Table 3.

Summary of studies employing proteomics in GB research.

Application	Aim	Tissue Type /Cell Line	Technique	Key Proteins	Key Pathways	Principle Insights	Reference
Pharmacoproteomics	To understand the extensive regulation of glioma metabolism in response to Delta-24-RGD (an E1A mutant oncolytic adenovirus) infection, by performing a cell-wide study of cytosolic, nuclear, and secreted proteomes during the early time course of the infection.	U87	Using iTRAQ, a shotgun comparative proteomic analysis of cytosolic fractions	Cytosolic proteins: Serine hydroxymethyltransferase, mitochondrial lactotransferrin Alpha-2-macroglobulin Proliferating cell nuclear antigen etc. Nuclear proteins: Programmed cell death protein 6 Replication factor C subunit 2 Annexin A2 Ribosome-binding protein 1 etc.	Proteostasis pathway Protein kinase C, ERK1/2, and p38 MAPK pathways	The findings assist in understanding the methods through which Delta-24-RGD exploits glioma proteome organization. Further exploration of this proteomic resource may lead to the development of complementary adenoviral-based vectors with increased specificity and efficacy against glioma.	[135]
Unraveling GB pathophysiology	To define the role of cat eye syndrome critical region protein 1 (CECR1) in tumor associated macrophages (TAMs) through a proteomic investigation of siRNA-mediated CECR1 silencing in THP-1-derived macrophages co-cultured with or without glial tumor cells.	U87 THP-1 cells (human monocytic cell line)	Mass spectrometry	ISG15 HLA-A HLA-B HLA-C TAP1 TAP2 TAPBP TIMP-1 WDFY1 SEPT7 S100A9 PLAU LAT2	MHC I antigen presenting pathway, Phagosome maturation, caveolin-mediated endocytosis, and type I interferon signaling pathways	CECR1-mediated molecular pathways and essential molecules operate in macrophages and glial TAMs (Tyro3, Axl, Mer, family of receptor tyrosine kinases). The proteome dataset might be used to create novel therapeutic targets for future immunotherapy research in the treatment of malignant (glial) cancers and autoimmune illnesses.	[136]
Unraveling GB pathophysiology	The constitutively active epidermal growth factor receptor (EGFRvIII) is an oncogenic factor that fuels GB aggressiveness and is ascribable to the release of extracellular vesicles (EVs). Researchers aimed to examine the effect of this oncogene on the profile of glioma EVs.	U373 U373vIII	MS	CD44/BSG TSPAN8 CD151 CD81 CD9 SDCB1 Actin, GAPDH CD44 ITGA6, ITGB4 TGFB1 Laminins, collagens	Vesiculation pathways	CD44/BSG were co-localized in cellular filopodia and EVs generated by EGFRvIII-expressing cells were double positive for these proteins. Oncogenic EGFRvIII alters the proteome and uptake of EVs related to GB.	[137]
Developmental therapeutics	To perform a comparison of the ligandomes of GSC and patient samples with the goal of discovering GSC-associated targets that are also present on primary patient malignancies.	Primary GB Peripheral blood mononuclear cells (PBMC) GSC cell lines: GS-2 GS-5 GS-9	LC–MS/MS	Cancer testis antigen (CTA) SERPINE1 FABP7 PTGFRN ALFPERITV (ATAT1) RLAPFVYLL (HEPACAM) SILDIVTKV (RFTN2)	Not available	The study identified a novel panel of T cell antigens characterized by the exclusive identification of malignant specimens, a substantial prevalence of presentation, and presence on the GSC compartment by mapping the HLA peptidome of glioblastoma and GSC. Epitopes of functional CD8 T-cell responses were identified, making them excellent candidates for immunotherapy.	[138]
Biomarker discovery	To investigate, in a cellular rat model, the line GL261.	3T3-L1 adipocyte cell line GL-261 murine model	MALDI-TOF-MS	Arbonic anhydrase Aldose reductase Endocan HGF IGF-I IL-6 IL-11 LIF PAI-1 SerpinE1 TNF-α TIMP-1 VEGF	Not available	STI1, hnRNPs, and PGK1, overexpressed otherwise in cancer, were under expressed. Carbonic anhydrase and aldose reductase, both of which play significant roles in inflammation, and cancer metabolism, are also reduced in glioma cells cultured in an adipokine-enriched environment, displaying a paradoxical association of a protective function between fat and cancer.	[139]
Biomarker discovery	To utilize SWATH-MS and quantitative targeted absolute proteomics to find plasma biomarker candidates for GB patients (QTAP).	Cyst fluid samples of IDH wildtype GB Non-cancerous brain tissue samples	SWATH-MS LC–MS/MS	LRG1 C9 CRP SERPINA3 APOB GSN IGHA1 APOA4	Not detected	To evaluate the links between biomarker candidates and GB Biology, the study looked at associations between biomarker candidate plasma concentrations and clinical presentation (tumor size, overall survival time, etc.) in patients. LRG1, CRP, and C9 plasma concentrations all revealed strong positive relationships with tumor growth.	[140]
Biomarker discovery	To identify and describe the effective biomarkers present in the small extracellular vesicles (sEVs) to improve GB diagnosis, and ultimately, patient prognosis.	Blood samples from GB patients and controls	MS, MS/MS	VWF FCGBP C3 PROS1 SERPINA1	B-cell receptor signaling pathway Pathways involved in complement activation, innate immune response, and platelet degranulation	Overall, the development of a non-invasive liquid biopsy method for the discovery of valuable biomarkers that could considerably enhance GB diagnosis and, as a result, patients’ prognosis, and quality of life, is promoted through this study.	[141]
Developmental therapeutics	To study GB- associated surfaceome by comparing it to the surfaceome of astrocyte cell lines in order to find new GB-specific targets.	NCH82 U-87 MG	MALDI-mass spectrometry	Plaur B41 alpha chain (HLA-b) A-24 alpha chain (HLA-a) DP beta 1 chain (hla-dpb1). CADM3 CADM4 NRCAM	Cell contact, cell adhesion, vascularization, and proliferation pathways	11 distinct potential GB targets were discovered, including 5 altered proteins such as MHC I, CYBA, EGFR, and RELL1.	[142]
Optimize GB datasets	To boost the translational importance of the Q-Cell datasets and to create a platform for academics to conduct rigorous preclinical neuro-oncology research.	Primary GB characterized cell line (Q-Cell)	LC–MS	BAH1 GSN JK2 MMK1 MN1 NNMT PLP2 PRDX6 RN1 SB2b SB2 SOD2 SERPINE1 WK1	PI3K and mTOR signaling pathways TCA cycle, NFKB, and MAPK signaling.	In-depth proteomic characterization of the GB Q-Cell resource was obtained, serving as a dataset for future biological and preclinical research.	[143]
Establishing research methodology	To develop methods to analyze the proteome of small extracellular vesicles (sEVs) from low serum volume that is obtained from mice, to perform a longitudinal analysis of disease models.	Adult C57BL/6J mice murine glioma GL261 cell line	LC–MS/MS	Tetraspanins integrins Sdcbp Hspa8 Cd9 Itga2 Anxa4, Anxa5, Anxa7 Vamp8 Lrp1 Cpn1 Mhy9 Tln1 Tfrc, CD71 Apoc4	PI3K/AKT pathway	The methodology allowed for the identification and quantification of 274 protein groups. The longitudinal study discovered 25 altered proteins in GB serum sEVs, including proteins previously linked to GB development and metastasis.	[144]
Identification of resistance mechanism	To investigate the cytoplasmic proteome of U87 GB cells treated with TMZ, using bioinformatic approaches to thoroughly evaluate the raw data.	U87	Liquid chromatography–electrospray ionization–tandem mass spectrometry (LC–ESI–MS/MS)	DHX9 HNRNPR RPL3 HNRNPA3 SF1 DDX5 EIF5B BTF RPL8	Thyroid hormone, p53 and the PI3K-Akt signaling pathways Regulation of actin cytoskeleton	Dysregulation of spliceosome-related proteins SF-1, DDX5, and HNRNPR may all contribute to a disruption in DHX9 synthesis, eventually leading to GB TMZ resistance.	[145]
Morphoproteomics	To create a spatially conserved proteomic atlas of GB by meticulous microdissection and LC–MS/MS profiling of the traditional histomorphologic characteristics of the malignancy.	MYC-enriched cell lines (3-CI-AHPC, CD-437)	LC–MS/MS	Immunoglobulin CD276 (B7-H3) AKAP12 PTPRZ1	Hypoxia pathway axis	Various glioblastoma locations may be divided into subpopulations in which glioma cells favor migration and infiltration above proliferation and growth.	[146]