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Halder A, Biswas D, Chauhan A, Saha A, Auromahima S, Yadav D, Nissa MU, Iyer G, Parihari S, Sharma G, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clin Proteomics 2023; 20:41. [PMID: 37770851 PMCID: PMC10540342 DOI: 10.1186/s12014-023-09426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Meningiomas are the most prevalent primary brain tumors. Due to their increasing burden on healthcare, meningiomas have become a pivot of translational research globally. Despite many studies in the field of discovery proteomics, the identification of grade-specific markers for meningioma is still a paradox and requires thorough investigation. The potential of the reported markers in different studies needs further verification in large and independent sample cohorts to identify the best set of markers with a better clinical perspective. METHODS A total of 53 fresh frozen tumor tissue and 51 serum samples were acquired from meningioma patients respectively along with healthy controls, to validate the prospect of reported differentially expressed proteins and claimed markers of Meningioma mined from numerous manuscripts and knowledgebases. A small subset of Glioma/Glioblastoma samples were also included to investigate inter-tumor segregation. Furthermore, a simple Machine Learning (ML) based analysis was performed to evaluate the classification accuracy of the list of proteins. RESULTS A list of 15 proteins from tissue and 12 proteins from serum were found to be the best segregator using a feature selection-based machine learning strategy with an accuracy of around 80% in predicting low grade (WHO grade I) and high grade (WHO grade II and WHO grade III) meningiomas. In addition, the discriminant analysis could also unveil the complexity of meningioma grading from a segregation pattern, which leads to the understanding of transition phases between the grades. CONCLUSIONS The identified list of validated markers could play an instrumental role in the classification of meningioma as well as provide novel clinical perspectives in regard to prognosis and therapeutic targets.
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Affiliation(s)
- Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Adrita Saha
- Motilal Nehru National Institute of Technology, Allahabad, 211004, UP, India
| | - Shreeman Auromahima
- Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Deeksha Yadav
- CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, New Delhi, 110025, India
| | - Mehar Un Nissa
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Gayatri Iyer
- Koita Centre for Digital Health, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shashwati Parihari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, India
| | | | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 185 Berry St., Suite 290, San Francisco, CA, 94107, USA.
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Ghantasala S, Pai MGJ, Biswas D, Gahoi N, Mukherjee S, KP M, Nissa MU, Srivastava A, Epari S, Shetty P, Moiyadi A, Srivastava S. Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors. Front Oncol 2021; 11:548243. [PMID: 34055594 PMCID: PMC8162214 DOI: 10.3389/fonc.2021.548243] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Saicharan Ghantasala
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, India
| | - Medha Gayathri J. Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Nikita Gahoi
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, India
| | - Shuvolina Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Manubhai KP
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre’s – Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Prakash Shetty
- Homi Bhabha National Institute, Mumbai, India
- Department of Neurosurgery, Tata Memorial Centre’s – Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Aliasgar Moiyadi
- Homi Bhabha National Institute, Mumbai, India
- Department of Neurosurgery, Tata Memorial Centre’s – Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Ruiz-Romero C, Lam MPY, Nilsson P, Önnerfjord P, Utz PJ, Van Eyk JE, Venkatraman V, Fert-Bober J, Watt FE, Blanco FJ. Mining the Proteome Associated with Rheumatic and Autoimmune Diseases. J Proteome Res 2019; 18:4231-4239. [PMID: 31599600 DOI: 10.1021/acs.jproteome.9b00360] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A steady increase in the incidence of osteoarthritis and other rheumatic diseases has been observed in recent decades, including autoimmune conditions such as rheumatoid arthritis, spondyloarthropathies, systemic lupus erythematosus, systemic sclerosis, and Sjögren's syndrome. Rheumatic and autoimmune diseases (RADs) are characterized by the inflammation of joints, muscles, or other connective tissues. In addition to often experiencing debilitating mobility and pain, RAD patients are also at a higher risk of suffering comorbidities such as cardiovascular or infectious events. Given the socioeconomic impact of RADs, broad research efforts have been dedicated to these diseases worldwide. In the present work, we applied literature mining platforms to identify "popular" proteins closely related to RADs. The platform is based on publicly available literature. The results not only will enable the systematic prioritization of candidates to perform targeted proteomics studies but also may lead to a greater insight into the key pathogenic processes of these disorders.
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Affiliation(s)
- Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR), Unidad de Proteómica, INIBIC - Complejo Hospitalario Universitario de A Coruña, SERGAS , Universidad de A Coruña , A Coruña 15006 , Spain
| | - Maggie P Y Lam
- Department of Medicine, Division of Cardiology, Consortium for Fibrosis Research and Translation, Anschutz Medical Campus , University of Colorado Denver , Aurora , Colorado 80045 , United States
| | - Peter Nilsson
- Division of Affinity Proteomics, SciLifeLab, Department of Protein Science , KTH Royal Institute of Technology , Stockholm 17121 , Sweden
| | - Patrik Önnerfjord
- Department of Clinical Sciences, Section for Rheumatology and Molecular Skeletal Biology , Lund University , Lund 22184 , Sweden
| | - Paul J Utz
- Division of Immunology and Rheumatology , Stanford University School of Medicine ; Palo Alto , California 94304 , United States
| | - Jennifer E Van Eyk
- Department of Medicine and The Heart Institute , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Vidya Venkatraman
- Department of Medicine and The Heart Institute , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Justyna Fert-Bober
- Department of Medicine and The Heart Institute , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Fiona E Watt
- Arthritis Research UK Centre for Osteoarthritis Pathogenesis, Kennedy Institute of Rheumatology , University of Oxford , Oxford OX3 7FY , United Kingdom
| | - Francisco J Blanco
- Grupo de Investigación de Reumatología, INIBIC-Complejo Hospitalario Universitario de A Coruña, SERGAS , Departamento de Medicina Universidad de A Coruña , A Coruña 15006 , Spain
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Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V. Proteomic characterization of human exhaled breath condensate. J Breath Res 2018; 12:021001. [PMID: 29189203 DOI: 10.1088/1752-7163/aa9e71] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To improve biomedical knowledge and to support biomarker discovery studies, it is essential to establish comprehensive proteome maps for human tissues and biofluids, and to make them publicly accessible. In this study, we performed an in-depth proteomics characterization of exhaled breath condensate (EBC), a sample obtained non-invasively by condensation of exhaled air that contains submicron droplets of airway lining fluid. Two pooled samples of EBC, each obtained from 10 healthy donors, were processed using a straightforward protocol based on sample lyophilization, in-gel digestion and liquid chromatography tandem-mass spectrometry analysis. Two 'technical' control samples were processed in parallel to the pooled samples to correct for exogenous protein contamination. A total of 229 unique proteins were identified in EBC among which 153 proteins were detected in both EBC pooled samples. A detailed bioinformatics analysis of these 153 proteins showed that most of the proteins identified corresponded to proteins secreted in the respiratory tract (lung, bronchi). Eight proteins were salivary proteins. Our dataset is described and has been made accessible through the ProteomeXchange database (dataset identifier: PXD007591) and is expected to be useful for future MS-based biomarker studies using EBC as the diagnostic specimen.
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Affiliation(s)
- Maud Lacombe
- Université Grenoble-Alpes, F-38000, Grenoble, France. CEA, BIG, Biologie à Grande Echelle, F-38054, Grenoble, France. Inserm, Unité 1038, F-38054, Grenoble, France
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Jimenez CR, Zhang H, Kinsinger CR, Nice EC. The cancer proteomic landscape and the HUPO Cancer Proteome Project. Clin Proteomics 2018; 15:4. [PMID: 29416445 PMCID: PMC5785860 DOI: 10.1186/s12014-018-9180-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/17/2018] [Indexed: 01/05/2023] Open
Abstract
The Human Cancer Proteome Project (Cancer-HPP) is an international initiative organized by HUPO whose key objective is to decipher the human cancer proteome through a coordinated effort by cancer proteome researchers around the world. The ultimate goal is to map the entire human cancer proteome to disclose tumor biology and drive improved diagnostics, treatment and management of cancer. Here we report the progress in the cancer proteomics field to date, and discuss future proteomic developments that will be needed to optimally delineate cancer phenotypes and advance the molecular characterization of this significant disease that is one of the leading causes of death worldwide.
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Affiliation(s)
- Connie R Jimenez
- 1OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Hui Zhang
- 2Department of Pathology, Mass Spectrometry Core Facility, Center for Biomarker Discovery and Translation, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Christopher R Kinsinger
- 3Office of the Clinical Proteomic, Tumor Analysis Consortium at the National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Edouard C Nice
- 4Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800 Australia
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Tholey A, Taylor NL, Heazlewood JL, Bendixen E. We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project. J Proteome Res 2017; 16:4273-4280. [DOI: 10.1021/acs.jproteome.7b00408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Nicolas L. Taylor
- Australian
Research Council Centre of Excellence in Plant Energy Biology, School
of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Joshua L. Heazlewood
- School
of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Emøke Bendixen
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, 8000 Aarhus, Denmark
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