The emergence of omics technologies over the last decade has helped in advancement of research and our understanding of complex diseases like brain cancers. However, barring genomics, no other omics technology has been able to find utility in clinical settings. The recent advancements in mass spectrometry instrumentation have resulted in proteomics technologies becoming more sensitive and reliable. Targeted proteomics, a relatively new branch of mass spectrometry-based proteomics has shown immense potential in addressing the shortcomings of the standard molecular biology-based techniques like Western blotting and Immunohistochemistry. In this study we demonstrate the utility of Multiple reaction monitoring (MRM), a targeted proteomics approach, in quantifying peptides from proteins like Apolipoprotein A1 (APOA1), Apolipoprotein E (APOE), Prostaglandin H2 D-Isomerase (PTGDS), Vitronectin (VTN) and Complement C3 (C3) in cerebrospinal fluid (CSF) collected from Glioma and Meningioma patients. Additionally, we also report transitions for peptides from proteins – Vimentin (VIM), Cystatin-C (CST3) and Clusterin (CLU) in surgically resected Meningioma tissues; Annexin A1 (ANXA1), Superoxide dismutase (SOD2) and VIM in surgically resected Glioma tissues; and Microtubule associated protein-2 (MAP-2), Splicing factor 3B subunit 2 (SF3B2) and VIM in surgically resected Medulloblastoma tissues. To our knowledge, this is the first study reporting the use of MRM to validate proteins from three types of brain malignancies and two different bio-specimens. Future studies involving a large cohort of samples aimed at accurately detecting and quantifying peptides of proteins with roles in brain malignancies could potentially result in a panel of proteins showing ability to classify and grade tumors. Successful application of these techniques could ultimately offer alternative strategies with increased accuracy, sensitivity and lower turnaround time making them translatable to the clinics.

Exosomes are directly involved in governing physiological and pathological processes of an organism by horizontal transfer of functional molecules (proteins, microRNA, etc.) from producing to receiving cells. We explored the relationship of proteins from plasma exosomes, and exosomes from the total blood of healthy females (HFs) and breast cancer patients (BCPs), with crucial steps of tumor progression: EMT, cell proliferation, invasion, cell migration, stimulation of angiogenesis, and immune response. A proteomic analysis of exosomes isolated from samples using ultrafiltration and ultracentrifugation was performed. Their nature has been verified using cryo-electron microscopy and flow cytometry. Bioinformatics analysis showed that 84% of common exosomal proteins were of cytoplasmic and vesicle origin. They perform functions of protein binding and signaling receptor binding, and facilitated the processes of the regulated exocytosis and vesicle-mediated transport. Half of the identified exosomal proteins from blood of HFs and BCPs are involved in crucial steps of the tumor progression: EMT, cell proliferation, invasion, cell migration stimulation of angiogenesis, and immune response. Moreover, we found that protein cargo of exosomes from HF total blood was enriched with proteins inhibiting EMT, cell migration, and invasion. Tumor diagnostic/prognostic protein markers accounted for 47% of the total composition of cell-surface-associated exosomes (calculated as the difference between the total blood exosomes and plasma exosomes) from BCP blood. Breast cancer-associated proteins were equally represented in the blood cell-surface-associated exosomes and in the plasma exosomes from BCPs. However, hyper-expressed proteins predominate in the blood cell-surface-associated exosomes as compared to the plasma exosomes (64 vs. 14%). Using breast cancer proteins data from the Human Protein Atlas (HPA) (www.proteinatlas.org/), three favorable (SERPINA1, KRT6B, and SOCS3), and one unfavorable (IGF2R) prognostic protein markers were found in the BCP total blood exosomes. Identified exosomal proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or novel therapeutic targets.