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Pillai U J, Cherian L, Taunk K, Iype E, Dutta M. Identification of antiviral phytochemicals from cranberry as potential inhibitors of SARS-CoV-2 main protease (M pro). Int J Biol Macromol 2024; 261:129655. [PMID: 38266830 DOI: 10.1016/j.ijbiomac.2024.129655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Cranberry phytochemicals are known to possess antiviral activities. In the current study, we explored the therapeutic potential of cranberry against SARS-CoV-2 by targeting its main protease (Mpro) enzyme. Firstly, phytochemicals of cranberry origin were identified from three independent databases. Subsequently, virtual screening, using molecular docking and molecular dynamics simulation approaches, led to the identification of three lead phytochemicals namely, cyanidin 3-O-galactoside, β-carotene and epicatechin. Furthermore, in vitro enzymatic assays revealed that cyanidin 3-O-galactoside had the highest inhibitory potential with IC50 of 9.98 μM compared to the other two phytochemicals. Cyanidin 3-O-galactoside belongs to the class of anthocyanins. Anthocyanins extracted from frozen cranberry also exhibited the highest inhibitory potential with IC50 of 23.58 μg/ml compared to the extracts of carotenoids and flavanols, the class for β-carotene and epicatechin, respectively. Finally, we confirm the presence of the phytochemicals in the cranberry extracts using targeted LC-MS/MS analysis. Our results, therefore, indicate that the identified cranberry-derived bioactive compounds as well as cranberry could be used for therapeutic interventions against SARS-CoV-2.
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Affiliation(s)
- Jisha Pillai U
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates
| | - Lucy Cherian
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates
| | - Khushman Taunk
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Eldhose Iype
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Mainak Dutta
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates.
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Taunk K, Paul D, Dabhi R, Venkatesh C, Jajula S, Naik V, Tamhankar A, Naiya T, Kumar Santra M, Rapole S. A single step and rapid protein extraction protocol developed for cell lines and tissues: Compatible for gel based and gel free proteomic approaches. Methods 2023; 220:29-37. [PMID: 37918646 DOI: 10.1016/j.ymeth.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
Proteins are crucial research molecules in modern biology. Almost every biological research area needs protein-based assays to answer the research questions. The study of the total protein content of a biological sample known as Proteomics, is one of the highly rated qualitative and quantitative approach to address numerous biological problems including clinical research. The key step to successfully generate high quality proteomics data is the efficient extraction of proteins from biological samples. Although different methods are in use for protein extraction from a wide variety of samples, however, because of their prolonged protocol and multiple steps involved, final protein yield is sacrificed. Here, we have shown the development of a simple single step method for extraction of proteins from mammalian cell lines as well as tissue samples in an effective and reproducible manner. This method is based on lysis of samples directly in a modified lysis buffer without CHAPS (7 M Urea, 2 M Thiourea, and 10 mM Tris-Cl; pH 8.5) that is compatible with gel based and gel free approaches. This developed protocol is reliable and should be useful for a wide range of proteomic studies involving various biological samples.
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Affiliation(s)
- Khushman Taunk
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India; Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, West Bengal, India
| | - Debasish Paul
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Raju Dabhi
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | | | - Saikiran Jajula
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Venkateshwarlu Naik
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Anup Tamhankar
- Department of Surgical Oncology, Deenanath Mangeshkar Hospital and Research Centre, Erandawne, Pune 411004, Maharashtra, India
| | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, West Bengal, India
| | - Manas Kumar Santra
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India.
| | - Srikanth Rapole
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India.
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Sugandhi S, Rajmane V, Taunk K, Jadhav S, Nema V, Rapole S, Mande SC. The role of thioredoxin proteins in Mycobacterium tuberculosis probed by proteome-wide target profiling. Biochem Biophys Rep 2023; 35:101512. [PMID: 37521372 PMCID: PMC10371808 DOI: 10.1016/j.bbrep.2023.101512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Mycobacterium tuberculosis encounters diverse microenvironments, including oxidative assault (ROS and RNS), when it attempts to establish itself within its human host. Therefore, redox sensory and regulation processes are assumed significant importance, as these are essential processes for M. tuberculosis to survive under these hostile conditions. M. tuberculosis contains thioredoxin system to maintain redox homeostasis, which establish a balance between the thiol/dithiol couple. Still very less is known about it. In the present study, we attempted to capture the targets of all the M. tuberculosis thioredoxin proteins (viz., TrxB and TrxC) and a thioredoxin-like protein, NrdH, under aerobic and hypoxic conditions by performing thioredoxin trapping chromatography followed by mass spectrometry. We found that TrxC captured the maximum number of targets in both the physiological conditions and most of the targets of TrxB and NrdH showing overlap with targets of TrxC, indicating that TrxC acts as main thioredoxin. Further the PANTHER classification system provides involvement of targets in various metabolic processes and Gene Ontology analysis suggests that glutamine biosynthetic process and Fe-S cluster biosynthesis are the most enriched processes in the target list of TrxC and TrxB respectively. Also, we suggest that the thioredoxin system might play an important role under hypoxia by targeting those proteins which are responsible to sense and maintain hypoxic conditions. Furthermore, our studies establish a link between TrxB and iron-sulfur cluster biogenesis in M. tuberculosis. Ultimately, these findings open a new direction to target the thioredoxin system for screening new anti-mycobacterial drug targets.
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Affiliation(s)
- Sapna Sugandhi
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Vyankatesh Rajmane
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Khushman Taunk
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Sushama Jadhav
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Srikanth Rapole
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Shekhar C. Mande
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
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Taunk K, Porto-Figueira P, Pereira JAM, Taware R, da Costa NL, Barbosa R, Rapole S, Câmara JS. Urinary Volatomic Expression Pattern: Paving the Way for Identification of Potential Candidate Biosignatures for Lung Cancer. Metabolites 2022; 12:36. [PMID: 35050157 PMCID: PMC8780352 DOI: 10.3390/metabo12010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 12/24/2022] Open
Abstract
The urinary volatomic profiling of Indian cohorts composed of 28 lung cancer (LC) patients and 27 healthy subjects (control group, CTRL) was established using headspace solid phase microextraction technique combined with gas chromatography mass spectrometry methodology as a powerful approach to identify urinary volatile organic metabolites (uVOMs) to discriminate among LC patients from CTRL. Overall, 147 VOMs of several chemistries were identified in the intervention groups-including naphthalene derivatives, phenols, and organosulphurs-augmented in the LC group. In contrast, benzene and terpenic derivatives were found to be more prevalent in the CTRL group. The volatomic data obtained were processed using advanced statistical analysis, namely partial least square discriminative analysis (PLS-DA), support vector machine (SVM), random forest (RF), and multilayer perceptron (MLP) methods. This resulted in the identification of nine uVOMs with a higher potential to discriminate LC patients from CTRL subjects. These were furan, o-cymene, furfural, linalool oxide, viridiflorene, 2-bromo-phenol, tricyclazole, 4-methyl-phenol, and 1-(4-hydroxy-3,5-di-tert-butylphenyl)-2-methyl-3-morpholinopropan-1-one. The metabolic pathway analysis of the data obtained identified several altered biochemical pathways in LC mainly affecting glycolysis/gluconeogenesis, pyruvate metabolism, and fatty acid biosynthesis. Moreover, acetate and octanoic, decanoic, and dodecanoic fatty acids were identified as the key metabolites responsible for such deregulation. Furthermore, studies involving larger cohorts of LC patients would allow us to consolidate the data obtained and challenge the potential of the uVOMs as candidate biomarkers for LC.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind, SPPU Campus, Pune 411007, India; (K.T.); (R.T.)
| | - Priscilla Porto-Figueira
- CQM—Centro de Química da Madeira, Centro de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal; (P.P.-F.); (J.A.M.P.)
| | - Jorge A. M. Pereira
- CQM—Centro de Química da Madeira, Centro de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal; (P.P.-F.); (J.A.M.P.)
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind, SPPU Campus, Pune 411007, India; (K.T.); (R.T.)
| | - Nattane Luíza da Costa
- Instituto de Informática, Alameda Palmeiras, Quadra D, Campus Samambaia, Universidade Federal de Goiás, Goiânia 74690-900, GO, Brazil; (N.L.d.C.); (R.B.)
| | - Rommel Barbosa
- Instituto de Informática, Alameda Palmeiras, Quadra D, Campus Samambaia, Universidade Federal de Goiás, Goiânia 74690-900, GO, Brazil; (N.L.d.C.); (R.B.)
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind, SPPU Campus, Pune 411007, India; (K.T.); (R.T.)
| | - José S. Câmara
- CQM—Centro de Química da Madeira, Centro de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal; (P.P.-F.); (J.A.M.P.)
- Faculdade de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal
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Behera S, Reddy RR, Taunk K, Rapole S, Pharande RR, Suryawanshi AR. Delineation of altered brain proteins associated with furious rabies virus infection in dogs by quantitative proteomics. J Proteomics 2021; 253:104463. [PMID: 34954397 DOI: 10.1016/j.jprot.2021.104463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/02/2021] [Accepted: 12/19/2021] [Indexed: 11/24/2022]
Abstract
Rabies is a fatal zoonotic disease caused by rabies virus (RABV). Despite the existence of control measures, dog-transmitted human rabies accounts for ˃95% reported cases due to unavailability of sensitive diagnostic methods, inadequate understanding of disease progression and absence of therapeutics. In addition, host factors and their role in RABV infection are poorly understood. In this study, we used 8-plex iTRAQ coupled with HRMS approach to identify differentially abundant proteins (DAPs) of dog brain associated with furious rabies virus infection. Total 40 DAPs including 26 down-regulated and 14 up-regulated proteins were statistically significant in infected samples. GO annotation and IPA showed that calcium signaling and calcium transport, efficient neuronal function, metabolic pathway associated proteins were mostly altered during this infection. Total 34 proteins including 10 down-regulated proteins pertaining to calcium signaling and calcium transport pathways were successfully verified by qRT-PCR and two proteins were verified by western blot, thereby suggesting these pathways may play an important role in this infection. This study provides the map of altered brain proteins and some insights into the molecular pathophysiology associated with furious rabies virus infection. However, further investigations are required to understand their role in disease mechanism. SIGNIFICANCE: Transmission of rabies by dogs poses the greatest hazard world-wide and the rare survival of post-symptomatic patients as well as severe neurological and immunological problems pose a question to understand the molecular mechanism involved in rabies pathogenesis. However, information regarding host factors and their function in RABV infection is still inadequate. Our study has used an advanced quantitative proteomics approach i.e. 8-plex iTRAQ coupled with HRMS and identified 40 DAPs in furious rabies infected dog brain tissues compared to the controls. Further analysis showed that calcium signaling and transport pathway, efficient neuronal functions and metabolic pathway associated brain proteins were most altered during furious rabies virus infection. This data provides a map of altered brain proteins which may have role in furious rabies virus infection. Hence, this will improve our understanding of the molecular pathogenesis of RABV infection.
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Affiliation(s)
- Suchismita Behera
- Clinical Proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India; Regional Centre for Biotechnology, Faridabad, India
| | - R Rajendra Reddy
- Clinical Proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Pune, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Pune, India
| | | | - Amol Ratnakar Suryawanshi
- Clinical Proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India; Regional Centre for Biotechnology, Faridabad, India.
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Khan MZ, Singha B, Ali MF, Taunk K, Rapole S, Gourinath S, Nandicoori VK. Redox homeostasis in Mycobacterium tuberculosis is modulated by a novel actinomycete-specific transcription factor. EMBO J 2021; 40:e106111. [PMID: 34018220 PMCID: PMC8280819 DOI: 10.15252/embj.2020106111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved diverse cellular processes in response to the multiple stresses it encounters within the infected host. We explored available TnSeq datasets to identify transcription factors (TFs) that are essential for Mtb survival inside the host. The analysis identified a single TF, Rv1332 (AosR), conserved across actinomycetes with a so‐far uncharacterized function. AosR mitigates phagocyte‐derived oxidative and nitrosative stress, thus promoting mycobacterial growth in the murine lungs and spleen. Oxidative stress induces formation of a single intrasubunit disulphide bond in AosR, which in turn facilitates AosR interaction with an extracytoplasmic‐function sigma factor, SigH. This leads to the specific upregulation of the CysM‐dependent non‐canonical cysteine biosynthesis pathway through an auxiliary intragenic stress‐responsive promoter, an axis critical in detoxifying host‐derived oxidative and nitrosative radicals. Failure to upregulate AosR‐dependent cysteine biosynthesis during the redox stress causes differential expression of 6% of Mtb genes. Our study shows that the AosR‐SigH pathway is critical for detoxifying host‐derived oxidative and nitrosative radicals to enhance Mtb survival in the hostile intracellular environment.
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Chanukuppa V, Taware R, Taunk K, Chatterjee T, Sharma S, Somasundaram V, Rashid F, Malakar D, Santra MK, Rapole S. Proteomic Alterations in Multiple Myeloma: A Comprehensive Study Using Bone Marrow Interstitial Fluid and Serum Samples. Front Oncol 2021; 10:566804. [PMID: 33585190 PMCID: PMC7879980 DOI: 10.3389/fonc.2020.566804] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
Multiple myeloma (MM) is a plasma cell-associated cancer and exists as the second most common hematological malignancy worldwide. Although researchers have been working on MM, a comprehensive quantitative Bone Marrow Interstitial Fluid (BMIF) and serum proteomic analysis from the same patients’ samples is not yet reported. The present study involves the investigation of alterations in the BMIF and serum proteome of MM patients compared to controls using multipronged quantitative proteomic approaches viz., 2D-DIGE, iTRAQ, and SWATH-MS. A total of 279 non-redundant statistically significant differentially abundant proteins were identified by the combination of three proteomic approaches in MM BMIF, while in the case of serum 116 such differentially abundant proteins were identified. The biological context of these dysregulated proteins was deciphered using various bioinformatic tools. Verification experiments were performed in a fresh independent cohort of samples using immunoblotting and mass spectrometry based SRM assays. Thorough data evaluation led to the identification of a panel of five proteins viz., haptoglobin, kininogen 1, transferrin, and apolipoprotein A1 along with albumin that was validated using ELISA in a larger cohort of serum samples. This panel of proteins could serve as a useful tool in the diagnosis and understanding of the pathophysiology of MM in the future.
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Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Lab, National Centre for Cell Science, Pune, India.,Savitribai Phule Pune University, Pune, India
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Pune, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Pune, India
| | | | | | | | | | | | - Manas K Santra
- Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Pune, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Pune, India
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Taware R, More TH, Bagadi M, Taunk K, Mane A, Rapole S. Lipidomics investigations into the tissue phospholipidomic landscape of invasive ductal carcinoma of the breast. RSC Adv 2021; 11:397-407. [PMID: 35423059 PMCID: PMC8690848 DOI: 10.1039/d0ra07368g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/27/2020] [Indexed: 12/24/2022] Open
Abstract
The need of identifying alternative therapeutic targets for invasive ductal carcinoma (IDC) of the breast with high specificity and sensitivity for effective therapeutic intervention is crucial for lowering the risk of fatality. Lipidomics has emerged as a key area for the discovery of potential candidates owing to its several shared pathways between cancer cell proliferation and survival. In the current study, we performed comparative phospholipidomic analysis of IDC, benign and control tissue samples of the breast to identify the significant lipid alterations associated with malignant transformation. A total of 33 each age-matched tissue samples from malignant, benign and control were analyzed to identify the altered phospholipids by using liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM/MS). A combination of univariate and multivariate statistical approaches was used to select the phospholipid species with the highest contribution in group segregation. Furthermore, these altered phospholipids were structurally confirmed by tandem mass spectrometry. A total of 244 phospholipids were detected consistently at quantifiable levels, out of which 32 were significantly altered in IDC of the breast. Moreover, in pairwise comparison of IDC against benign and control samples, 11 phospholipids were found to be significantly differentially expressed. Particularly, LPI 20:3, PE (22:1/22:2), LPE 20:0 and PC (20:4/22:4) were observed to be most significantly associated with IDC tissue samples. Apart from that, we also identified that long-chain unsaturated fatty acids were enriched in the IDC tissue samples as compared to benign and control samples, indicating its possible association with the invasive phenotype. Identification of tissue phospholipid alternations associated with invasive ductal carcinoma of breast.![]()
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Affiliation(s)
- Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Tushar H. More
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Muralidhararao Bagadi
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Anupama Mane
- Grant Medical Foundation, Ruby Hall Clinic, Pune-411001, MH, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
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Kalita B, Bano S, Vavachan VM, Taunk K, Seshadri V, Rapole S. Application of mass spectrometry based proteomics to understand diabetes: A special focus on interactomics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2020; 1868:140469. [DOI: 10.1016/j.bbapap.2020.140469] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/07/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
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Taunk K, Kalita B, Kale V, Chanukuppa V, Naiya T, Zingde SM, Rapole S. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics 2020; 17:433-451. [PMID: 32576061 DOI: 10.1080/14789450.2020.1787157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic. AREAS COVERED This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed. EXPERT OPINION The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | - Vaikhari Kale
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | | | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Surekha M Zingde
- CH3-53, Kendriya Vihar, Sector 11, Kharghar , Navi Mumbai, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
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Chanukuppa V, Paul D, Taunk K, Chatterjee T, Sharma S, Shirolkar A, Islam S, Santra MK, Rapole S. Proteomics and functional study reveal marginal zone B and B1 cell specific protein as a candidate marker of multiple myeloma. Int J Oncol 2020; 57:325-337. [PMID: 32377723 DOI: 10.3892/ijo.2020.5056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/10/2020] [Indexed: 11/06/2022] Open
Abstract
Multiple myeloma (MM) is a plasma cell‑associated cancer and accounts for 13% of all hematological malignancies, worldwide. MM still remains an incurable plasma cell malignancy with a poor prognosis due to a lack of suitable markers. Therefore, discovering novel markers and targets for diagnosis and therapeutics of MM is essential. The present study aims to identify markers associated with MM malignancy using patient‑derived MM mononuclear cells (MNCs). Label‑free quantitative proteomics analysis revealed a total of 192 differentially regulated proteins, in which 79 proteins were upregulated and 113 proteins were found to be downregulated in MM MNCs as compared to non‑hematological malignant samples. The identified differentially expressed candidate proteins were analyzed using various bioinformatics tools, including Ingenuity Pathway Analysis (IPA), Protein Analysis THrough Evolutionary Relationships (PANTHER), Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Database for Annotation, Visualization and Integrated Discovery (DAVID) to determine their biological context. Among the 192 candidate proteins, marginal zone B and B1 cell specific protein (MZB1) was investigated in detail using the RPMI-8226 cell line model of MM. The functional studies revealed that higher expression of MZB1 is associated with promoting the progression of MM pathogenesis and could be established as a potential target for MM in the future.
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Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Laboratory, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Debasish Paul
- Savitribai Phule Pune University, Pune, Maharashtra 411007, India
| | - Khushman Taunk
- Proteomics Laboratory, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Tathagata Chatterjee
- Army Hospital (Research and Referral), Dhaula Kuan, New Delhi, Delhi 110010, India
| | | | - Amey Shirolkar
- Proteomics Laboratory, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Sehbanul Islam
- Savitribai Phule Pune University, Pune, Maharashtra 411007, India
| | - Manas K Santra
- Cancer Biology and Epigenetics Laboratory, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Srikanth Rapole
- Proteomics Laboratory, National Centre for Cell Science, Pune, Maharashtra 411007, India
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Taware R, Taunk K, Kumar TVS, Pereira JAM, Câmara JS, Nagarajaram HA, Kundu GC, Rapole S. Extracellular volatilomic alterations induced by hypoxia in breast cancer cells. Metabolomics 2020; 16:21. [PMID: 31980945 DOI: 10.1007/s11306-020-1635-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/03/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The metabolic shift induced by hypoxia in cancer cells has not been explored at volatilomic level so far. The volatile organic metabolites (VOMs) constitute an important part of the metabolome and their investigation could provide us crucial aspects of hypoxia driven metabolic reconfiguration in cancer cells. OBJECTIVE To identify the altered volatilomic response induced by hypoxia in metastatic/aggressive breast cancer (BC) cells. METHODS BC cells were cultured under normoxic and hypoxic conditions and VOMs were extracted using HS-SPME approach and profiled by standard GC-MS system. Univariate and multivariate statistical approaches (p < 0.05, Log2 FC ≥ 0.58/≤ - 0.58, PC1 > 0.13/< - 0.13) were applied to select the VOMs differentially altered after hypoxic treatment. Metabolic pathway analysis was also carried out in order to identify altered metabolic pathways induced by the hypoxia in the selected BC cells. RESULTS Overall, 20 VOMs were found to be significantly altered (p < 0.05, PC1 > 0.13/< - 0.13) upon hypoxic exposure to BC cells. Further, cell line specific volatilomic alterations were extracted by comparative metabolic analysis of aggressive (MDA-MB-231) vs. non-aggressive (MCF-7) cells incubated under hypoxia and normoxia. In this case, 15 and 12 VOMs each were found to be significantly altered in aggressive cells when exposed to hypoxic and normoxic condition respectively. Out of these, 9 VOMs were found to be uniquely associated with hypoxia, 6 were specific to normoxia and 6 were found common to both the conditions. Formic acid was identified as the most prominent molecule with higher abundance levels in aggressive as compared to non-aggressive cells in both conditions. Furthermore, metabolic pathway analyses revealed that fatty acid biosynthesis and nicotinate and nicotinamide metabolism were significantly altered in aggressive as compared to non-aggressive cells in normoxia and hypoxia respectively. CONCLUSIONS Higher formate overflow was observed in aggressive cells compared to non-aggressive cells incubated under both the conditions, reinforcing its correlation with aggressive and invasive cancer type. Moreover, under hypoxia, aggressive cells preferred to be bioenergetically more efficient whereas, under normoxia, fatty acid biosynthesis was favoured when compared to non-aggressive cells.
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Affiliation(s)
- Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Totakura V S Kumar
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science (NCCS), Ganeshkhind, Pune, 411007, India
| | - Jorge A M Pereira
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020105, Funchal, Portugal
| | - José S Câmara
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020105, Funchal, Portugal
- Faculdade de Ciências Exatas E da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
| | - H A Nagarajaram
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Gopal C Kundu
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science (NCCS), Ganeshkhind, Pune, 411007, India
- School of Biotechnology, KIIT Deemed to be University, Institute of Eminence, Bhubaneswar, 751024, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
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Chanukuppa V, Paul D, Taunk K, Chatterjee T, Sharma S, Kumar S, Santra MK, Rapole S. XPO1 is a critical player for bortezomib resistance in multiple myeloma: A quantitative proteomic approach. J Proteomics 2019; 209:103504. [PMID: 31465861 DOI: 10.1016/j.jprot.2019.103504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/26/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023]
Abstract
Among the blood cancers, 13% mortality is caused by Multiple myeloma (MM) type of hematological malignancy. In spite of therapeutic advances in chemotherapy treatment, still MM remains an incurable disease is mainly due to emergence of chemoresistance. At present time, FDA approved bortezomib is the first line drug for MM treatment. However, like other chemotherapy, MM patients are acquiring resistance against bortezomib. The present study aims to identify and validate bortezomib resistant protein targets in MM using iTRAQ and label free quantitative proteomic approaches. 112 differentially expressed proteins were commonly found in both approaches with similar differential expression pattern. Exportin-1 (XPO1) protein was selected for further validation as its significant high expression was observed in both iTRAQ and label free analysis. Bioinformatic analysis of these common differentially expressed proteins showed a clear cluster of proteins such as SMC1A, RCC2, CSE1, NUP88, NUP50, TPR, HSPA14, DYNLL1, RAD21 and RANBP2 being associated with XPO1. Functional studies like cell count assay, flow cytometry assay and soft agar assay proved that XPO1 knock down in RPMI 8226R cell line results in re-sensitization to bortezomib drug. The mass spectrometry data are available via ProteomeXchange with identifier PXD013859. BIOLOGICAL SIGNIFICANCE: Multiple myeloma (MM) is a type of hematological malignancy which constitutes about 13% of all blood cell related malignancies. Chemoresistance is one of the major obstacles for the successful treatment for MM. Bortezomib is a first proteasome inhibitor drug, widely used in MM treatment. The present study aims to identify and validate bortezomib resistant protein targets in MM. Here, we identified 112 candidate proteins to be associated with bortezomib resistance using global quantitative proteomic analysis. Among these candidate proteins, we show that XPO1 plays crucial role in emerging bortezomib resistance using functional studies like cell count assay, flow cytometry assay and soft agar assay. XPO1 could be a potential therapeutic target for MM and development of inhibitors of XPO1 might help to cure MM.
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Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India
| | - Debasish Paul
- Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India; Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | | | | | - Saravanan Kumar
- Thermo Fisher Scientific India Pvt. Ltd, Whitefield, Bangalore 560066, KA, India
| | - Manas K Santra
- Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India.
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Chanukuppa V, Taware R, Chatterjee T, Sharma S, More TH, Taunk K, Kumar S, Santra MK, Rapole S. Current Understanding of the Potential of Proteomics and Metabolomics Approaches in Cancer Chemoresistance: A Focus on Multiple Myeloma. Curr Top Med Chem 2019; 18:2584-2598. [DOI: 10.2174/1568026619666181130111202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/17/2018] [Accepted: 11/17/2018] [Indexed: 11/22/2022]
Abstract
Chemoresistance is one of the major hurdles in cancer treatment leading to recurrence of cancer
and affects the overall survival of patients. Cancer chemoresistance can be associated with various
phenomena including modulation of vital cellular pathways. Unrevealing these alterations could provide
a better understanding of chemoresistance and assist in the identification of new targets to overcome it.
Recent advances in the field of proteomics and metabolomics have substantially helped in the
identification of potential targets for chemoresistance in various cancers. This review highlights the potential
of proteomics and metabolomics research to explore the putative targets associated with cancer
chemoresistance with a special focus on Multiple Myeloma (MM). MM is a type of hematological malignancy
which constitutes about 13% of all blood cell cancers. The therapeutic advancements for MM
have increased the median overall survival rate to over 3-fold in the last one and half decade. Although
in recent times, significant improvements in the overall survival rate of MM are achieved, MM remains
an incurable disease with unpredictable refractory mechanisms. In spite of therapeutic advances,
chemoresistance thrives to be a major hurdle in the treatment of multiple myeloma which demands a
better understanding of chemoresistance. In this review, we have attempted to highlight the potential
applications of proteomics and metabolomics research in the understanding of chemoresistance in MM.
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Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | | | | | - Tushar H. More
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
| | - Saravanan Kumar
- Thermo Fisher Scientific India Pvt. Ltd., Whitefield, Bangalore-560066, Karnataka, India
| | - Manas K. Santra
- Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune-411007, MH, India
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Chanukuppa V, More TH, Taunk K, Taware R, Chatterjee T, Sharma S, Rapole S. Serum metabolomic alterations in multiple myeloma revealed by targeted and untargeted metabolomics approaches: a pilot study. RSC Adv 2019; 9:29522-29532. [PMID: 35531512 PMCID: PMC9071903 DOI: 10.1039/c9ra04458b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Multiple myeloma (MM) is the second most prevalent hematological malignancy characterized by rapid proliferation of plasma cells, which leads to overproduction of antibodies. MM affects around 15% of all hemato-oncology cases across the world. The present study involves identification of metabolomic alterations in the serum of an MM cohort compared to healthy controls using both LC-MRM/MS based targeted and GC-MS based untargeted approaches. Several MM specific serum metabolomic signatures were observed in this study. A total of 54 metabolites were identified as being significantly altered in MM cohort, out of which, 26 metabolites were identified from LC-MRM/MS based targeted analysis, whereas 28 metabolites were identified from the GC-MS based untargeted analysis. Receiver operating characteristic (ROC) curve analysis demonstrated that six metabolites each from both the datasets can be projected as marker metabolites to discriminate MM subjects with higher specificity and sensitivity. Moreover, pathway analysis deciphered that several metabolic pathways were altered in MM including pyrimidine metabolism, purine metabolism, amino acid metabolism, nitrogen metabolism, sulfur metabolism, and the citrate cycle. Comprehensively, this study contributes valuable information regarding MM induced serum metabolite alterations and their pathways, which could offer further insights into this cancer. This study presents the potential of serum metabolomics approach towards the segregation of multiple myeloma cohort from healthy controls.![]()
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Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Lab
- National Centre for Cell Science
- Pune-411007
- India
- Savitribai Phule Pune University
| | - Tushar H. More
- Proteomics Lab
- National Centre for Cell Science
- Pune-411007
- India
- Savitribai Phule Pune University
| | - Khushman Taunk
- Proteomics Lab
- National Centre for Cell Science
- Pune-411007
- India
| | - Ravindra Taware
- Proteomics Lab
- National Centre for Cell Science
- Pune-411007
- India
| | | | | | - Srikanth Rapole
- Proteomics Lab
- National Centre for Cell Science
- Pune-411007
- India
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More TH, Taware R, Taunk K, Chanukuppa V, Naik V, Mane A, Rapole S. Investigation of altered urinary metabolomic profiles of invasive ductal carcinoma of breast using targeted and untargeted approaches. Metabolomics 2018; 14:107. [PMID: 30830381 DOI: 10.1007/s11306-018-1405-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/01/2018] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Invasive ductal carcinoma (IDC) is a type of breast cancer, usually detected in advanced stages due to its asymptomatic nature which ultimately leads to low survival rate. Identification of urinary metabolic adaptations induced by IDC to understand the disease pathophysiology and monitor therapy response would be a helpful approach in clinical settings. Moreover, its non-invasive and cost effective strategy better suited to minimize apprehension among high risk population. OBJECTIVE This study aims toward investigating the urinary metabolic alterations of IDC by targeted (LC-MRM/MS) and untargeted (GC-MS) approaches for the better understanding of the disease pathophysiology and monitoring therapy response. METHODS Urinary metabolic alterations of IDC subjects (63) and control subjects (63) were explored by targeted (LC-MRM/MS) and untargeted (GC-MS) approaches. IDC specific urinary metabolomics signature was extracted by applying both univariate and multivariate statistical tools. RESULTS Statistical analysis identified 39 urinary metabolites with the highest contribution to metabolomic alterations specific to IDC. Out of which, 19 metabolites were identified from targeted LC-MRM/MS analysis, while 20 were identified from the untargeted GC-MS analysis. Receiver operator characteristic (ROC) curve analysis evidenced 6 most discriminatory metabolites from each type of approach that could differentiate between IDC subjects and controls with higher sensitivity and specificity. Furthermore, metabolic pathway analysis depicted several dysregulated pathways in IDC including sugar, amino acid, nucleotide metabolism, TCA cycle etc. CONCLUSIONS: Overall, this study provides valuable inputs regarding altered urinary metabolites which improved our knowledge on urinary metabolomic alterations induced by IDC. Moreover, this study identified several dysregulated metabolic pathways which offer further insight into the disease pathophysiology.
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Affiliation(s)
- Tushar H More
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, MH, India
- Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, MH, India
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, MH, India
| | - Venkatesh Chanukuppa
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, MH, India
- Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, MH, India
| | - Venkateshwarlu Naik
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, MH, India
| | - Anupama Mane
- Grant Medical Foundation, Ruby Hall Clinic, Pune, 411001, MH, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, MH, India.
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Cavaco C, Pereira JAM, Taunk K, Taware R, Rapole S, Nagarajaram H, Câmara JS. Screening of salivary volatiles for putative breast cancer discrimination: an exploratory study involving geographically distant populations. Anal Bioanal Chem 2018; 410:4459-4468. [PMID: 29732495 DOI: 10.1007/s00216-018-1103-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/05/2018] [Accepted: 04/20/2018] [Indexed: 01/08/2023]
Abstract
Saliva is possibly the easiest biofluid to analyse and, despite its simple composition, contains relevant metabolic information. In this work, we explored the potential of the volatile composition of saliva samples as biosignatures for breast cancer (BC) non-invasive diagnosis. To achieve this, 106 saliva samples of BC patients and controls in two distinct geographic regions in Portugal and India were extracted and analysed using optimised headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME/GC-MS, 2 mL acidified saliva containing 10% NaCl, stirred (800 rpm) for 45 min at 38 °C and using the CAR/PDMS SPME fibre) followed by multivariate statistical analysis (MVSA). Over 120 volatiles from distinct chemical classes, with significant variations among the groups, were identified. MVSA retrieved a limited number of volatiles, viz. 3-methyl-pentanoic acid, 4-methyl-pentanoic acid, phenol and p-tert-butyl-phenol (Portuguese samples) and acetic, propanoic, benzoic acids, 1,2-decanediol, 2-decanone, and decanal (Indian samples), statistically relevant for the discrimination of BC patients in the populations analysed. This work defines an experimental layout, HS-SPME/GC-MS followed by MVSA, suitable to characterise volatile fingerprints for saliva as putative biosignatures for BC non-invasive diagnosis. Here, it was applied to BC samples from geographically distant populations and good disease separation was obtained. Further studies using larger cohorts are therefore very pertinent to challenge and strengthen this proof-of-concept study. Graphical abstract ᅟ.
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Affiliation(s)
- Carina Cavaco
- CQM-UMa - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
| | - Jorge A M Pereira
- CQM-UMa - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal.
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Hampapathalu Nagarajaram
- Laboratory of Computational Biology, Centre for DNA Fingerprinting & Diagnostics (CDFD), Nampally, Hyderabad, 500001, India.,Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India
| | - José S Câmara
- CQM-UMa - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal.,Faculdade de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
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More TH, RoyChoudhury S, Christie J, Taunk K, Mane A, Santra MK, Chaudhury K, Rapole S. Metabolomic alterations in invasive ductal carcinoma of breast: A comprehensive metabolomic study using tissue and serum samples. Oncotarget 2018; 9:2678-2696. [PMID: 29416801 PMCID: PMC5788669 DOI: 10.18632/oncotarget.23626] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/08/2017] [Indexed: 01/05/2023] Open
Abstract
Invasive ductal carcinoma (IDC) is the most common type of breast cancer and the leading cause of breast cancer related mortality. In the present study, metabolomic profiles of 72 tissue samples and 146 serum samples were analysed using targeted liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM/MS) and untargeted gas chromatography mass spectrometry (GC-MS) approaches. Combination of univariate and multivariate statistical treatment identified significant alterations of 42 and 32 metabolites in tissue and serum samples of IDC, respectively when compared to control. Some of the metabolite changes from tissue were also reflected in serum, indicating a bi-directional interaction of metabolites in IDC. Additionally, 8 tissue metabolites and 9 serum metabolites showed progressive change from control to benign to IDC suggesting their possible role in malignant transformation. We have identified a panel of three metabolites viz. tryptophan, tyrosine, and creatine in tissue and serum, which could be useful in screening of IDC subjects from both control and benign. The metabolomic alterations in IDC showed perturbations in purine and pyrimidine metabolism, amino sugar metabolism, amino acid metabolism, fatty acid biosynthesis etc. Comprehensively, this study provides valuable insights into metabolic adaptations of IDC, which can help to identify diagnostic markers as well as potential therapeutic targets.
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Affiliation(s)
- Tushar H. More
- Proteomics Lab, National Center for Cell Science, Ganeshkhind, Pune 411007, MH, India
- Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India
| | - Sourav RoyChoudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Joel Christie
- Proteomics Lab, National Center for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Center for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Anupama Mane
- Grant Medical Foundation, Ruby Hall Clinic, Pune 411001, MH, India
| | - Manas K. Santra
- Cancer Biology and Epigenetics Lab, National Center for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Srikanth Rapole
- Proteomics Lab, National Center for Cell Science, Ganeshkhind, Pune 411007, MH, India
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Taunk K, Taware R, More TH, Porto-Figueira P, Pereira JAM, Mohapatra R, Soneji D, Câmara JS, Nagarajaram HA, Rapole S. A non-invasive approach to explore the discriminatory potential of the urinary volatilome of invasive ductal carcinoma of the breast. RSC Adv 2018; 8:25040-25050. [PMID: 35542123 PMCID: PMC9082450 DOI: 10.1039/c8ra02083c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/24/2018] [Indexed: 01/13/2023] Open
Abstract
A non-invasive urinary volatilomics approach for exploring the IDC type breast cancer.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab
- National Centre for Cell Science
- Pune 411007
- India
| | - Ravindra Taware
- Proteomics Lab
- National Centre for Cell Science
- Pune 411007
- India
| | - Tushar H. More
- Proteomics Lab
- National Centre for Cell Science
- Pune 411007
- India
| | - Priscilla Porto-Figueira
- CQM – Centro de Química da Madeira
- Universidade da Madeira
- Campus Universitário da Penteada
- Funchal 9000-390
- Portugal
| | - Jorge A. M. Pereira
- CQM – Centro de Química da Madeira
- Universidade da Madeira
- Campus Universitário da Penteada
- Funchal 9000-390
- Portugal
| | - Rajkishore Mohapatra
- Laboratory of Computational Biology
- Centre for DNA Fingerprinting & Diagnostics (CDFD)
- Hyderabad
- India
| | - Dharmesh Soneji
- Malignant Disease Treatment Centre
- Military Hospital (Cardio Thoracic Centre)
- Armed Forces Medical College
- Pune 411040
- India
| | - José S. Câmara
- CQM – Centro de Química da Madeira
- Universidade da Madeira
- Campus Universitário da Penteada
- Funchal 9000-390
- Portugal
| | - H. A. Nagarajaram
- Laboratory of Computational Biology
- Centre for DNA Fingerprinting & Diagnostics (CDFD)
- Hyderabad
- India
- Department of Biotechnology & Bioinformatics
| | - Srikanth Rapole
- Proteomics Lab
- National Centre for Cell Science
- Pune 411007
- India
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Gajbhiye A, Dabhi R, Taunk K, Jagadeeshaprasad MG, RoyChoudhury S, Mane A, Bayatigeri S, Chaudhury K, Santra MK, Rapole S. Multipronged quantitative proteomics reveals serum proteome alterations in breast cancer intrinsic subtypes. J Proteomics 2017; 163:1-13. [DOI: 10.1016/j.jprot.2017.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/29/2022]
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Gajbhiye A, Dabhi R, Taunk K, Vannuruswamy G, RoyChoudhury S, Adhav R, Seal S, Mane A, Bayatigeri S, Santra MK, Chaudhury K, Rapole S. Urinary proteome alterations in HER2 enriched breast cancer revealed by multipronged quantitative proteomics. Proteomics 2016; 16:2403-18. [DOI: 10.1002/pmic.201600015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/27/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Akshada Gajbhiye
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
- Savitribai Phule Pune University; Ganeshkhind Pune Maharashtra India
| | - Raju Dabhi
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Khushman Taunk
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Sourav RoyChoudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Ragini Adhav
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Anupama Mane
- Grant Medical Foundation; Ruby Hall Clinic; Pune Maharashtra India
| | | | - Manas K. Santra
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Koel Chaudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Srikanth Rapole
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
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Paul D, Chanukuppa V, Reddy PJ, Taunk K, Adhav R, Srivastava S, Santra MK, Rapole S. Global proteomic profiling identifies etoposide chemoresistance markers in non-small cell lung carcinoma. J Proteomics 2016; 138:95-105. [DOI: 10.1016/j.jprot.2016.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 12/31/2015] [Accepted: 02/11/2016] [Indexed: 02/05/2023]
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Pendharkar N, Gajbhiye A, Taunk K, RoyChoudhury S, Dhali S, Seal S, Mane A, Abhang S, Santra MK, Chaudhury K, Rapole S. Quantitative tissue proteomic investigation of invasive ductal carcinoma of breast with luminal B HER2 positive and HER2 enriched subtypes towards potential diagnostic and therapeutic biomarkers. J Proteomics 2015; 132:112-30. [PMID: 26642762 DOI: 10.1016/j.jprot.2015.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/16/2015] [Accepted: 11/26/2015] [Indexed: 02/09/2023]
Abstract
Worldwide, breast cancer is one of the frequently diagnosed cancers in women with high mortality if not diagnosed at early stage. Although biomarker discoveries through various proteomic approaches have been studied in breast cancer, a limited number of studies have explored the invasive ductal carcinoma with Luminal B HER2 positive (LB) and HER2 enriched (HE) subtypes. The present study employed the complementary quantitative proteomic approaches to find a panel of markers that could discriminate LB and HE subtypes as well as early (ES) and late stages (LS) of these subtypes. A total of 67 and 68 differentially expressed proteins were identified by DIGE for the subtype and stage wise categories, respectively. Multivariate statistical analysis was employed to identify the set of most significant proteins, which could discriminate between these two subtypes and also early and late stages under study. Immunoblotting and MRM based validation in a separate cohort of samples confirmed that panel of biosignatures for LB are APOA1, GELS, HS90B, EF1A1, NHRF1 and PRDX3 and for HE are PRDX1, CATD, CALR, ATPB and CH60. For the diagnosis of early and late stages the potential markers are TPM4, CATD, PRDX3, ANXA3, HSPB1 and CALR, TRFE, GELS, CH60, CAPG, NHRF1, 1433G, GRP78 respectively.
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Affiliation(s)
- Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India; B. J. Medical College, Sassoon Hospital, Pune 411001, MH, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Sourav RoyChoudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | | | - Anupama Mane
- Grant Medical Foundation, Ruby Hall Clinic, Pune 411001, MH, India
| | | | - Manas K Santra
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India.
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Pereira J, Porto-Figueira P, Cavaco C, Taunk K, Rapole S, Dhakne R, Nagarajaram H, Câmara JS. Breath analysis as a potential and non-invasive frontier in disease diagnosis: an overview. Metabolites 2015; 5:3-55. [PMID: 25584743 PMCID: PMC4381289 DOI: 10.3390/metabo5010003] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/12/2014] [Indexed: 02/06/2023] Open
Abstract
Currently, a small number of diseases, particularly cardiovascular (CVDs), oncologic (ODs), neurodegenerative (NDDs), chronic respiratory diseases, as well as diabetes, form a severe burden to most of the countries worldwide. Hence, there is an urgent need for development of efficient diagnostic tools, particularly those enabling reliable detection of diseases, at their early stages, preferably using non-invasive approaches. Breath analysis is a non-invasive approach relying only on the characterisation of volatile composition of the exhaled breath (EB) that in turn reflects the volatile composition of the bloodstream and airways and therefore the status and condition of the whole organism metabolism. Advanced sampling procedures (solid-phase and needle traps microextraction) coupled with modern analytical technologies (proton transfer reaction mass spectrometry, selected ion flow tube mass spectrometry, ion mobility spectrometry, e-noses, etc.) allow the characterisation of EB composition to an unprecedented level. However, a key challenge in EB analysis is the proper statistical analysis and interpretation of the large and heterogeneous datasets obtained from EB research. There is no standard statistical framework/protocol yet available in literature that can be used for EB data analysis towards discovery of biomarkers for use in a typical clinical setup. Nevertheless, EB analysis has immense potential towards development of biomarkers for the early disease diagnosis of diseases.
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Affiliation(s)
- Jorge Pereira
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, Funchal 9000-390, Portugal.
| | - Priscilla Porto-Figueira
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, Funchal 9000-390, Portugal.
| | - Carina Cavaco
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, Funchal 9000-390, Portugal.
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Rahul Dhakne
- Laboratory of Computational Biology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Andhra Pradesh 500 001, India.
| | - Hampapathalu Nagarajaram
- Laboratory of Computational Biology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Andhra Pradesh 500 001, India.
| | - José S Câmara
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, Funchal 9000-390, Portugal.
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Dutta M, Subramani E, Taunk K, Gajbhiye A, Seal S, Pendharkar N, Dhali S, Ray CD, Lodh I, Chakravarty B, Dasgupta S, Rapole S, Chaudhury K. Mass spectrometry and bioinformatics analysis data. Data Brief 2014. [PMID: 26217699 PMCID: PMC4459760 DOI: 10.1016/j.dib.2014.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
2DE and 2D-DIGE based proteomics analysis of serum from women with endometriosis revealed several proteins to be dysregulated. A complete list of these proteins along with their mass spectrometry data and subsequent bioinformatics analysis are presented here. The data is related to “Investigation of serum proteome alterations in human endometriosis” by Dutta et al. [1].
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Affiliation(s)
- Mainak Dutta
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Elavarasan Subramani
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | | | - Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Chaitali Datta Ray
- Institute of Post Graduate Medical Education & Research, Obstetrics & Gynecology, Kolkata, West Bengal, India
| | - Indrani Lodh
- Institute of Reproductive Medicine, Sector-III, Kolkata, West Bengal, India
| | | | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
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Dutta M, Subramani E, Taunk K, Gajbhiye A, Seal S, Pendharkar N, Dhali S, Ray CD, Lodh I, Chakravarty B, Dasgupta S, Rapole S, Chaudhury K. Investigation of serum proteome alterations in human endometriosis. J Proteomics 2014; 114:182-96. [PMID: 25449831 DOI: 10.1016/j.jprot.2014.10.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 10/23/2014] [Accepted: 10/29/2014] [Indexed: 12/26/2022]
Abstract
UNLABELLED Endometriosis is a common benign gynecological disease, characterized by proliferation of functional endometrial glands and stroma outside the uterine cavity. The present study involves investigation of alterations in the serum proteome of endometriosis patients compared to healthy controls using 2DE and 2D-DIGE combined with MALDI TOF/TOF-MS. Comparison of serum proteome of endometriosis patients and healthy subjects revealed 25 significant differentially expressed proteins. Gene ontology and network analysis, performed using PANTHER, DAVID, WebGestalt and STRING, revealed that the differentially expressed proteins are majorly involved in response to stimulus, immune system, metabolic, localization and cellular processes. For serum diagnostic marker identification, several robust statistical screening procedures were applied to identify the set of the most significant proteins responsible for successful diagnosis of different endometriosis stages. Partial least squares (PLS) based marker selection tool and orthogonal partial least squares-discriminant analysis (OPLS-DA) were used to identify the most significant proteins for disease prediction. Western blotting validation in a separate cohort of patients revealed that haptoglobin (HP), Ig kappa chain C region (IGKC), alpha-1B-glycoprotein (A1BG) can be considered effective serum protein markers for the diagnosis of Stage II, III and IV endometriosis. For diagnosis of Stage I, only IGKC and HP seemed promising. BIOLOGICAL SIGNIFICANCE Globally, about 12 in 100 women of reproductive age are diagnosed with endometriosis. The pathogenesis of the disease still remains unclear, leading to non-specific therapeutic approaches for disease management. Moreover, there is a delay of 8-12years in correct diagnosis after the initial onset of symptoms leading to a considerable impact on the woman's lifestyle. Also, the gold standard for diagnosis of endometriosis, laparoscopy, is an invasive procedure. The value of a noninvasive or semi-invasive diagnostic test for endometriosis with easily accessible fluids such as plasma, serum, urine, and saliva is, therefore, rightfully recognized. The present study is expected to considerably improve the understanding of the disease pathogenesis along with improved diagnostics and therapeutic approaches leading to better management of the disease.
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Affiliation(s)
- Mainak Dutta
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Elavarasan Subramani
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | | | - Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Chaitali Datta Ray
- Institute of Post Graduate Medical Education & Research, Obstetrics & Gynecology, Kolkata, West Bengal, India
| | - Indrani Lodh
- Institute of Reproductive Medicine, Sector-III, Kolkata, West Bengal, India
| | | | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India.
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