1
|
Tomanelli M, Florio T, Vargas GC, Pagano A, Modesto P. Domestic Animal Models of Central Nervous System Tumors: Focus on Meningiomas. Life (Basel) 2023; 13:2284. [PMID: 38137885 PMCID: PMC10744527 DOI: 10.3390/life13122284] [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: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023] Open
Abstract
Intracranial primary tumors (IPTs) are aggressive forms of malignancies that cause high mortality in both humans and domestic animals. Meningiomas are frequent adult IPTs in humans, dogs, and cats, and both benign and malignant forms cause a decrease in life quality and survival. Surgery is the primary therapeutic approach to treat meningiomas, but, in many cases, it is not resolutive. The chemotherapy and targeted therapy used to treat meningiomas also display low efficacy and many side effects. Therefore, it is essential to find novel pharmacological approaches to increase the spectrum of therapeutic options for meningiomas. This review analyzes the similarities between human and domestic animal (dogs and cats) meningiomas by evaluating the molecular and histological characteristics, diagnosis criteria, and treatment options and highlighting possible research areas to identify novel targets and pharmacological approaches, which are useful for the diagnosis and therapy of this neoplasia to be used in human and veterinary medicine.
Collapse
Affiliation(s)
- Michele Tomanelli
- Department of Experimental Medicine, University of Genova, 16132 Genova, Italy; (G.C.V.); (A.P.)
| | - Tullio Florio
- Pharmacology Section, Department of Internal Medicine (DIMI), University of Genova, 16126 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Gabriela Coronel Vargas
- Department of Experimental Medicine, University of Genova, 16132 Genova, Italy; (G.C.V.); (A.P.)
| | - Aldo Pagano
- Department of Experimental Medicine, University of Genova, 16132 Genova, Italy; (G.C.V.); (A.P.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Paola Modesto
- National Reference Center for Veterinary and Comparative Oncology, Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, 10154 Torino, Italy
| |
Collapse
|
2
|
Biswas D, Halder A, Barpanda A, Ghosh S, Chauhan A, Bhat L, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma. Cells 2023; 12:2483. [PMID: 37887327 PMCID: PMC10604908 DOI: 10.3390/cells12202483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Meningioma, a primary brain tumor, is commonly encountered and accounts for 39% of overall CNS tumors. Despite significant progress in clinical research, conventional surgical and clinical interventions remain the primary treatment options for meningioma. Several proteomics and transcriptomics studies have identified potential markers and altered biological pathways; however, comprehensive exploration and data integration can help to achieve an in-depth understanding of the altered pathobiology. This study applied integrated meta-analysis strategies to proteomic and transcriptomic datasets comprising 48 tissue samples, identifying around 1832 common genes/proteins to explore the underlying mechanism in high-grade meningioma tumorigenesis. The in silico pathway analysis indicated the roles of extracellular matrix organization (EMO) and integrin binding cascades in regulating the apoptosis, angiogenesis, and proliferation responsible for the pathobiology. Subsequently, the expression of pathway components was validated in an independent cohort of 32 fresh frozen tissue samples using multiple reaction monitoring (MRM), confirming their expression in high-grade meningioma. Furthermore, proteome-level changes in EMO and integrin cell surface interactions were investigated in a high-grade meningioma (IOMM-Lee) cell line by inhibiting integrin-linked kinase (ILK). Inhibition of ILK by administrating Cpd22 demonstrated an anti-proliferative effect, inducing apoptosis and downregulating proteins associated with proliferation and metastasis, which provides mechanistic insight into the disease pathophysiology.
Collapse
Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Susmita Ghosh
- Leibniz-Institut für Analytische Wissenschaften—ISAS, 44227 Dortmund, Germany;
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Lipika Bhat
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed-to-be University, Mumbai 400056, India;
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai 400012, India;
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai 400012, India; (P.S.); (A.M.)
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Tata Memorial Centre, Mumbai 400012, India; (P.S.); (A.M.)
| | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, East Rd., Cambridge CB1 1PT, UK;
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| |
Collapse
|
3
|
Xu N, Yu Y, Duan C, Wei J, Sun W, Jiang C, Jian B, Cao W, Jia L, Ma X. Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children. Clin Proteomics 2023; 20:10. [PMID: 36918772 PMCID: PMC10012572 DOI: 10.1186/s12014-023-09401-4] [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: 12/01/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma with poor prognosis in children. The 5-year survival rate for early RMS has improved, whereas it remains unsatisfactory for advanced patients. Urine can rapidly reflect changes in the body and identify low-abundance proteins. Early screening of tumor markers through urine in RMS allows for earlier treatment, which is associated with better outcomes. METHODS RMS patients under 18 years old, including those newly diagnosed and after surgery, were enrolled. Urine samples were collected at the time points of admission and after four cycles of chemotherapy during follow-up. Then, a two-stage workflow was established. (1) In the discovery stage, differential proteins (DPs) were initially identified in 43 RMS patients and 12 healthy controls (HCs) using a data-independent acquisition method. (2) In the verification stage, DPs were further verified as biomarkers in 54 RMS patients and 25 HCs using parallel reaction monitoring analysis. Furthermore, a receiver operating characteristic (ROC) curve was used to construct the protein panels for the diagnosis of RMS. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software were used to perform bioinformatics analysis. RESULTS A total of 251 proteins were significantly altered in the discovery stage, most of which were enriched in the head, neck and urogenital tract, consistent with the most common sites of RMS. The most overrepresented biological processes from GO analysis included immunity, inflammation, tumor invasion and neuronal damage. Pathways engaging the identified proteins revealed 33 common pathways, including WNT/β-catenin signaling and PI3K/AKT signaling. Finally, 39 proteins were confirmed as urinary biomarkers for RMS, and a diagnostic panel composed of 5 candidate proteins (EPS8L2, SPARC, HLA-DRB1, ACAN, and CILP) was constructed for the early screening of RMS (AUC: 0.79, 95%CI = 0.66 ~ 0.92). CONCLUSIONS These findings provide novel biomarkers in urine that are easy to translate into clinical diagnosis of RMS and illustrate the value of global and targeted urine proteomics to identify and qualify candidate biomarkers for noninvasive molecular diagnosis.
Collapse
Affiliation(s)
- Na Xu
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.,Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Chao Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Jing Wei
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Wei Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chiyi Jiang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Binglin Jian
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Wang Cao
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Lulu Jia
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China.
| | - Xiaoli Ma
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.
| |
Collapse
|
4
|
Barpanda A, Halder A, Dhote A, Parihari S, Kantharia C, Srivastava S. Colon Adenocarcinoma Quantitative Proteomics Reveals Dysregulation in Key Cancer Signaling Pathways and a Candidate Protein Marker Panel. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:75-85. [PMID: 36730729 DOI: 10.1089/omi.2022.0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Colorectal cancer (CRC) is reportedly the second leading cause of cancer death worldwide. By the end of the decade, there will likely be more than one million fatalities worldwide from this cancer, with an estimated 2.2 million additional cases. We need new ways of thinking about cancer research. One approach is to deploy systems science using quantitative proteomics to obtain postgenomic and functional insights into cancer. The present study compares the tissue proteome of CRC (n = 10) with the matched peritumoral controls (n = 10) in samples obtained from the Indian subcontinent. When compared with the controls, a list of 22 substantially altered protein candidates was identified, which were associated with the growth, survival, and metastasis of the tumor. A list of the unique peptides from top significant proteins, including olfactomedin-4, alanyl aminopeptidase, and grancalcin was further validated using a parallel reaction monitoring-based targeted proteomics approach. In addition, biological pathway analysis showed perturbation in key biological processes, including dysregulation in purine metabolism, MYC targets in cancer, DNA repair, and replication, and leukocyte transendothelial migration, among others. The protein panel reported herein is also shown to be dysregulated in CRC and warrants further research toward understanding pathobiology, diagnostics, and therapeutics development in CRC.
Collapse
Affiliation(s)
- Abhilash Barpanda
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ankit Halder
- Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ayushi Dhote
- Saint Francis de Sales College, Nagpur, Maharashtra, India
| | - Shashwati Parihari
- Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Chetan Kantharia
- Department of Surgical Gastroenterology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| |
Collapse
|
5
|
Mukherjee A, Ghosh S, Biswas D, Rao A, Shetty P, Epari S, Moiyadi A, Srivastava S. Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:512-520. [PMID: 36036964 DOI: 10.1089/omi.2022.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated VIM, AHNAK, and CLU from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.
Collapse
Affiliation(s)
- Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Susmita Ghosh
- 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
| | - Aishwarya Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | | | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| |
Collapse
|
6
|
Takase H, Yamamoto T. Bone Invasive Meningioma: Recent Advances and Therapeutic Perspectives. Front Oncol 2022; 12:895374. [PMID: 35847854 PMCID: PMC9280135 DOI: 10.3389/fonc.2022.895374] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Meningioma is the most common primary neoplasm of the central nervous system (CNS). Generally, these tumors are benign and have a good prognosis. However, treatment can be challenging in cases with aggressive variants and poor prognoses. Among various prognostic factors that have been clinically investigated, bone invasion remains controversial owing to a limited number of assessments. Recent study reported that bone invasion was not associated with WHO grades, progression, or recurrence. Whereas, patients with longer-recurrence tended to have a higher incidence of bone invasion. Furthermore, bone invasion may be a primary preoperative predictor of the extent of surgical resection. Increasing such evidence highlights the potential of translational studies to understand bone invasion as a prognostic factor of meningiomas. Therefore, this mini-review summarizes recent advances in pathophysiology and diagnostic modalities and discusses future research directions and therapeutic strategies for meningiomas with bone invasion.
Collapse
Affiliation(s)
- Hajime Takase
- Center for Novel and Exploratory Clinical Trials (Y-NEXT), Yokohama City University Hospital, Yokohama, Japan
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- *Correspondence: Hajime Takase, ; orcid.org/0000-0001-5813-1386
| | - Tetsuya Yamamoto
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| |
Collapse
|
7
|
Rana R, Sharma S, Ganguly NK. Comprehensive overview of extracellular vesicle proteomics in meningioma: future strategy. Mol Biol Rep 2021; 48:8061-8074. [PMID: 34687392 PMCID: PMC8536918 DOI: 10.1007/s11033-021-06740-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/15/2021] [Indexed: 11/09/2022]
Abstract
Background Meningioma arising from meninges is one among the various types of brain tumors. Others are, astrocytomas originating from astrocyte, oligodendrogliomas originating from oligodendrocyte, Ependymomas originating from ependymal cells and medulloblastomas originating from neurons. Current knowledge of molecular biology, genetics and epigenetics of meningioma is not sufficient. Therefore, In depth understanding of the mechanism of meningioma formation and progression is needed for its treatment and management. Grade I Grade I meningiomas are majorly classified as grade I, grade II and grade III. Meningioma can be indolent, slow growing or can be invasive and metastatic which can recurre. Grade I meningioma can be removed by surgery in comparison to invasive meningioma which may recurre with high propensity. This property of recurrence is responsible for high morbidity and mortality. Meningioma are majorly classified into three classes namely grade I, grade II, grade III. Protein biomarkers are considered as promising candidates for the diagnosis of meningioma. Study Various studies done on differential expression of proteins have shown increased expression of EGFR, NEK9, EPS812, CKAP4, SET and STAT2, in all the three grades of meningioma. Additionally, some proteins like HK2 are overexpressed in grade II and grade III meningioma than in grade I meningioma. Protein Markers, found on extracellular vesicles of different grades of meningioma can serve the same purpose. A test done on a sample of any kind of body fluid like blood, tear, saliva, urine etc. for recognizing the circulating cancer cells or DNA and extracellular vesicles released from them to help detecting the early stage of cancer is known as liquid biopsy. Solid biopsy has several limitations as compared to liquid biopsy. This is because the samples can be easily collected and studied in case of liquid biopsy. Exosomes are related with liquid biopsy and hence provide platform for better diagnosis, prognosis and treatment of any type of cancer including meningioma. Exosomal tetraspanin are important example of exosomal biomarkers. The tetraspanin network is a molecular scaffold which connects various proteins for signal transduction. Conclusion This study tells about the utility of proper knowledge of extracellular vesicle proteins and their profiles in different grades, which can help in better understanding of pathogenesis, diagnosis, prognosis and treatment of meningioma. In Addition to use of these proteins as biomarkers, role of exosomes in currently available therapeutic approaches has been discussed.
Collapse
Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, 110060, India.
| | - Swati Sharma
- Department of Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | | |
Collapse
|
8
|
Mukherjee S, Biswas D, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. Comprehensive proteomic analysis reveals distinct functional modules associated with skull base and supratentorial meningiomas and perturbations in collagen pathway components. J Proteomics 2021; 246:104303. [PMID: 34174477 DOI: 10.1016/j.jprot.2021.104303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/31/2021] [Accepted: 06/05/2021] [Indexed: 12/18/2022]
Abstract
Meningiomas are brain tumors that originate from the meninges and has been primarily classified into three grades by the current WHO guidelines. Although widely prevalent and can be managed by surgery there are instances when the tumors are located in difficult regions. This results in considerable challenges for complete surgical resection and further clinical management. While the genetic signature of the skull base tumors is now known to be different from the non-skull base tumors, there is a lack of information at the functional aspects of these tumors at the proteomic level. Thus, the current study thereby aims to obtain mechanistic insights between the two radiologically distinct groups of meningiomas, namely the skull base & supratentorial (non-skull base-NSB) regions. We have employed a comprehensive mass spectrometry-based label-free quantitative proteomic analysis in Skull base and supratentorial meningiomas. Further, we have used an Artificial Neural Networking employing a sparse Multilayer perceptron (MLP) architecture to predict protein concordance. A patient-derived spectral library has been employed for a novel peptide-level validation of proteins that are specific to the radiological regions using the SRM assay based targeted proteomics approach. The comprehensive proteomics enabled the identification of nearly 4000 proteins with high confidence (1%FDR ≥ 2 unique peptides) among which 170 proteins were differentially abundant in Skull base vs Supratentorial tumors (p-value ≤0.05). In silico analysis enabled mapping of the major alterations and hinted towards an overall perturbation of extracellular matrix and collagen biosynthesis components in the non-skull base meningiomas and a prominent perturbation of molecular trafficking in the skull base meningiomas. Therefore, this study has yielded novel insights into the functional association of the proteins that are differentially abundant in the two radiological subgroups. SIGNIFICANCE: In the current study, we have performed label-free proteomic analysis on fresh frozen tissue of 14 Supratentorial (NSB) and 7 Skull base meningiomas to assess perturbations in the global proteome, we have further employed an in-depth in silico analysis to map the pathways that have enabled functional mapping of the differentially abundant proteins in the Skull base and Supratentorial tumors. The findings from the above were also subjected to a machine learning-based neural networking to find out the proteins that have the most concordance of occurrence to determine the most influential proteins of the network. We further validated the differential abundance of identified protein markers in a larger patient cohort of Skull base and Supratentorial employing targeted proteomics approach to validate key protein candidates emerging from ours and other recent studies. The previous studies that have explored the skull base and convexity meningiomas have been able to reveal alterations in the genetic mutations in these tumor types. However, there are not many studies that have explored the functional aspects of these tumors, especially at the proteome level. We have attempted for the first time to map the functional modules associated with altered proteins in these tumors and have been able to identify that there is a possibility that the Skull base meningiomas to be considerably different from the Non-skull base (NSB) tumors in terms of the perturbed pathways. Our study employed global as well as targeted proteomics to examine the proteomic alterations in these two tumor groups. The study indicates that proteins that were more abundant in Skull base tumors were part of molecular transport components, non-skull base proteins majorly mapped to the components of extracellular matrix remodeling pathways. In conclusion, this study substantiates the distinction in the proteomic signatures in the skull base and supratentorial meningiomas paving way for further investigation of the identified markers for determining if some of these proteins can be used for therapeutic interventions for cases that pose considerable challenges for complete resection.
Collapse
Affiliation(s)
- Shuvolina Mukherjee
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai, 400076, Maharashtra, India; Department of Immunotechnology, Lund University, Medicon Village, 22100 Lund, Sweden
| | - Deeptarup Biswas
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai, 400076, Maharashtra, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, Dr. E Borges Road, Parel, Mumbai 400 012, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, Dr. E Borges Road, Parel, Mumbai 400 012, India
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, Dr. E Borges Road, Parel, Mumbai 400 012, India
| | - Graham Roy Ball
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Sanjeeva Srivastava
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai, 400076, Maharashtra, India.
| |
Collapse
|
9
|
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: 18] [Impact Index Per Article: 6.0] [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.
Collapse
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
| |
Collapse
|