Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors

• DOI: 10.3389/fonc.2021.548243
• Publication Date: 2021-05-14T14:37:45Z
• Authors: Saicharan Ghantasala; Medha Gayathri J....; Deeptarup Biswas; Nikita Gahoi; Shuvolina Mukherjee; Manubhai KP; Mehar Un Nissa; Alisha Srivastava; Sridhar Epari; Prakash Shetty; Aliasgar Moiyadi; Sanjeeva Srivastava
• Keywords: Proteomics; FOS: Computer and information sciences; targeted proteomics; multiple reaction monitoring; S100 Proteins: Structure, Function, and Pathology; Protein Identification; Proteome; Bioinformatics; Tandem mass spectrometry; Omics; Apoptosis; Cancer research; Biochemistry; Gene; Mass Spectrometry; Computational biology; 03 medical and health sciences; Tandem Mass Spectrometry; Biochemistry, Genetics and Molecular Biology; Health Sciences; Quantitative proteomics; Molecular Biology; Biology; RC254-282; Spectroscopy; Chromatography; 0303 health sciences; Role of Clusterin in Cancer and Disease; Mass spectrometry; Neoplasms. Tumors. Oncology. Including cancer and carcinogens; Life Sciences; Glioma; Mass Spectrometry Techniques with Proteins; 3. Good health; gliomas; Chemistry; Clusterin; Oncology; Calcium Modulated Proteins; Physical Sciences; Selected reaction monitoring; Medicine; Meningioma; Medulloblastoma

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.