. doi: 10.1016/j.mcpro.2021.100129.
   PubMed Web of Science ®Google Scholar
• Biswas D, Kumari N, Lachén-Montes M, et al. Deep phosphoproteome landscape of interhemispheric functionality of neuroanatomical regions of the human brain. J Proteome Res [Internet]. 2023;22(4):1043–1055. [cited 2023 Jul 1]. doi: 10.1021/acs.jproteome.2c00244
   PubMed Web of Science ®Google Scholar
• Zhang X, Maity TK, Ross KE, et al. Alterations in the global proteome and phosphoproteome in third generation EGFR TKI resistance reveal drug targets to circumvent resistance. Cancer Res [Internet]. 2021;81(11):3051–3066. [cited 2023 Jul 1]. doi: 10.1158/0008-5472.CAN-20-2435
   PubMed Web of Science ®Google Scholar
• Vázquez-Blomquist D, Hardy-Sosa A, Baez SC, et al. Proteomics and phospho-proteomics profiling of the Co-Formulation of type I and II interferons, HeberFERON, in the glioblastoma-derived cell line U-87 MG. Cells [Internet]. 2022;11(24):4068. [cited 2023 Jul 1]. doi: 10.3390/cells11244068
   Google Scholar
• Whiteaker JR, Sharma K, Hoffman MA, et al. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP kinase, and AKT signaling. Cell Rep Met [Internet]. 2021;1(3):100015. [cited 2023 Jul 1]. Available from: https://pubmed.ncbi.nlm.nih.gov/34671754/
   PubMedGoogle Scholar
• Veillon L, Fakih C, Abou-El-Hassan H, et al. Glycosylation changes in brain Cancer. ACS Chem Neurosci [Internet]. 2018;9(1):51–72. doi: 10.1021/acschemneuro.7b00271
   PubMed Web of Science ®Google Scholar
• Sethi MK, Downs M, Shao C, et al. In-depth matrisome and glycoproteomic analysis of human brain glioblastoma versus control tissue. Mol Cell Proteom [Internet]. 2022;21(4):100216. [cited 2023 Jul 1]. doi: 10.1016/j.mcpro.2022.100216
   PubMed Web of Science ®Google Scholar
• Henson JW, Cordon-Cardo C, Posner JB. P-glycoprotein expression in brain tumors. J Neurooncol [Internet]. 1992;14(1):37–43. [cited 2023 Jul 1]. doi: 10.1007/BF00170943.
   PubMed Web of Science ®Google Scholar
• Liao C, Wang Q, An J, et al. CD44 glycosylation as a therapeutic target in oncology. Front Oncol [Internet]. 2022;12. [cited 2023 Jul 1]. doi: 10.3389/fonc.2022.883831
   Web of Science ®Google Scholar
• Liu X, Chen X, Shi L, et al. The third-generation EGFR inhibitor AZD9291 overcomes primary resistance by continuously blocking ERK signaling in glioblastoma. J Exp Clin Cancer Res [Internet]. 2019;38(1). [cited 2023 Jul 1]. doi: 10.1186/s13046-019-1235-7
   Google Scholar
• Sharanek A, Raco L, Soleimani VD, et al. Subcellular fractionation of brain tumor stem cells. Methods Cell Biol [Internet]. 2022;170:47–58 [cited 2023 Jul 1]. Available from: https://pubmed.ncbi.nlm.nih.gov/35811103/
   Google Scholar
• Rose M, Cardon T, Aboulouard S, et al. Surfaceome proteomic of glioblastoma revealed potential targets for immunotherapy. Front Immunol [Internet]. 2021;12. [cited 2023 Jul 1]. doi: 10.3389/fimmu.2021.746168
   Web of Science ®Google Scholar
• Calvo SE, Mootha VK. The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet [Internet]. 2010;11(1):25–44. [cited 2023 Jul 1]. doi: 10.1146/annurev-genom-082509-141720.
   PubMedGoogle Scholar
• Duhamel M, Drelich L, Wisztorski M, et al. Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun [Internet]. 2022;13(1). [cited 2023 Jul 1]. doi: 10.1038/s41467-022-34208-6
   PubMed Web of Science ®Google Scholar
• Wang N, Li X, Wang R, et al. Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment. Biotechnol J [Internet]. 2021;16(9). [cited 2023 Jul 1]. doi: 10.1002/biot.202100041
   Web of Science ®Google Scholar
• Okawa S, Gagrica S, Blin C, et al. Proteome and Secretome characterization of glioblastoma-derived neural stem cells. Stem Cells [Internet]. 2017;35(4):967–980. [cited 2023 Jul 1]. doi: 10.1002/stem.2542
   PubMed Web of Science ®Google Scholar
• Piñero J, Bravo Á, Queralt-Rosinach N, et al. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res [Internet]. 2017;45(D1):D833–D839. [cited 2023 Oct 27]. doi: 10.1093/nar/gkw943
   PubMed Web of Science ®Google Scholar
• Szklarczyk D et al . (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res, 51(D1), D638–D646. 10.1093/nar/gkac1000
   PubMed Web of Science ®Google Scholar
• Louis DN, Perry A, Wesseling P, et al. The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro Oncol [Internet]. 2021;23(8):1231–1251. [cited 2023 Jul 1]. Available from: https://pubmed.ncbi.nlm.nih.gov/34185076/
   PubMed Web of Science ®Google Scholar
• Yanovich-Arad G, Ofek P, Yeini E, et al. Proteogenomics of glioblastoma associates molecular patterns with survival. Cell Rep. 2021;34(9):108787. doi: 10.1016/j.celrep.2021.108787
   PubMed Web of Science ®Google Scholar
• Buehler M, Yi X, Ge W, et al. Quantitative proteomic landscapes of primary and recurrent glioblastoma reveal a protumorigeneic role for FBXO2-dependent glioma-microenvironment interactions. Neuro Oncol [Internet]. 2023;25(2):290–302. [cited 2023 Jul 1]. doi: 10.1093/neuonc/noac169
   PubMed Web of Science ®Google Scholar
• Miyauchi E, Furuta T, Ohtsuki S, et al. Identification of blood biomarkers in glioblastoma by SWATH mass spectrometry and quantitative targeted absolute proteomics. PLoS One. 2018;13(3):e0193799. [cited 2023 Jul 1]. doi: 10.1371/journal.pone.0193799
   PubMed Web of Science ®Google Scholar
• Mason JT. Proteomic analysis of FFPE tissue: barriers to clinical impact. Expert Rev Proteom. 2016;13(9):801–803. cited 2021 Jul 19. [Internet] Available from: https://www.tandfonline.com/doi/abs/10.1080/14789450.2016.1221346.
   PubMed Web of Science ®Google Scholar
• Coscia F, Doll S, Bech JM, et al. A streamlined mass spectrometry–based proteomics workflow for large-scale FFPE tissue analysis. J Pathol [Internet]. 2020;251(1):100–112. [cited 2021 Jul 19]. doi: 10.1002/path.5420
   PubMed Web of Science ®Google Scholar
• Föll MC, Fahrner M, Oria VO, et al. Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization. Clinical Proteomics [Internet]. 2018;15(1):1–15. [cited 2021 Jul 19]. Available from: https://link.springer.com/articles/10.1186/s12014-018-9188-y
   PubMedGoogle Scholar
• Choudhary R, Elabbas A, Vyas A, et al. Utilization of Cerebrospinal fluid proteome analysis in the diagnosis of meningioma: a systematic review. Cureus [Internet]. 2021;13 [cited 2023 Jul 1]. Available from: https://pubmed.ncbi.nlm.nih.gov/34966627/
   Web of Science ®Google Scholar
• Liu J, Xia C, Wang G. Multi-omics analysis in initiation and progression of meningiomas: from pathogenesis to diagnosis. Front Oncol [Internet]. 2020;10. [cited 2023 Jul 1]. doi: 10.3389/fonc.2020.01491
   Web of Science ®Google Scholar
• Abbritti RV, Polito F, Cucinotta M, et al. Meningiomas and proteomics: focus on New potential biomarkers and molecular pathways. Cancer Genom Proteom [Internet]. 2016;13:369. [cited 2023 Jul 1]. Available from: /pmc/articles/PMC5070626/.
   PubMed Web of Science ®Google Scholar
• Kim JH, Lee SK, Yoo YC, et al. Proteome analysis of human cerebrospinal fluid as a diagnostic biomarker in patients with meningioma. Med Sci Monit. 2012;18(11):BR450–BR460. doi: 10.12659/MSM.883538
   PubMed Web of Science ®Google Scholar
• Mukherjee A, Ghosh S, Biswas D, et al. Clinical proteomics for meningioma: an Integrated workflow for Quantitative proteomics and biomarker validation in formalin-fixed paraffin-embedded tissue samples. OMICS [Internet]. 2022;26(9):512–520. [cited 2023 Jul 1]. doi: 10.1089/omi.2022.0082
   PubMed Web of Science ®Google Scholar
• Halder A, Biswas D, Chauhan A, et al. A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clin Proteomics [Internet]. 2023;20(1). [cited 2023 Oct 27]. doi: 10.1186/s12014-023-09426-9
   PubMed Web of Science ®Google Scholar
• Ramaswamy V, Taylor MD. Medulloblastoma: from myth to molecular. J Clin Oncol. 2017;35(21):2355–2363. doi: 10.1200/JCO.2017.72.7842
   PubMed Web of Science ®Google Scholar
• Zomerman WW, Plasschaert SLA, Conroy S, et al. Identification of two protein-signaling states delineating transcriptionally heterogeneous human medulloblastoma. Cell Rep. 2018;22(12):3206–3216. doi: 10.1016/j.celrep.2018.02.089
   PubMed Web of Science ®Google Scholar
• Forget A, Martignetti L, Puget S, et al. Aberrant ERBB4-SRC signaling as a hallmark of Group 4 medulloblastoma revealed by integrative phosphoproteomic profiling. Cancer Cell. 2018;34(3):379–395.e7. doi: 10.1016/j.ccell.2018.08.002
   PubMed Web of Science ®Google Scholar
• Rivero-Hinojosa S, Lau LS, Stampar M, et al. Proteomic analysis of medulloblastoma reveals functional biology with translational potential. Acta Neuropathol Commun [Internet]. 2018;6(1):48. [cited 2023 Jul 1]. doi: 10.1186/s40478-018-0548-7
   PubMedGoogle Scholar
• Narayan V, Jaiswal J, Sugur H, et al. Proteomic profiling of medulloblastoma reveals novel proteins differentially expressed within each molecular subgroup. Clin Neurol Neurosur [Internet]. 2020;196:106028 [cited 2023 Jul 1]. doi: 10.1016/j.clineuro.2020.106028
   PubMed Web of Science ®Google Scholar
• Kp M, Kumar A, Biswas D, et al. The proteomic analysis shows enrichment of RNA surveillance pathways in adult SHH and extensive metabolic [Internet]reprogramming in Group 3 medulloblastomas. Brain Tumor Pathol. 2021;38(2):96–108. [cited 2021 Feb 8]. doi: 10.1007/s10014-020-00391-x
   PubMed Web of Science ®Google Scholar
• Hao X, Guo Z, Sun H, et al. Urinary protein biomarkers for pediatric medulloblastoma. J Proteomics [Internet] 2020;225:103832. [cited 2020 Jul 7]. Available from: https://pubmed.ncbi.nlm.nih.gov/32474013/.
   PubMed Web of Science ®Google Scholar
• Low SYY, Bte Syed Sulaiman N, Tan EEK, et al. Cerebrospinal fluid cytokines in metastatic group 3 and 4 medulloblastoma. BMC Cancer [Internet]. 2020;20(1). [cited 2023 Jul 1]. doi: 10.1186/s12885-020-07048-0
   PubMed Web of Science ®Google Scholar
• Reichl B, Niederstaetter L, Boegl T, et al. Determination of a tumor-promoting microenvironment in recurrent medulloblastoma: a multi-omics study of Cerebrospinal fluid. Cancers (Basel) [Internet]. 2020;12(6):1350. [cited 2023 Jul 1]. doi: 10.3390/cancers12061350
   PubMed Web of Science ®Google Scholar
• Zhao M, Liu Y, Ding G, et al. Online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer. BMC Genomics [Internet]. 2021;22(1). [[cited 2023 Jul 1]]. doi: 10.1186/s12864-021-07793-x
   Web of Science ®Google Scholar
• Aizer AA, Lamba N, Ahluwalia MS, et al. Brain metastases: a society for Neuro-oncology (SNO) consensus review on current management and future directions. Neuro Oncol [Internet]. 2022;24(10):1613–1646. [cited 2023 Jul 1]. doi: 10.1093/neuonc/noac118
   PubMed Web of Science ®Google Scholar
• Fernández-Irigoyen J, Corrales F, Santamaría E. The human brain proteome project: biological and technological challenges. Methods Mol Biol [Internet]. 2019;2044:3–23. [[cited 2023 Jul 1]]. Available from: https://pubmed.ncbi.nlm.nih.gov/31432403/
   PubMedGoogle Scholar
• Rudnick PA, Markey SP, Roth J, et al. A Description of the clinical proteomic tumor analysis Consortium (CPTAC) common data analysis pipeline. J Proteome Res [Internet]. 2016;15(3):1023–1032. [cited 2023 Jul 1]. doi: 10.1021/acs.jproteome.5b01091
   PubMed Web of Science ®Google Scholar
• Wang Q, Ding SL, Li Y, et al. The allen mouse brain common coordinate framework: a 3D reference Atlas. Cell [Internet]. 2020;181(4):936–953.e20. [cited 2023 Jul 1]. doi: 10.1016/j.cell.2020.04.007
   Google Scholar
• Bota M, Swanson LW. Collating and Curating Neuroanatomical Nomenclatures: principles and use of the brain architecture knowledge management system (BAMS). Front Neuroinf [Internet]. 2010;4 [cited 2023 Jul 1]. Available from: https://pubmed.ncbi.nlm.nih.gov/20407640/.
   Google Scholar
• Najafi H, Naseri M, Zahiri J, et al. Identification of the molecular events involved in the development of Prefrontal Cortex through the analysis of RNA-Seq data from BrainSpan. ASN Neuro [Internet]. 2019;11:175909141985462 [cited 2023 Jul 1]. doi: 10.1177/1759091419854627
   Web of Science ®Google Scholar
• Liu L, Zhang Y, Niu G, et al. BrainBase: a curated knowledgebase for brain diseases. Nucleic Acids Res [Internet]. 2022;50(D1):D1131–D1138. [cited 2023 Jul 1]. doi: 10.1093/nar/gkab987
   PubMed Web of Science ®Google Scholar
• Biswas D, Vinayak S, Chauahan A, et al. BrainProt(TM) 3.0: understanding human brain diseases using comprehensively curated & integrated OMICS datasets. Biorxiv [Internet]. 2023 [cited 2023 Jul 1]. Available from: https://www.biorxiv.org/content/10.1101/2023.06.21.545851v1
   Google Scholar
• Liu J, Xia C, Wang G. Multi-omics analysis in initiation and progression of meningiomas: from pathogenesis to diagnosis. Front Oncol [Internet]. 2020;10:1491. [cited 2023 Jul 1]. Available from. doi: 10.3389/fonc.2020.01491.
   PubMed Web of Science ®Google Scholar
• Francesca Petralia A, Tignor N, Reva B, et al. Integrated proteogenomic characterization across major histological types of pediatric brain Cancer ll resource integrated proteogenomic characterization across major histological types of pediatric brain Cancer. 2020 [[cited 2021 Jul 10]]. Available from: doi: 10.1016/j.cell.2020.10.044
   Google Scholar
• Lyne SB, Yamini B. An alternative pipeline for glioblastoma therapeutics: a systematic review of drug repurposing in glioblastoma. Cancers (Basel) [Internet]. 2021;13(8):1953. [[cited 2023 Jul 1]]. Available from: 10.3390/cancers13081953.
   PubMed Web of Science ®Google Scholar
• Ma Y, Xi Z, Liang S. Integrated analysis of Multiomics data identified molecular subtypes and oxidative stress-related prognostic biomarkers in glioblastoma multiforme. Oxid Med Cell Longev. 2022;2022:1–15. doi: 10.1155/2022/9993319
   Web of Science ®Google Scholar
• Wang H, Diaz AK, Shaw TI, et al. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nat Commun. 2019;10(1):10. doi: 10.1038/s41467-019-11661-4
   PubMedGoogle Scholar
• Ravi VM, Will P, Kueckelhaus J, et al. Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma. Cancer Cell [Internet]. 2022;40(6):639–655.e13. [cited 2023 Jul 2]. doi: 10.1016/j.ccell.2022.05.009
   PubMed Web of Science ®Google Scholar
• Harmancl AS, Youngblood MW, Clark VE, et al. Integrated genomic analyses of de novo pathways underlying atypical meningiomas. Nat Commun [Internet]. 2017;8(1). [cited 2023 Jul 2]. Available from: https://pubmed.ncbi.nlm.nih.gov/28195122/
   Google Scholar
• McLendon R, Friedman A, Bigner D, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455:1061–1068.
   PubMed Web of Science ®Google Scholar
• Westermark B. Platelet-derived growth factor in glioblastoma—driver or biomarker? Ups J Med Sci. 2014;119(4):298–305. doi: 10.3109/03009734.2014.970304
   PubMed Web of Science ®Google Scholar
• Shamsdin SA, Mehrafshan A, Rakei SM, et al. Evaluation of VEGF, FGF and PDGF and serum levels of inflammatory cytokines in patients with glioma and meningioma in southern Iran. Asian Pac J Cancer Prev. 2019;20(10):2883–2890. doi: 10.31557/APJCP.2019.20.10.2883
   PubMedGoogle Scholar
• Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Sci (1979). 2008;321(5897):1807–1812. doi: 10.1126/science.1164382
   PubMed Web of Science ®Google Scholar
• Colardo M, Segatto M, Di Bartolomeo S. Targeting rtk-pi3k-mtor axis in gliomas: an update. Int J Mol Sci. 2021;22(9):22. doi: 10.3390/ijms22094899
   Web of Science ®Google Scholar
• Brennan CW, Verhaak RGW, McKenna A, et al. The somatic genomic landscape of glioblastoma. Cell. 2013;155(2):462. doi: 10.1016/j.cell.2013.09.034
   PubMed Web of Science ®Google Scholar
• Mao H, Lebrun DG, Yang J, et al. Deregulated signaling pathways in glioblastoma multiforme: molecular mechanisms and therapeutic targets. Cancer Invest. 2012;30(1):48–56. doi: 10.3109/07357907.2011.630050
   PubMed Web of Science ®Google Scholar
• Moodie SA, Willumsen BM, Weber MJ, et al. Complexes of Ras⋅GTP with raf-1 and mitogen-activated protein kinase kinase. Sci (1979). 1993;260(5114):1658–1661. doi: 10.1126/science.8503013
   PubMed Web of Science ®Google Scholar
• Lo H-W. Targeting Ras-RAF-ERK and its interactive pathways as a novel therapy for malignant gliomas. Curr Cancer Drug Targets. 2010;10(8):840–848. doi: 10.2174/156800910793357970
   PubMed Web of Science ®Google Scholar
• Serra R, Mangraviti A. A systematic view of pediatric medulloblastoma proteomics-current state of the field and future directions. [cited 2023 Apr 30]. doi: 10.1007/s00381-020-04988-7
   Google Scholar
• El-Habr EA, Levidou G, Trigka EA, et al. Complex interactions between the components of the PI3K/AKT/mTOR pathway, and with components of MAPK, JAK/STAT and notch-1 pathways, indicate their involvement in meningioma development. Virchows Arch [Internet]. 2014;465(4):473–485. [cited 2023 Jul 1]. doi: 10.1007/s00428-014-1641-3
   PubMed Web of Science ®Google Scholar
• Cui Y, Groth S, Troutman S, et al. The NF2 tumor suppressor merlin interacts with Ras and RasGAP, which may modulate Ras signaling. Oncogene. 2019;38(36):6370–6381. doi: 10.1038/s41388-019-0883-6
   PubMed Web of Science ®Google Scholar
• Wang Z, Wang W, Xu S, et al. The role of MAPK signaling pathway in the her-2-positive meningiomas. Oncol Rep. 2016;36(2):685–695. doi: 10.3892/or.2016.4849
   PubMed Web of Science ®Google Scholar
• Pecina-Slaus N, Cicvara-Pecina T, Kafka A. Epithelial-to-mesenchymal transition: possible role in meningiomas. Front Biosci - Elite. 2012;E4(3):889–896. doi: 10.2741/e427
   Google Scholar
• Lu YB, Sun TJ, Chen YT, et al. Targeting the epithelial-to-mesenchymal transition in Cancer stem cells for a better clinical outcome of glioma. Technol Cancer Res Treat. 2020;19:153303382094805. doi: 10.1177/1533033820948053
   Web of Science ®Google Scholar
• Rowitch DH, St-Jacques B, Lee SMK, et al. Sonic hedgehog regulates proliferation and inhibits differentiation of CNS precursor cells. J Neurosci. 1999;19(20):8954–8965. doi: 10.1523/JNEUROSCI.19-20-08954.1999
   PubMed Web of Science ®Google Scholar
• Shahi MH, Lorente A, Castresana JS. Hedgehog signalling in medulloblastoma, glioblastoma and neuroblastoma. Oncol Rep. 2008;19:681–688. doi: 10.3892/or.19.3.681
   PubMed Web of Science ®Google Scholar
• Pietsch T, Waha A, Koch A, et al. Medulloblastomas of the desmoplastic variant carry mutations of the human homologue of drosophila patched. Cancer Res. 1997;57(11):2085–2088.
   PubMed Web of Science ®Google Scholar
• Raffel C, Jenkins RB, Frederick L, et al. Sporadic medulloblastomas contain PTCH mutations. Cancer Res. 1997;57(5):842–845.
   PubMed Web of Science ®Google Scholar
• Dong J, Gailani MR, Pomeroy SL, et al. Identification of PATCHED mutations in medulloblastomas by direct sequencing. Hum Mutat. 2000;16(1):89–90. doi: 10.1002/1098-1004(200007)16:1<89:AID-HUMU18>3.0.CO;2-7
   PubMedGoogle Scholar
• Taylor MD, Liu L, Raffel C, et al. Mutations in SUFU predispose to medulloblastoma. Nat Genet. 2002;31(3):306–310. doi: 10.1038/ng916
   PubMed Web of Science ®Google Scholar
• Santoni M, Burattini L, Nabissi M, et al. Essential Role of Gli Proteins in Glioblastoma Multiforme. Curr Protein Pept Sci. 2013;14(2):133–140. doi: 10.2174/1389203711314020005
   PubMed Web of Science ®Google Scholar
• Kiecker C, Niehrs C. A morphogen gradient of Wnt/β-catenin signalling regulates anteroposterior neural patterning in xenopus. Development. 2001;128(21):4189–4201. doi: 10.1242/dev.128.21.4189
   PubMed Web of Science ®Google Scholar