Abstract
Background IDH-wildtype glioblastoma (GBM) is the most prevalent primary brain cancer with a 5-year survival rate below 10%. Despite combined treatment through extensive resection and radiochemotherapy, nine out of ten patients develop recurrences. The lack of targeted treatment options and reliable diagnostic markers for recurrent tumors remain major challenges.
Methods & Aims In this study, we present the proteomic characterization of tissue and serum from 55 initial GBM tumors and five matching recurrences, which we investigated for proteomic tumor subtypes and proteomic signatures associated with recurrence.
Results Primary tumors revealed four distinct subgroups through hierarchical clustering: a neuronal cluster with elevated mature neuron markers, an innate immunity cluster with increased protease expression, a mixed cluster, and a stem-cell cluster. Neurodevelopmental and inflammatory processes were identified as key factors influencing clustering, with proteolytic activity increasing relative to the degree of inflammation. An analysis comprising proteins with lower coverage confirmed and expanded this pattern. Patients in the neuronal cluster exhibited significantly longer survival compared to those in the stem-cell cluster. In a patient-matched differential expression analysis, five recurrent tumors displayed significantly altered protein expression compared to their primary counterparts, emphasizing the proteomic plasticity of recurrent tumors. Investigation of serum proteomes before and after surgery, using a depletion-based protocol, revealed highly patient-specific and stable proteome compositions, despite a notable increase in inflammation markers post-surgery. However, the levels of circulating proteolytic products matched to the proteolytic activity within the tissue and one fragment of proteolysis activated receptor 2 (PAR2) consistently dropped in abundance after removal of inflamed tumors.
Conclusion Overall, we describe a large proteomic GBM cohort. We identified distinct tumor subgroups, molecular patterns of recurrence, and matching proteomic patterns in the bloodstream, which may improve risk prediction for recurrent GBM.
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- ABC
- Ammonium Bicarbonate
- AGC
- Automatic Gain Control
- ALB
- Albumin
- BCA
- Bicinchonic Acid Assay
- BLBP
- Fatty acid-binding protein, brain
- CAA
- 2-Chloroacetamide
- CD163
- Scavenger receptor cysteine-rich type 1 protein M130
- CPHM
- Cox Proportional Hazards Model
- CT
- Computer Tomography
- CTSG
- Cathepsin G
- DIA
- Data Independent Acquisition
- EDTA
- Ethylenediaminetetraacetic acid
- EGFR
- Epidermal growth factor receptor
- ENO2
- Gamma-enolase
- FCN1
- Ficolin-1
- FDR
- False Discovery Rate
- GBM
- Glioblastoma Multiforme
- GFAP
- Glial fibrillary acidic protein
- HCD
- Higher-energy collisional dissociation
- HEPES
- 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HPLC
- High Pressure Liquid Chromatography
- HR
- Hazard Ratio
- HRAS
- GTPase HRas
- IDH
- Isocitrate Dehydrogenase
- IQR
- Inter-Quartile Range
- iRTs
- Indexed Retention Time Standards
- KRAS
- GTPase KRas
- L1CAM
- Neural cell adhesion molecule L1
- LC-MS/MS
- Liquid-Chromatography Tandem Mass-Spectrometry
- LFQ
- Label-Free Quantification
- LPA
- Apolipoprotein (a)
- LTQ
- Linear Quadrupole Ion Trap Mass-Spectrometer
- LUM
- Lumican
- LysC
- Lysyl Endopeptidase C
- LYZ
- Lysozyme C
- MAP2
- Microtubule-associated protein 2
- MARS
- Multi Affinity Removal System
- MNG
- Meningioma
- MRC1
- Macrophage mannose receptor 1
- MRI
- Magnetic Resonance Imaging
- mRNA
- Messenger Ribonucleic Acid
- mTOR
- Mammalian Target of Rapamycine
- NCAM1
- Neural cell adhesion molecule 1
- NES
- Nestin
- nLC
- Nanoflow Liquid Chromatography
- NOTCH1
- Neurogenic locus notch homolog protein 1
- NTRK2
- BDNF/NT-3 growth factors receptor
- NTRK3
- NT-3 growth factor receptor
- PAR2
- Proteolysis Activated Receptor 2
- PCA
- Principal Component Analysis
- PLS-DA
- Partial-Least Squares Discriminant Analysis
- PMSF
- Phenylmethylsulfonyl Fluoride
- postOP
- Collection after Surgery
- preOP
- Collection before Surgery
- PLA2G7
- Platelet-activating factor acetylhydrolase
- PTEN
- Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
- RTN4
- Reticulon-4
- SDS
- Sodium Dodecyl Sulfate
- SOX10
- Transcription factor SOX-10
- SOX2
- Transcription factor SOX-2
- SP3
- Single-Pot Solid-Phase-Enhanced Sample Preparation
- SYP
- Synaptophysin
- SYT
- Synaptotagmin-1
- TCEP
- Tris(2-carboxyethyl)phosphine hydrochloride
- TFA
- Trifluoroacetic acid
- TMZ
- Temozolomide
- UMAP
- Uniform Manifold Approximation and Projection for Dimension Reduction
- VNN1
- Pantetheinase
- WHO
- World Health Organization
- ZEB1
- Zinc finger E-box-binding homeobox 1