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Article ; Online: A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy.

Pai, Medha Gayathri J / Biswas, Deeptarup / Verma, Ayushi / Srivastava, Sanjeeva

2023 Volume 20, Issue 12, Page(s) 381–395

Abstract: Introduction: Brain tumors are complex and heterogeneous malignancies with significant challenges in diagnosis, prognosis, and therapy. Proteomics, the large-scale study of proteins and their functions, has emerged as a powerful tool to comprehensively ... ...

Abstract	Introduction: Brain tumors are complex and heterogeneous malignancies with significant challenges in diagnosis, prognosis, and therapy. Proteomics, the large-scale study of proteins and their functions, has emerged as a powerful tool to comprehensively investigate the molecular mechanisms underlying brain tumor regulation. Areas covered: This review explores brain tumors from a proteomic standpoint, highlighting recent progress and insights gained through proteomic methods. It delves into the proteomic techniques employed and underscores potential biomarkers for early detection, prognosis, and treatment planning. Recent PubMed Central proteomic studies (2017-present) are discussed, summarizing findings on altered protein expression, post-translational changes, and protein interactions. This sheds light on brain tumor signaling pathways and their significance in innovative therapeutic approaches. Expert opinion: Proteomics offers immense potential for revolutionizing brain tumor diagnosis and therapy. To unlock its full benefits, further translational research is crucial. Combining proteomics with other omics data enhances our grasp of brain tumors. Validating and translating proteomic biomarkers are vital for better patient results. Challenges include tumor complexity, lack of curated proteomic databases, and the need for collaboration between researchers and clinicians. Overcoming these challenges requires investment in technology, data sharing, and translational research.
MeSH term(s)	Humans ; Proteomics/methods ; Proteome/genetics ; Prognosis ; Biomarkers/metabolism ; Brain Neoplasms/diagnosis ; Brain Neoplasms/genetics ; Brain Neoplasms/therapy
Chemical Substances	Proteome ; Biomarkers
Language	English
Publishing date	2023-12-30
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2299100-1
ISSN	1744-8387 ; 1478-9450
ISSN (online)	1744-8387
ISSN	1478-9450
DOI	10.1080/14789450.2023.2283498
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Article ; Online: Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue.

Ghantasala, Saicharan / Pai, Medha Gayathri J / Srivastava, Sanjeeva

Journal of visualized experiments : JoVE

2021 , Issue 174

Abstract: The proteomic analysis of the human brain tissue over the last decade has greatly enhanced our understanding of the brain. However, brain related disorders continue to be a major contributor of deaths around the world, necessitating the need for even ... ...

Abstract	The proteomic analysis of the human brain tissue over the last decade has greatly enhanced our understanding of the brain. However, brain related disorders continue to be a major contributor of deaths around the world, necessitating the need for even greater understanding of their pathobiology. Traditional antibody-based techniques like western blotting or immunohistochemistry suffer from being low-throughput besides being labor-intensive and qualitative or semi-quantitative. Even conventional mass spectrometry-based shotgun approaches fail to provide conclusive evidence to support a certain hypothesis. Targeted proteomics approaches are largely hypothesis driven and differ from the conventional shotgun proteomics approaches that have been long in use. Multiple reaction monitoring is one such targeted approach that requires the use of a special mass spectrometer called the tandem quadrupole mass spectrometer or triple quadrupole mass spectrometer. In the current study, we have systematically highlighted the major steps involved in performing a successful tandem quadrupole mass spectrometry-based proteomics workflow using human brain tissue with an aim to introduce this workflow to a broader research community.
MeSH term(s)	Brain ; Humans ; Proteins ; Proteomics ; Tandem Mass Spectrometry ; Workflow
Chemical Substances	Proteins
Language	English
Publishing date	2021-08-28
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/61833
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Article ; Online: Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda.

Pinto, Nevil / Nissa, Mehar Un / Yashwanth, B S / Sathiyanarayanan, A / Pai, Medha Gayathri J / Srivastava, Sanjeeva / Goswami, Mukunda

Comparative biochemistry and physiology. Part D, Genomics & proteomics

2024 Volume 50, Page(s) 101221

Abstract: Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and ... ...

Abstract	Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after Et infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and Et infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after Et infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against Et.
Language	English
Publishing date	2024-02-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2212119-5
ISSN	1878-0407 ; 1744-117X
ISSN (online)	1878-0407
ISSN	1744-117X
DOI	10.1016/j.cbd.2024.101221
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Article: Quantitative proteomics workflow using multiple reaction monitoring based detection of proteins from human brain tissue

Ghantasala, Saicharan / Pai, Medha Gayathri J / Srivastava, Sanjeeva

Journal of visualized experiments. 2021 Aug. 28, , no. 174

2021

Abstract	The proteomic analysis of the human brain tissue over the last decade has greatly enhanced our understanding of the brain. However, brain related disorders continue to be a major contributor of deaths around the world, necessitating the need for even greater understanding of their pathobiology. Traditional antibody-based techniques like western blotting or immunohistochemistry suffer from being low-throughput besides being labor-intensive and qualitative or semi-quantitative. Even conventional mass spectrometry-based shotgun approaches fail to provide conclusive evidence to support a certain hypothesis. Targeted proteomics approaches are largely hypothesis driven and differ from the conventional shotgun proteomics approaches that have been long in use. Multiple reaction monitoring is one such targeted approach that requires the use of a special mass spectrometer called the tandem quadrupole mass spectrometer or triple quadrupole mass spectrometer. In the current study, we have systematically highlighted the major steps involved in performing a successful tandem quadrupole mass spectrometry-based proteomics workflow using human brain tissue with an aim to introduce this workflow to a broader research community.
Keywords	brain ; humans ; immunohistochemistry ; mass spectrometry ; proteomics ; spectrometers
Language	English
Dates of publication	2021-0828
Size	p. e61833.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/61833
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Article ; Online: Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples.

Banerjee, Arghya / Pai, Medha Gayathri J / Singh, Avinash / Nissa, Mehar Un / Srivastava, Sanjeeva

STAR protocols

2022 Volume 3, Issue 1, Page(s) 101177

Abstract: With new emerging SARS-CoV-2 strains and their increased pathogenicity, diagnosis has become more challenging. Molecular diagnosis often involves the use of nasopharyngeal swabs and subsequent real-time PCR-based tests. Although this test is the gold ... ...

Abstract	With new emerging SARS-CoV-2 strains and their increased pathogenicity, diagnosis has become more challenging. Molecular diagnosis often involves the use of nasopharyngeal swabs and subsequent real-time PCR-based tests. Although this test is the gold standard, it has several limitations; therefore, more complementary assays are required. This protocol describes how to identify SARS-CoV-2 protein from patients' nasopharyngeal swab samples. We first introduce the approach of label-free quantitative proteomics. We then detail target verification by triple quadrupole mass spectrometry (MS)-based targeted proteomics. For complete details on the use and execution of this profile, please refer to Bankar et al. (2021).
MeSH term(s)	COVID-19/metabolism ; Female ; Humans ; Male ; Nasopharynx/metabolism ; Nasopharynx/virology ; Proteomics ; SARS-CoV-2/metabolism ; Specimen Handling ; Tandem Mass Spectrometry ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins
Language	English
Publishing date	2022-02-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101177
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Article ; Online: IL-17A Orchestrates Reactive Oxygen Species/HIF1α-Mediated Metabolic Reprogramming in Psoriasis.

Dhamija, Bhavuk / Marathe, Soumitra / Sawant, Vinanti / Basu, Moumita / Attrish, Diksha / Mukherjee, Ditipriya / Kumar, Sushant / Pai, Medha Gayathri J / Wad, Siddhi / Sawant, Abhijeet / Nayak, Chitra / Venkatesh, Kareenhalli V / Srivastava, Sanjeeva / Barthel, Steven R / Purwar, Rahul

Journal of immunology (Baltimore, Md. : 1950)

2023 Volume 212, Issue 2, Page(s) 302–316

Abstract: Immune cell-derived IL-17A is one of the key pathogenic cytokines in psoriasis, an immunometabolic disorder. Although IL-17A is an established regulator of cutaneous immune cell biology, its functional and metabolic effects on nonimmune cells of the skin, ...

Abstract	Immune cell-derived IL-17A is one of the key pathogenic cytokines in psoriasis, an immunometabolic disorder. Although IL-17A is an established regulator of cutaneous immune cell biology, its functional and metabolic effects on nonimmune cells of the skin, particularly keratinocytes, have not been comprehensively explored. Using multiomics profiling and systems biology-based approaches, we systematically uncover significant roles for IL-17A in the metabolic reprogramming of human primary keratinocytes (HPKs). High-throughput liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy revealed IL-17A-dependent regulation of multiple HPK proteins and metabolites of carbohydrate and lipid metabolism. Systems-level MitoCore modeling using flux-balance analysis identified IL-17A-mediated increases in HPK glycolysis, glutaminolysis, and lipid uptake, which were validated using biochemical cell-based assays and stable isotope-resolved metabolomics. IL-17A treatment triggered downstream mitochondrial reactive oxygen species and HIF1α expression and resultant HPK proliferation, consistent with the observed elevation of these downstream effectors in the epidermis of patients with psoriasis. Pharmacological inhibition of HIF1α or reactive oxygen species reversed IL-17A-mediated glycolysis, glutaminolysis, lipid uptake, and HPK hyperproliferation. These results identify keratinocytes as important target cells of IL-17A and reveal its involvement in multiple downstream metabolic reprogramming pathways in human skin.
MeSH term(s)	Cells, Cultured ; Humans ; Interleukin-17/metabolism ; Metabolic Reprogramming/genetics ; Reactive Oxygen Species/metabolism ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Keratinocytes/cytology ; Cell Proliferation/genetics ; Male ; Female ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Up-Regulation ; Lipid Metabolism ; Psoriasis/genetics ; Psoriasis/metabolism
Chemical Substances	Interleukin-17 ; Reactive Oxygen Species ; HIF1A protein, human ; Hypoxia-Inducible Factor 1, alpha Subunit
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.2300319
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Article: Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai.

Rajoria, Sakshi / Nair, Divya / Suvarna, Kruthi / Pai, Medha Gayathri J / Salkar, Akanksha / Palanivel, Viswanthram / Verma, Ayushi / Barpanda, Abhilash / Awasthi, Gaurav / Doshi, Hastyn / Dhara, Vivek / Burli, Ananya / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

Advances in experimental medicine and biology

2023 Volume 1412, Page(s) 175–195

Abstract: Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second ... ...

Abstract	Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Proteomics/methods ; India/epidemiology ; Ritonavir
Chemical Substances	Ritonavir (O3J8G9O825)
Language	English
Publishing date	2023-06-28
Publishing country	United States
Document type	Journal Article
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-031-28012-2_9
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Article: Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors.

Ghantasala, Saicharan / Pai, Medha Gayathri J / Biswas, Deeptarup / Gahoi, Nikita / Mukherjee, Shuvolina / Kp, Manubhai / Nissa, Mehar Un / Srivastava, Alisha / Epari, Sridhar / Shetty, Prakash / Moiyadi, Aliasgar / Srivastava, Sanjeeva

Frontiers in oncology

2021 Volume 11, Page(s) 548243

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 ... ...

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.
Language	English
Publishing date	2021-05-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2021.548243
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Article ; Online: Proteomic investigation reveals dominant alterations of neutrophil degranulation and mRNA translation pathways in patients with COVID-19.

Bankar, Renuka / Suvarna, Kruthi / Ghantasala, Saicharan / Banerjee, Arghya / Biswas, Deeptarup / Choudhury, Manisha / Palanivel, Viswanthram / Salkar, Akanksha / Verma, Ayushi / Singh, Avinash / Mukherjee, Amrita / Pai, Medha Gayathri J / Roy, Jyotirmoy / Srivastava, Alisha / Badaya, Apoorva / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

iScience

2021 Volume 24, Issue 3, Page(s) 102135

Abstract: The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of nasopharyngeal swab samples from patients with COVID-19 to study the host response by ... ...

Abstract	The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of nasopharyngeal swab samples from patients with COVID-19 to study the host response by employing simple extraction strategies. Few of the host proteins such as interleukin-6, L-lactate dehydrogenase, C-reactive protein, Ferritin, and aspartate aminotransferase were found to be upregulated only in COVID-19-positive patients using targeted multiple reaction monitoring studies. The most important pathways identified by enrichment analysis were neutrophil degranulation, interleukin-12 signaling pathways, and mRNA translation of proteins thus providing the detailed investigation of host response in COVID-19 infection. Thus, we conclude that mass spectrometry-detected host proteins have a potential for disease severity progression; however, suitable validation strategies should be deployed for the clinical translation. Furthermore, the
Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.102135
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Article: Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential.

Suvarna, Kruthi / Biswas, Deeptarup / Pai, Medha Gayathri J / Acharjee, Arup / Bankar, Renuka / Palanivel, Viswanthram / Salkar, Akanksha / Verma, Ayushi / Mukherjee, Amrita / Choudhury, Manisha / Ghantasala, Saicharan / Ghosh, Susmita / Singh, Avinash / Banerjee, Arghya / Badaya, Apoorva / Bihani, Surbhi / Loya, Gaurish / Mantri, Krishi / Burli, Ananya /

Roy, Jyotirmoy / Srivastava, Alisha / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

Frontiers in physiology

2021 Volume 12, Page(s) 652799

Abstract: The pestilential pathogen SARS-CoV-2 has led to a seemingly ceaseless pandemic of COVID-19. The healthcare sector is under a tremendous burden, thus necessitating the prognosis of COVID-19 severity. This in-depth study of plasma proteome alteration ... ...

Abstract	The pestilential pathogen SARS-CoV-2 has led to a seemingly ceaseless pandemic of COVID-19. The healthcare sector is under a tremendous burden, thus necessitating the prognosis of COVID-19 severity. This in-depth study of plasma proteome alteration provides insights into the host physiological response towards the infection and also reveals the potential prognostic markers of the disease. Using label-free quantitative proteomics, we performed deep plasma proteome analysis in a cohort of 71 patients (20 COVID-19 negative, 18 COVID-19 non-severe, and 33 severe) to understand the disease dynamics. Of the 1200 proteins detected in the patient plasma, 38 proteins were identified to be differentially expressed between non-severe and severe groups. The altered plasma proteome revealed significant dysregulation in the pathways related to peptidase activity, regulated exocytosis, blood coagulation, complement activation, leukocyte activation involved in immune response, and response to glucocorticoid biological processes in severe cases of SARS-CoV-2 infection. Furthermore, we employed supervised machine learning (ML) approaches using a linear support vector machine model to identify the classifiers of patients with non-severe and severe COVID-19. The model used a selected panel of 20 proteins and classified the samples based on the severity with a classification accuracy of 0.84. Putative biomarkers such as angiotensinogen and SERPING1 and ML-derived classifiers including the apolipoprotein B, SERPINA3, and fibrinogen gamma chain were validated by targeted mass spectrometry-based multiple reaction monitoring (MRM) assays. We also employed an
Language	English
Publishing date	2021-04-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2021.652799
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