Proteomic analysis of gliomas

The Big Picture of Glioblastoma Malignancy: A Meta-Analysis of Glioblastoma Proteomics to Identify Altered Biological Pathways

Glioblastoma is a highly malignant cancer with no effective treatment. It is vital to elucidate the mechanisms which drive glioblastoma in order to identify therapeutic targets. The differences in protein expression between glioblastoma, grade I-III glioma, and normal brain tissue reflect the functional alterations driving malignancy. However, proteomic analysis of glioblastoma has been hampered by the heterogeneity of glioblastoma and the variety of methodology used in its study. To reduce these inconsistencies, we performed a meta-analysis of the literature published since 2015, including 14 datasets from eight papers comparing the whole proteome of glioblastoma to normal brain or grade I-III glioma. We found that 154 proteins were commonly upregulated and 116 proteins were commonly downregulated in glioblastoma compared to normal brain. Meanwhile, 240 proteins were commonly upregulated and 125 proteins were commonly downregulated in glioblastoma compared to grade I-III glioma. Functional enrichment analysis revealed upregulation of proteins involved in mRNA splicing and the immune system and downregulation of proteins involved in synaptic signaling and glucose and glutamine metabolism. The identification of these altered biological pathways provides a basis for deeper investigation in the pursuit of an effective treatment for glioblastoma.

Rapid Proteomic Profiling by MALDI-TOF Mass Spectrometry for Better Brain Tumor Classification

PURPOSE

Glioblastoma is one of the most aggressive primary brain cancers. The precise grading of tumors is important to adopt the best follow-up treatment but complementary methods to histopathological diagnosis still lack in achieving an unbiased and reliable classification.

EXPERIMENTAL DESIGN

To progress in the field, a rapid Matrix Assisted Laser Desorption Ionization - Time of Flight Mass spectrometry (MALDI-TOF MS) protocole, devised for the identification and taxonomic classification of microorganisms and based on the analysis of whole cell extracts, was applied to glioma cell lines.

RESULTS

The analysis of different human glioblastoma cell lines permitted to identify distinct proteomic profiles thus demonstrating the ability of MALDI-TOF to distinguish different malignant cell types.

CONCLUSIONS AND CLINICAL RELEVANCE

In the study, the authors showed the ability of MALDI-TOF profiling to discriminate glioblastoma cell lines, demonstrating that this technique could be used in complement to histological tumor classification. The proposed procedure is rapid and inexpensive and could be used to improve brain tumors classification and help propose a personalized and more efficient treatment.

Circulating Tumor Biomarkers in Meningiomas Reveal a Signature of Equilibrium Between Tumor Growth and Immune Modulation

Meningiomas are primary central nervous system (CNS) tumors that originate from the arachnoid cells of the meninges. Recurrence occurs in higher grade meningiomas and a small subset of Grade I meningiomas with benign histology. Currently, there are no established circulating tumor markers which can be used for diagnostic and prognostic purposes in a non-invasive way for meningiomas. Here, we aimed to identify potential biomarkers of meningioma in patient sera. For this purpose, we collected preoperative (n = 30) serum samples from the meningioma patients classified as Grade I (n = 23), Grade II (n = 4), or Grade III (n = 3). We used a high-throughput, multiplex immunoassay cancer panel comprising of 92 cancer-related protein biomarkers to explore the serum protein profiles of meningioma patients. We detected 14 differentially expressed proteins in the sera of the Grade I meningioma patients in comparison to the age- and gender-matched control subjects (n = 12). Compared to the control group, Grade I meningioma patients showed increased serum levels of amphiregulin (AREG), CCL24, CD69, prolactin, EGF, HB-EGF, caspase-3, and decreased levels of VEGFD, TGF-α, E-Selectin, BAFF, IL-12, CCL9, and GH. For validation studies, we utilized an independent set of meningioma tumor tissue samples (Grade I, n = 20; Grade II, n = 10; Grade III, n = 6), and found that the expressions of amphiregulin and Caspase3 are significantly increased in all grades of meningiomas either at the transcriptional or protein level, respectively. In contrast, the gene expression of VEGF-D was significantly lower in Grade I meningioma tissue samples. Taken together, our study identifies a meningioma-specific protein signature in blood circulation of meningioma patients and highlights the importance of equilibrium between tumor-promoting factors and anti-tumor immunity.

Proteomics analysis of human brain glial cell proteome by 2D gel

INTRODUCTION

Proteomics is increasingly employed in both neurological and oncological research, and applied widely in every area of neuroscience research including brain cancer. Astrocytomas are the most common glioma and can occur in most parts of the brain and occasionally in the spinal cord. Patients with high-grade astrocytomas have a life expectancy of <1 year even after surgery, chemotherapy, and radiotherapy.

MATERIALS AND METHODS

We extracted proteins from tumors and normal brain tissues and then evaluated the protein purity by Bradford test and spectrophotometry method. In this study, we separated proteins by the two-dimensional (2DG) gel electrophoresis method, and the spots were analyzed and compared using statistical data.

RESULTS

On each analytical 2D gel, an average of 800 spots was observed. In this study, 164 spots exhibited up-regulation of expression level, whereas the remaining 179 spots decreased in astrocytoma tumor relative to normal tissue. RESULTS demonstrate that functional clustering and principal component analysis (PCA) has considerable merits in aiding the interpretation of proteomic data. Proteomics is a powerful tool in identifying multiple proteins that are altered following a neuropharmacological intervention in a disease of the central nervous system (CNS).

CONCLUSION

2-D gel and cluster analysis have important roles in the diagnostic management of astrocytoma patients, providing insight into tumor biology. The application of proteomics to CNS research has invariably been very successful in yielding large amounts of data.

Quantitative proteomic analysis of meningiomas for the identification of surrogate protein markers

Meningiomas are the most common non-glial tumors of the brain and spine. Pathophysiology and definite histological grading of meningiomas are frequently found to be deceptive due to their unusual morphological features and locations. Here for the first time we report a comprehensive serum proteomic analysis of different grades of meningiomas by using multiple quantitative proteomic and immunoassay-based approaches to obtain mechanistic insights about disease pathogenesis and identify grade specific protein signatures. In silico functional analysis revealed modulation of different vital physiological pathways including complement and coagulation cascades, metabolism of lipids and lipoproteins, immune signaling, cell growth and apoptosis and integrin signaling in meningiomas. ROC curve analysis demonstrated apolipoprotein E and A-I and hemopexin as efficient predictors for meningiomas. Identified proteins like vimentin, alpha-2-macroglobulin, apolipoprotein B and A-I and antithrombin-III, which exhibited a sequential increase in different malignancy grades of meningiomas, could serve as potential predictive markers.

Identification of novel tumor-associated cell surface sialoglycoproteins in human glioblastoma tumors using quantitative proteomics

Glioblastoma multiform (GBM) remains clinical indication with significant “unmet medical need”. Innovative new therapy to eliminate residual tumor cells and prevent tumor recurrences is critically needed for this deadly disease. A major challenge of GBM research has been the identification of novel molecular therapeutic targets and accurate diagnostic/prognostic biomarkers. Many of the current clinical therapeutic targets of immunotoxins and ligand-directed toxins for high-grade glioma (HGG) cells are surface sialylated glycoproteins. Therefore, methods that systematically and quantitatively analyze cell surface sialoglycoproteins in human clinical tumor samples would be useful for the identification of potential diagnostic markers and therapeutic targets for malignant gliomas. In this study, we used the bioorthogonal chemical reporter strategy (BOCR) in combination with label-free quantitative mass spectrometry (LFQ-MS) to characterize and accurately quantify the individual cell surface sialoproteome in human GBM tissues, in fetal, adult human astrocytes, and in human neural progenitor cells (NPCs). We identified and quantified a total of 843 proteins, including 801 glycoproteins. Among the 843 proteins, 606 (72%) are known cell surface or secreted glycoproteins, including 156 CD-antigens, all major classes of cell surface receptor proteins, transporters, and adhesion proteins. Our findings identified several known as well as new cell surface antigens whose expression is predominantly restricted to human GBM tumors as confirmed by microarray transcription profiling, quantitative RT-PCR and immunohistochemical staining. This report presents the comprehensive identification of new biomarkers and therapeutic targets for the treatment of malignant gliomas using quantitative sialoglycoproteomics with clinically relevant, patient derived primary glioma cells.

Proteomic analysis of glioma chemoresistance

Malignant glioma is the most common and destructive form of primary brain tumor. Along with surgery and radiation, chemotherapy remains as the major treatment modality. The emergence of drug resistance, however, often leads to a therapeutic failure in the treatment of glioma, precluding long-term survival of the patients. A proteomic approach has recently been adapted for the mechanistic analysis of glioma drug resistance. The proteomic analysis of drug-resistant glioma led to the discovery of novel biomarkers that can be used for the prognosis of glioma as well as for monitoring the drug response or resistance of glioma. These proteomics-based biomarkers can also be a druggable target that one can exploit for successful glioma chemotherapy. In this review, recent reports on proteomic analysis of glioma from the perspective of chemoresistance are discussed with a focus on the proteome profiles of glioma cells that are resistant to the alkylating agent, 1, 3-bis (2-chloroethyl)-1-nitrosourea (BCNU), as a prime example. Among numerous proteins that were up- or down-regulated in drug-resistant glioma cells, lipocalin 2 (LCN2) and integrin β3 (ITGB3) were identified as key proteins that determine the survival and death of glioma cells. LCN2, ITGB3, and other proteins identified by proteomic analysis could be utilized to overcome glioma chemoresistance.

Over-expression of cofilin-1 and phosphoglycerate kinase 1 in astrocytomas involved in pathogenesis of radioresistance

INTRODUCTION

Astrocytoma is among the most common intracranial tumors and radiotherapy is typically used after its resection. One of the outstanding problems encountered in the treatment is radioresistance. The lack of efficient biomarkers for evaluating the radiosensitivity of glioma precludes advances in treatment of astrocytoma and remains the most fatal cancer.

METHODS

To identify potential biomarkers for assessing the radioresistance of astrocytomas, the following study investigated the proteome of astrocytoma in surgical samples from 15 typical patients. The patients were divided into 2 groups: radioresistant vs. radiosensitive (controls). Proteome was assessed using two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS). Western blot was adopted to confirm the differential expression of proteins.

RESULTS

A total of 36 proteins were expressed differently between the 2 groups, represented by cofilin-1 and phosphoglycerate kinase 1 (PGK1), which up-regulated significantly in radioresistant astrocytomas though there was no obvious morphological change of tumors. Western blot analysis revealed elevated levels of protein extracts in radioresistant astrocytomas compared with the radiosensitive group.

CONCLUSIONS

The results indicated cofilin-1 enhances the motility of tumor cells which is important invasive potential of malignancy. PGK1 is metabolic enzyme and seems to be correlated with the negative prognosis following radiotherapy. Thus, cofilin-1 and PGK1 might be involved in the radioresistant phenotype and are potential biomarkers for developing better therapeutic methods.

Quantitative proteomic Isotope-Coded Protein Label (ICPL) analysis reveals alteration of several functional processes in the glioblastoma

Glioblastoma (GB), the most frequent primary tumor of the central nervous system, remains one of the most lethal human cancers despite intensive researches. Current paradigm in the study of GB has been focused on inter-patient variability and on trying to isolate new classification elements or prognostic factors. Here, using ICPL, a technique for protein relative quantification by mass spectrometry, we investigated protein expression between the four regions of GB on clinically relevant biopsies from 5 patients. We identified 584 non-redundant proteins and 31 proteins were found to be up-regulated in the tumor region compared to the peri-tumoral brain tissue, among which, 24 proteins belong to an interaction network linked to 4 biological processes. The core of this network is mainly constituted of interactions between beta-actin (ACTB) with heat shock proteins (HSP90AA1, HSPA8) and 14-3-3 proteins (YWHAZ, YWHAG, YWHAB). A cluster of three isoforms of the sodium pump α-subunit (ATP1A1, ATP1A2, ATP1A3) was also identified outside this network. The differential expression observed for ACTB and 14-3-3γ was further validated by western blot and/or immunohistochemistry. Our study confirms the identity of previously proposed molecular targets, highlights several functional processes altered in GB such as energy metabolism and synaptic transmission and could thus provide added value to new therapeutic trails.

Differential analysis of glioblastoma multiforme proteome by a 2D-DIGE approach

Background

Genomics, transcriptomics and proteomics of glioblastoma multiforme (GBM) have recently emerged as possible tools to discover therapeutic targets and biomarkers for new therapies including immunotherapy. It is well known that macroscopically complete surgical excision, radiotherapy and chemotherapy have therapeutic limitations to improve survival in these patients. In this study, we used a differential proteomic-based technique (2D-Difference Gel Electrophoresis) coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to identify proteins that may serve as brain tumor antigens in new therapeutic assays. Five samples of patients presenting a GBM and five samples of microscopically normal brain tissues derived from brain epileptic surgery specimen were labeled and run in 2D-PAGE (Two-Dimensional Polyacrylamide Gel Electrophoresis) with an internal pool sample on each gel. Five gels were matched and compared with DIA (Difference In-gel Analysis) software. Differential spots were picked, in-gel digested and peptide mass fingerprints were obtained.

Results

From 51 protein-spots significantly up-regulated in GBM samples, mass spectrometry (MS) identified twenty-two proteins. The differential expression of a selected protein set was first validated by western-blotting, then tested on large cohorts of GBM specimens and non-tumor tissues, using immunohistochemistry and real-time RT-PCR.

Conclusions

Our results confirmed the importance of previously described proteins in glioma pathology and their potential usefulness as biological markers but also revealed some new interesting targets for future therapies.

Serum angiogenic profile of patients with glioblastoma identifies distinct tumor subtypes and shows that TIMP-1 is a prognostic factor

Angiogenesis plays a key role in glioblastoma biology and antiangiogenic agents are under clinical investigation with promising results. However, the angiogenic profiles of patients with glioblastoma and their clinical significance are not well understood. Here we characterize the serum angiogenic profile of patients with glioblastoma, and examine the prognostic significance of individual angiogenic factors. Serum samples from 36 patients with glioblastoma were collected on admission and simultaneously assayed for 48 angiogenic factors using protein microarrays. The data were analyzed using hierarchical cluster analysis. Vessel morphology was assessed histologically after immunostaining for the pan-endothelial marker CD31. Tumor samples were also immunostained for tissue inhibitor of metalloproteinase-1 (TIMP-1). Cluster analysis of the serum angiogenic profiles revealed 2 distinct subtypes of glioblastoma. The 2 subtypes had markedly different tumor microvessel densities. A low serum level of TIMP-1 was associated with significantly longer survival independent of patient age, performance status, or treatment. The serum angiogenic profile in patients with glioblastoma mirrors tumor biology and has prognostic value. Our data suggest the serum TIMP-1 level as an independent predictor of survival.

Correlations between in vivo (1)H MRS and ex vivo (1)H HRMAS metabolite measurements in adult human gliomas

PURPOSE

To assess how accurately ex vivo high-resolution magic angle spinning (HRMAS) proton magnetic resonance spectroscopy ((1)H MRS) from small biopsy tissues relate to in vivo (1)H MRS (from larger tumor volumes) in human astrocytomas.

MATERIALS AND METHODS

In vivo (PRESS, TE = 30 msec) and ex vivo (presaturation) (1)H spectra of 17 human astrocytomas (4 grade II, 1 grade III and 12 glioblastomas) were quantified using LCModel. Concentrations of 11 metabolites and 2 lipid/macromolecules were retrospectively compared, with histogram analysis of the in vivo MRI data used to evaluate tumor heterogeneity.

RESULTS

For homogeneous-appearing tumors, significant correlations were found between in vivo and ex vivo (1)H MRS concentrations of those metabolites known to be metabolically stable in postmortem tissues (eg, creatine, myo-inositol, total cholines, and the approximately 1.3 and 0.9 ppm lipids). Anaerobic glycolysis during biopsy surgical removal depletes the tissue of glucose, increasing alanine and lactate, and resulted in no correlation between these in vivo and ex vivo metabolite concentrations.

CONCLUSION

Within defined limitations, ex vivo astrocytoma biopsy HRMAS (1)H spectra have similar metabolic profiles to that obtained in vivo and therefore detailed ex vivo characterization of glioma biopsies can directly relate to the original tumor.

Glioma pathophysiology: insights emerging from proteomics

Proteomics is increasingly employed in both neurological and oncological research to provide insight into the molecular basis of disease but rarely has a coherent, novel pathophysiological insight emerged. Gliomas account for >50% of adult primary intracranial tumors, with malignant gliomas (anaplastic astrocytomas and glioblastoma multiforme) being the most common. In glioma, the application of proteomic technology has identified altered protein expression but without consistency of these alterations or their biological significance being established. A systematic review of multiple independent proteomic analyses of glioma has demonstrated alterations of 99 different proteins. Importantly 10 of the 99 proteins found differentially expressed in glioma [PHB, Hsp20, serum albumin, epidermal growth factor receptor (EGFR), EA-15, RhoGDI, APOA1, GFAP, HSP70, PDIA3] were identified in multiple publications. An assessment of protein-protein interactions between these proteins compiled using novel web-based technology, revealed a robust and cohesive network for glioblastoma. The protein network discovered (containing TP53 and RB1 at its core) compliments recent findings in genomic studies of malignant glioma. The novel perspective provided by network analysis indicates that the potential of this technology to explore crucial aspects of glioma pathophysiology can now be realized but only if the conceptual and technical limitations highlighted in this review are addressed.

Elucidating novel mechanisms of brain injury following subarachnoid hemorrhage: an emerging role for neuroproteomics

Subarachnoid hemorrhage (SAH) is a devastating neurological injury associated with significant patient morbidity and death. Since the first demonstration of cerebral vasospasm nearly 60 years ago, the preponderance of research has focused on strategies to limit arterial narrowing and delayed cerebral ischemia following SAH. However, recent clinical and preclinical data indicate a functional dissociation between cerebral vasospasm and neurological outcome, signaling the need for a paradigm shift in the study of brain injury following SAH. Early brain injury may contribute to poor outcome and early death following SAH. However, elucidation of the complex cellular mechanisms underlying early brain injury remains a major challenge. The advent of modern neuroproteomics has rapidly advanced scientific discovery by allowing proteome-wide screening in an objective, nonbiased manner, providing novel mechanisms of brain physiology and injury. In the context of neurosurgery, proteomic analysis of patient-derived CSF will permit the identification of biomarkers and/or novel drug targets that may not be intuitively linked with any particular disease. In the present report, the authors discuss the utility of neuroproteomics with a focus on the roles for this technology in understanding SAH. The authors also provide data from our laboratory that identifies high-mobility group box protein-1 as a potential biomarker of neurological outcome following SAH in humans.

Recruitment difficulties in brain tumour patients cause participation bias: findings from a neuropsychological study of adult inpatients with supratentorial intracranial tumours

PURPOSE

Patients who participate in questionnaire surveys, clinical studies and clinical trials can be different from patients who do not participate. The occurrence and direction of this response, participation or ascertainment bias is unpredictable, and can harm the external validity of medical research.

METHODS

We compared the characteristics of patients with intracranial tumours who participated in a psychological study of inspection time with the characteristics of patients who did not participate for a number of reasons.

RESULTS

Of 178 newly diagnosed adults with intracranial tumours, 136 (76%) were eligible, of whom 76 (56%) participated and 34 (25%) declined. There were no significant differences in terms of age and sex of the patients who participated and those who declined. When the participation group was combined with those who were ineligible and those who declined, the majority of patients in the combined cohort (n = 152) had a WHO grade III or IV glioma (high-grade glioma) (48.0%), and only 13.2% had a WHO grade I or II glioma (low-grade glioma). However, only 38.2% of those who participated had a WHO grade III or IV glioma, and 23.7% had a WHO grade I or II glioma. Comparisons of the participation vs. ineligible and declined groups revealed there was a significant difference (p = 0.002) between the ratio of high-grade to low-grade gliomas in the total and recruited cohorts. Comparisons of only the participation vs. declined groups approached significance (p = 0.051). WHO grade III and IV glioma patients were under-represented, and WHO grade I or II glioma patients were over-represented in the study group.

CONCLUSIONS

Noninterventional, non-therapeutic applied neuropsychological studies in neuro-oncology are susceptible to bias since the spectrum of neuropathologies in recruited patients can be significantly different from that of the total cohort. These data could help anticipate recruitment rates for applied neuropsychological studies in clinical neuro-oncology and may help anticipate likely selection biases amongst those who participate.

The utility of functional interaction and cluster analysis in CNS proteomics

Proteomic studies offer enormous potential for gaining insight into cellular dynamics and disease processes. An immediate challenge for enhancing the utility of proteomics in translational research lies in methods of handling and interpreting the large datasets generated. Publications rarely extend beyond lists of proteins, putatively altered derived from basic statistics. Here we describe two additional distinct approaches (with particular strengths and limitations) that will enhance the analysis of proteomic datasets. Arithmetic and functional cluster analyses have been performed on proteins found differentially regulated in human glioma. These two approaches highlight (i) subgroups of proteins that may be co-regulated and play a role in glioma pathophysiology, and (ii) functional protein interactions that may improve comprehension of the biological mechanisms involved. A coherent proteomic strategy which involves both arithmetic and functional clustering, (together with careful consideration of conceptual limitations), is imperative for quantitative proteomics to deliver and advance the biological understanding of disease of the CNS. A strategy which combines arithmetic analysis and bioinformatics of protein-protein interactions is both generally applicable and will facilitate the interpretation of proteomic data.

Molecular profiling in glioblastoma: prelude to personalized treatment

The purpose of this review is to provide an up-to-date summary of the current knowledge and understanding of the molecular alterations and pathways relevant to the clinical outcome of glioblastoma patients and their potential use in designing personalized treatment for these patients. This article also discusses the potential of molecular profiling as a diagnostic modality, possible therapeutic implications of MGMT promoter methylation, the targeted inhibition of angiogenesis, and assessment of the tumor's molecular background with respect to PI3K/AKT pathway activation and associated molecules (EGFR, EGFRvIII, PTEN).

Multifarious proteomic signatures and regional heterogeneity in glioblastomas

To investigate the underlying intratumoral diversity of molecular profiles in glioblastomas, a proteomic approach was introduced to compare samples from regions of different histological grade. Using two-dimensional gel electrophoresis (2DE) with matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), we compared prospectively collected tissue samples of different histological grade areas of three glioblastoma patients. Consistent results showing relatively high expression of ubiquitin carboxyl-terminal esterase L1 in low-histological-grade areas (Grade 2 > Grades 3 and 4) and high expression of transthyretin in high-histological-grade areas (Grade 2 < Grades 3 and 4) were demonstrated. These results were confirmed by western blot (WB) analysis and immunohistochemical staining. This study provided the evidence of multifarious proteomic signatures according to regional and histological heterogeneity in glioblastomas.