Abstract
Based on our previous proteomic study on Cavitating Ultrasound Aspirator (CUSA) fluid pools of Newly Diagnosed (ND) and Recurrent (R) glioblastomas (GBMs) of tumor core and periphery, as defined by 5-aminolevulinc acid (5-ALA) metabolite fluorescence, this work aims to apply a bioinformatic approach to investigate specifically into three sub-proteomes, i.e., Not Detected in Brain (NB), Cancer Related (CR) and Extracellular Vesicles (EVs) proteins following selected database classification. The study of these yet unexplored specific datasets aims to understand the high infiltration capability and relapse rate that characterizes this aggressive brain cancer. Out of the 587 proteins highly confidently identified in GBM CUSA pools, 53 proteins were classified as NB. Their gene ontology (GO) analysis showed the over-representation of blood coagulation and plasminogen activating cascade pathways, possibly compatible with Blood Brain Barrier damage in tumor disease and surgery bleeding. However, the NB group also included non-blood proteins and, specifically, histones correlated with oncogenesis. Concerning CR proteins, 159 proteins were found in the characterized GBM proteome. Their GO analysis highlighted the over-representation of many pathways, primarily glycolysis. Interestingly, while CR proteins were identified in ND-GBM exclusively in the tumor zones (fluorescence positive core and periphery zones) as predictable, conversely, in R-GBM they were unexpectedly characterized prevalently in the healthy zone (fluorescence negative tumor periphery). Relative to EVs protein classification, 60 proteins were found. EVs are over-released in tumor disease and are important in the transport of biological macromolecules. Furthermore, the presence of EVs in numerous body fluids makes them a possible low-invasive source of brain tumor biomarkers to be investigated. These results give new hints on the molecular features of GBM in trying to understand its aggressive behavior and open to more in-depth investigations to disclose potential disease biomarkers.
Highlights
Glioblastoma multiforme (GBM) is the most frequent brain tumor in adults and is classified as WHO grade IV tumor for its high grade of malignancy [1]
The lists of proteins identified in our previous study in the six pools of different tumor zones and GBM diagnosis, i.e., Newly Diagnosed (ND) CORE, A+ and A−, and R CORE, A+ and A− obtained by seven patients [1], have been further analyzed by bioinformatic approach to investigate three different specific protein classes, following the Human Protein Atlas [5] classification: (i) Proteins Not Detected in Brain (NB), which count 2908 elements; (ii) Cancer Related proteins (CR), which count 1659 elements; (iii) Extracellular Vesicles (EVs) proteins, which count 2035 elements
In the present investigation we found Apolipoprotein E (APOE) in the lists of Cancer Related and Extracellular Vesicles proteins, in both Newly Diagnosed and Recurrent pools and in all three zones
Summary
Glioblastoma multiforme (GBM) is the most frequent brain tumor in adults and is classified as WHO grade IV tumor for its high grade of malignancy [1]. In previous work we analyzed the proteomic profile of Cavitating Ultrasound Aspirator (CUSA) fluid from seven patients affected by Newly Diagnosed (ND) and Recurrent (R) GBM. The samples were collected from different zones of the tumor, according to the results obtained after administration of 5-aminolevulinic acid (A). The present investigation aims to deeply explore these proteomic data by applying a bioinformatic approach to investigate three sub-proteomes, including the Not Detected in Brain (NB), Cancer Related (CR) and Extracellular Vesicles (EVs) protein classes, following the Human Protein Atlas classification [5], and to compare their distribution inside the different tumor zones and the different GBM diagnosis, i.e., newly diagnosed tumor and relapse
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