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Lu X, Fu Y, Gu L, Zhang Y, Liao AY, Wang T, Jia B, Zhou D, Liao L. Integrated proteome and phosphoproteome analysis of gastric adenocarcinoma reveals molecular signatures capable of stratifying patient outcome. Mol Oncol 2022; 17:261-283. [PMID: 36520032 PMCID: PMC9892830 DOI: 10.1002/1878-0261.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Metastasis is one of the main causes of low survival rate of gastric cancer patients. Exploring key proteins in the progression of gastric adenocarcinoma (GAC) may provide new candidates for prognostic biomarker development and therapeutic intervention. We applied quantitative mass spectrometry to compare the proteome and phosphoproteome of primary tumor tissues between GAC patients with and without lymph node metastasis (LNM). We then performed an integrated analysis of the proteomic and transcriptomic data to reveal the molecular features. We quantified a total of 5536 proteins, and we found 218 upregulated and 49 downregulated proteins in tumor samples from patients with LNM compared to those without LNM. Clustering analysis identified a number of hub proteins that have been previously shown to play important roles in gastric cancer progression. We also found that two extracellular proteins, TNXB and SPON1, are overexpressed in patients with LNM, which correlates with poor survival of GAC patients. Overexpression of TNXB and SPON1 was validated by western blotting and immunohistochemistry. Furthermore, treating gastric cancer cells with anti-TNXB antibody significantly reduced cell migration. Finally, quantitative phosphoproteomic analysis combined with activity-based kinase capture revealed a number of activated kinases in primary tumor tissues from patients with LNM, among which GSK3 might be a new target that warrants further study. Our study provides a snapshot of the proteome and phosphoproteome of GAC tumor tissues that have metastatic potential, and identifies potential biomarkers for GAC progression.
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Affiliation(s)
- Xue Lu
- Shanghai Key Laboratory of Regulatory Biology, School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Yunyun Fu
- Shanghai Key Laboratory of Regulatory Biology, School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Lei Gu
- Department of General Surgery, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yunpeng Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life SciencesEast China Normal UniversityShanghaiChina
| | | | | | - Bin Jia
- Department of OncologyThe First Affiliated Hospital of Zhengzhou UniversityChina
| | - Donglei Zhou
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterChina,Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, School of Life SciencesEast China Normal UniversityShanghaiChina
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2
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Wang EJY, Chen IH, Kuo BYT, Yu CC, Lai MT, Lin JT, Lin LYT, Chen CM, Hwang T, Sheu JJC. Alterations of Cytoskeleton Networks in Cell Fate Determination and Cancer Development. Biomolecules 2022; 12:biom12121862. [PMID: 36551290 PMCID: PMC9775460 DOI: 10.3390/biom12121862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Cytoskeleton proteins have been long recognized as structural proteins that provide the necessary mechanical architecture for cell development and tissue homeostasis. With the completion of the cancer genome project, scientists were surprised to learn that huge numbers of mutated genes are annotated as cytoskeletal or associated proteins. Although most of these mutations are considered as passenger mutations during cancer development and evolution, some genes show high mutation rates that can even determine clinical outcomes. In addition, (phospho)proteomics study confirms that many cytoskeleton-associated proteins, e.g., β-catenin, PIK3CA, and MB21D2, are important signaling mediators, further suggesting their biofunctional roles in cancer development. With emerging evidence to indicate the involvement of mechanotransduction in stemness formation and cell differentiation, mutations in these key cytoskeleton components may change the physical/mechanical properties of the cells and determine the cell fate during cancer development. In particular, tumor microenvironment remodeling triggered by such alterations has been known to play important roles in autophagy, metabolism, cancer dormancy, and immune evasion. In this review paper, we will highlight the current understanding of how aberrant cytoskeleton networks affect cancer behaviors and cellular functions through mechanotransduction.
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Affiliation(s)
- Evan Ja-Yang Wang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - I-Hsuan Chen
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Brian Yu-Ting Kuo
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chia-Cheng Yu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114202, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung 403301, Taiwan
| | - Jen-Tai Lin
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
| | - Leo Yen-Ting Lin
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital, Taichung 404327, Taiwan
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Correspondence: ; Tel.: +886-7-5252000 (ext. 7102)
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3
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George IA, Sathe G, Ghose V, Chougule A, Chandrani P, Patil V, Noronha V, Venkataramanan R, Limaye S, Pandey A, Prabhash K, Kumar P. Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer. Front Cell Dev Biol 2022; 10:957983. [PMID: 36393868 PMCID: PMC9651967 DOI: 10.3389/fcell.2022.957983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/04/2022] [Indexed: 03/27/2024] Open
Abstract
Tongue squamous cell carcinoma is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. Most of the oral cavity cancer patients present in clinics with locally advanced unresectable tumors. Neoadjuvant treatment is beneficial for these individuals as it reduces the tumor size aiding complete resection. However, patients develop therapy resistance to the drug regimen. In this study, we explored the differential expression of proteins and altered phosphorylation in the neoadjuvant chemotherapy resistant tongue cancer patients. We integrated the proteomic and phosphoproteomic profiles of resistant (n = 4) and sensitive cohorts (n = 4) and demonstrated the differential expression and phosphorylation of proteins in the primary tissue of the respective subject groups. We observed differential and extensive phosphorylation of keratins such as KRT10 and KRT1 between the two cohorts. Furthermore, our study revealed a kinase signature associated with neoadjuvant chemotherapy resistance. Kinases such as MAPK1, AKT1, and MAPK3 are predicted to regulate the resistance in non-responders. Pathway analysis showed enrichment of Rho GTPase signaling and hyperphosphosphorylation of proteins involved in cell motility, invasion, and drug resistance. Targeting the kinases could help with the clinical management of neoadjuvant chemotherapy-resistant tongue cancer.
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Affiliation(s)
- Irene A. George
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, Bangalore, India
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vivek Ghose
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | | | | | | | | | - Sewanti Limaye
- Sir H.N. Reliance Foundation Hospital and Research Centre, Mumbai, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Prashant Kumar
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Karkinos Healthcare Pvt Ltd., Mumbai, India
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4
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Laforgue L, Fertin A, Usson Y, Verdier C, Laurent VM. Efficient deformation mechanisms enable invasive cancer cells to migrate faster in 3D collagen networks. Sci Rep 2022; 12:7867. [PMID: 35550548 PMCID: PMC9098560 DOI: 10.1038/s41598-022-11581-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer cell migration is a widely studied topic but has been very often limited to two dimensional motion on various substrates. Indeed, less is known about cancer cell migration in 3D fibrous-extracellular matrix (ECM) including variations of the microenvironment. Here we used 3D time lapse imaging on a confocal microscope and a phase correlation method to follow fiber deformations, as well as cell morphology and live actin distribution during the migration of cancer cells. Different collagen concentrations together with three bladder cancer cell lines were used to investigate the role of the metastatic potential on 3D cell migration characteristics. We found that grade-3 cells (T24 and J82) are characterized by a great diversity of shapes in comparison with grade-2 cells (RT112). Moreover, grade-3 cells with the highest metastatic potential (J82) showed the highest values of migration speeds and diffusivities at low collagen concentration and the greatest sensitivity to collagen concentration. Our results also suggested that the small shape fluctuations of J82 cells are the signature of larger migration velocities. Moreover, the displacement fields generated by J82 cells showed significantly higher fiber displacements as compared to T24 and RT112 cells, regardless of collagen concentration. The analysis of cell movements enhanced the fact that bladder cancer cells were able to exhibit different phenotypes (mesenchymal, amoeboid). Furthermore, the analysis of spatio-temporal migration mechanisms showed that cancer cells are able to push or pull on collagen fibers, therefore producing efficient local collagen deformations in the vicinity of cells. Our results also revealed that dense actin regions are correlated with the largest displacement fields, and this correlation is enhanced for the most invasive J82 cancer cells. Therefore this work opens up new routes to understand cancer cell migration in soft biological networks.
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Affiliation(s)
- Laure Laforgue
- Univ. Grenoble Alpes, CNRS, LIPhy, 38000, Grenoble, France.,Institute for Advanced Biosciences, INSERM U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Grenoble, 38000, France
| | - Arnold Fertin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Yves Usson
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Claude Verdier
- Univ. Grenoble Alpes, CNRS, LIPhy, 38000, Grenoble, France.
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Jain AP, Sambath J, Sathe G, George IA, Pandey A, Thompson EW, Kumar P. Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. J Transl Med 2022; 20:84. [PMID: 35148768 PMCID: PMC8832824 DOI: 10.1186/s12967-021-03227-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/30/2021] [Indexed: 12/31/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a dynamic and complex cellular process that is known to be hijacked by cancer cells to facilitate invasion, metastasis and therapeutic resistance. Several quantitative measures to assess the interplay between EMT and cancer progression are available, based on large scale genome and transcriptome data. However, these large scale multi-omics studies have repeatedly illustrated a lack of correlation in mRNA and protein abundances that may be influenced by diverse post-translational regulation. Hence, it is imperative to understand how changes in the EMT proteome are associated with the process of oncogenic transformation. To this effect, we developed a parallel reaction monitoring-based targeted proteomics method for quantifying abundances of EMT-associated proteins across cancer cell lines. Our study revealed that quantitative measurement of EMT proteome which enabled a more accurate assessment than transcriptomics data and revealed specific discrepancies against a backdrop of generally strong concordance between proteomic and transcriptomic data. We further demonstrated that changes in our EMT proteome panel might play a role in tumor transformation across cancer types. In future, this EMT panel assay has the potential to be used for clinical samples to guide treatment choices and to congregate functional information for the development and advancing novel therapeutics.
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Affiliation(s)
- Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
| | - Janani Sambath
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Erik W Thompson
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia. .,School-Biomedical Sciences, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India. .,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India. .,Somaiya Institute of Research and Consultancy (SIRAC), Somaiya Vidyavihar University (SVU), Vidyavihar, Mumbai, 400077, Maharashtra, India.
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6
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Wang G, Sun D, Li W, Xin Y. CircRNA_100290 promotes GC cell proliferation and invasion via the miR-29b-3p/ITGA11 axis and is regulated by EIF4A3. Cancer Cell Int 2021; 21:324. [PMID: 34182990 PMCID: PMC8240270 DOI: 10.1186/s12935-021-01964-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/04/2021] [Indexed: 12/29/2022] Open
Abstract
Background Circular RNAs (circRNAs) have been reported to be important regulators of the development and progression of various carcinomas. However, the role of circRNA_100290 in gastric cancer (GC) is still unclear. This study aimed to investigate the role of circRNA_100290 in GC invasion and metastasis and the possible underlying mechanism. Methods The expression of circRNA_100290 in GC cells and tissues was examined using quantitative real-time polymerase chain reaction (qRT-PCR). The role of circRNA_100290 in cell proliferation, migration, and invasion was evaluated in the AGS and HGC-27 cell lines in vitro. Bioinformatics tools, dual-luciferase reporter assays, Western blot assays and qRT-PCR were used to explore the pathways downstream of circRNA_100290. The mechanism underlying the regulation of circRNA_100290 expression was explored using RNA immunoprecipitation, qRT-PCR, and Western blot assays. Results The expression of circRNA_100290 was significantly upregulated in GC cells and 102 GC tissues, and high circRNA_100290 expression in GC was closely related to Borrmann’s type, lymph node metastasis and tumour-node-metastasis stage. In vitro, knockdown of circRNA_100290 in AGS and HGC-27 cells significantly inhibited cell proliferation, migration, and invasion. Mechanistically, a dual-luciferase reporter assay confirmed the direct interaction between circRNA_100290 and miR-29b-3p, which targets ITGA11, an oncogene that is closely related to epithelial–mesenchymal transition (EMT). In addition, EIF4A3, an RNA-binding protein (RBP), could inhibit the formation of circRNA_100290 by binding to the flanking sites of circRNA_100290. Low EIF4A3 expression in GC was related to a poor prognosis. Conclusions Elevated circRNA_100290 expression in GC promotes cell proliferation, invasion and EMT via the miR-29b-3p/ITGA11 axis and might be regulated by EIF4A3. CircRNA_100290 might be a promising biomarker and target for GC therapy. Graphical abstract ![]()
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Affiliation(s)
- Gang Wang
- Laboratory of Gastrointestinal Onco-Pathology, Cancer Institute, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province, China.,Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Lung Cancer Institute, 16766 Jingshi Road, Lixia District, Jinan, Shandong Province, China
| | - Dan Sun
- Laboratory of Gastrointestinal Onco-Pathology, Cancer Institute, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province, China
| | - Wenhui Li
- Laboratory of Gastrointestinal Onco-Pathology, Cancer Institute, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province, China
| | - Yan Xin
- Laboratory of Gastrointestinal Onco-Pathology, Cancer Institute, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province, China.
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7
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Gondkar K, Sathe G, Joshi N, Nair B, Pandey A, Kumar P. Integrated Proteomic and Phosphoproteomics Analysis of DKK3 Signaling Reveals Activated Kinase in the Most Aggressive Gallbladder Cancer. Cells 2021; 10:cells10030511. [PMID: 33670899 PMCID: PMC7997438 DOI: 10.3390/cells10030511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
DKK3 is a secreted protein, which belongs to a family of Wnt antagonists and acts as a potential tumor suppressor in gallbladder cancer. To further understand its tumor suppressor functions, we overexpressed DKK3 in 3 GBC cell lines. We have employed high-resolution mass spectrometry and tandem mass tag (TMT) multiplexing technology along with immobilized metal affinity chromatography to enrich phosphopeptides to check the downstream regulators. In this study, we reported for the first time the alteration in the phosphorylation of 14 kinases upon DKK3 overexpression. In addition, we observed DKK3 induced hyper phosphorylation of 2 phosphatases: PPP1R12A and PTPRA, which have not been reported previously. Canonical pathway analysis of altered molecules indicated differential enrichment of signaling cascades upon DKK3 overexpression in all the 3 cell lines. Protein kinase A signaling, Sirtuin signaling pathway, and Cell Cycle Control of Chromosomal Replication were observed to be differentially activated in the GBC cell lines. Our study revealed, DKK3 overexpression has differential effect based on the aggressive behavior of the cell lines. This study expands the understanding of DKK3-mediated signaling events and can be used as a primary factor for understanding the complex nature of this molecule.
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Affiliation(s)
- Kirti Gondkar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Neha Joshi
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Prashant Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
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8
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Sürmen MG, Sürmen S, Ali A, Musharraf SG, Emekli N. Phosphoproteomic strategies in cancer research: a minireview. Analyst 2020; 145:7125-7149. [PMID: 32996481 DOI: 10.1039/d0an00915f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.
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Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Syed Ghulam Musharraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
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9
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Puttamallesh VN, Deb B, Gondkar K, Jain A, Nair B, Pandey A, Chatterjee A, Gowda H, Kumar P. Quantitative Proteomics of Urinary Bladder Cancer Cell Lines Identify UAP1 as a Potential Therapeutic Target. Genes (Basel) 2020; 11:genes11070763. [PMID: 32650368 PMCID: PMC7397020 DOI: 10.3390/genes11070763] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/25/2022] Open
Abstract
Bladder carcinoma (BC) incidence and mortality rates are increasing worldwide. The development of novel therapeutic strategies is required to improve clinical management of this cancer. Aberrant protein expression may lead to cancer initiation and progression. Therefore, the identification of these potential protein targets and limiting their expression levels would provide alternative treatment options. In this study, we utilized a liquid-chromatography tandem mass spectrometry-based global proteomics approach to identify differentially expressed proteins in bladder cancer cell lines. A total of 3913 proteins were identified in this study, of which 479 proteins were overexpressed and 141 proteins were downregulated in 4 out of 6 BC cell lines when compared with normal human urothelial cell line (TERT-NHUC). We evaluated the role of UDP-N-acetylhexosamine pyrophosphorylase (UAP1) in bladder cancer pathogenesis. The silencing of UAP1 led to reduction in proliferation, invasion, colony formation and migration capability of bladder cancer cell lines. Thus, our study reveals UAP1 as a promising therapeutic target for bladder cancer.
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Affiliation(s)
- Vinuth N. Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Kirti Gondkar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Ankit Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (V.N.P.); (B.D.); (K.G.); (A.J.); (A.P.); (A.C.); (H.G.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
- Correspondence: ; Tel.: +91-80-28416140; Fax: +91-80-28416132
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10
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Kasarpalkar N, Deb B, Kumar P, Bhor VM. The Role of Integrin α 4β 7 Signaling in Human Immunodeficiency Virus-1 Pathogenesis and Viral Entry in Primary CD4 + T Cells As Revealed by Comparative Phosphoproteomic Signatures. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:437-450. [PMID: 32522079 DOI: 10.1089/omi.2019.0196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Integrin α4β7, a CD4 independent receptor of human immunodeficiency virus-1 (HIV-1) gp120, defines a subset of CD4+T cells preferentially targeted by HIV. It is also considered as a promising therapeutic target for HIV-1 infection. Despite its role in HIV acquisition and disease progression, HIV-1-mediated integrin α4β7 signaling has not been elucidated so far. In view of this, we determined phosphoproteomic signatures of HIV-1 gp120 signaling as well as signaling mediated by the integrin α4β7 ligand, mucosal vascular addressin cell adhesion molecule-1 (MAdCAM-1), in primary CD4+ T cells. This is the first comprehensive report on MAdCAM-1 signaling, which is believed to enhance HIV-1 replication. Importantly, we identified proteins associated with both classical and nonclassical integrin functions. We observed that HIV-1 gp120 signaling is associated with proteins that have previously not been associated with HIV-1 pathogenesis and thus, need to be explored further. There was a significant overlap in proteins identified by both MAdCAM-1 and HIV-1 gp120 signaling, which most likely represents cellular processes triggered upon interaction of HIV-1 gp120 with integrin α4β7. Pathway analysis revealed enrichment of processes that could facilitate viral replication as well as viral entry through endocytosis. Although these results warrant independent replication and further validation, they suggest the presence of additional potential therapeutic targets. These results also suggest that combinatorial approaches for targeting both HIV-1 gp120 and MAdCAM-1 signaling may be necessary for efficient control of HIV-1 infection as well as novel innovation strategies in HIV therapeutics.
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Affiliation(s)
- Nandini Kasarpalkar
- Department of Molecular Immunology and Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Vikrant M Bhor
- Department of Molecular Immunology and Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
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11
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Insights into the Multi-Dimensional Dynamic Landscape of Epithelial-Mesenchymal Plasticity through Inter-Disciplinary Approaches. J Clin Med 2020; 9:jcm9061624. [PMID: 32471235 PMCID: PMC7356048 DOI: 10.3390/jcm9061624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
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12
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Sugiyama N. Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. ACTA ACUST UNITED AC 2020; 9:A0082. [PMID: 32547896 PMCID: PMC7242781 DOI: 10.5702/massspectrometry.a0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation mediated by protein kinases is one of the most significant posttranslational modifications in many biological events. The function and physiological substrates of specific protein kinases, which are highly associated with known signal transduction elements or therapeutic targets, have been extensively studied using various approaches; however, most protein kinases have not yet been characterized. In recent decades, many techniques have been developed for the identification of in vitro and physiological substrates of protein kinases. In this review, I summarize recent studies profiling the characteristics of kinases using mass spectrometry-based proteomics, focusing on the large-scale identification of in vitro substrates of the human kinome using a quantitative phosphoproteomics approach.
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Affiliation(s)
- Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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13
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Deb B, Sengupta P, Sambath J, Kumar P. Bioinformatics Analysis of Global Proteomic and Phosphoproteomic Data Sets Revealed Activation of NEK2 and AURKA in Cancers. Biomolecules 2020; 10:biom10020237. [PMID: 32033228 PMCID: PMC7072708 DOI: 10.3390/biom10020237] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/18/2019] [Accepted: 12/25/2019] [Indexed: 12/15/2022] Open
Abstract
Tumor heterogeneity attributes substantial challenges in determining the treatment regimen. Along with the conventional treatment, such as chemotherapy and radiotherapy, targeted therapy has greater impact in cancer management. Owing to the recent advancements in proteomics, we aimed to mine and re-interrogate the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data sets which contain deep scale, mass spectrometry (MS)-based proteomic and phosphoproteomic data sets conducted on human tumor samples. Quantitative proteomic and phosphoproteomic data sets of tumor samples were explored and downloaded from the CPTAC database for six different cancers types (breast cancer, clear cell renal cell carcinoma (CCRCC), colon cancer, lung adenocarcinoma (LUAD), ovarian cancer, and uterine corpus endometrial carcinoma (UCEC)). We identified 880 phosphopeptide signatures for differentially regulated phosphorylation sites across five cancer types (breast cancer, colon cancer, LUAD, ovarian cancer, and UCEC). We identified the cell cycle to be aberrantly activated across these cancers. The correlation of proteomic and phosphoproteomic data sets identified changes in the phosphorylation of 12 kinases with unchanged expression levels. We further investigated phosphopeptide signature across five cancer types which led to the prediction of aurora kinase A (AURKA) and kinases-serine/threonine-protein kinase Nek2 (NEK2) as the most activated kinases targets. The drug designed for these kinases could be repurposed for treatment across cancer types.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (B.D.); (J.S.)
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Pratyay Sengupta
- Department of Biotechnology, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur, West Bengal 713209, India;
| | - Janani Sambath
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (B.D.); (J.S.)
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; (B.D.); (J.S.)
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence: ; Tel.: +91-802-841-6140; Fax: +91-802-841-6132
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14
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Gondkar K, Patel K, Patil Okaly GV, Nair B, Pandey A, Gowda H, Kumar P. Dickkopf Homolog 3 (DKK3) Acts as a Potential Tumor Suppressor in Gallbladder Cancer. Front Oncol 2019; 9:1121. [PMID: 31737564 PMCID: PMC6828847 DOI: 10.3389/fonc.2019.01121] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/09/2019] [Indexed: 01/19/2023] Open
Abstract
Gallbladder cancer (GBC) is a common malignancy of biliary tract cancers and its incidence has been rising rapidly worldwide. The prognosis for this disease is dismal as most of the symptoms are non-specific leading to a definitive diagnosis only at a late stage. Loss of DKK3 gene is associated with a possible tumor suppressor role in human cancers. The role and regulation of DKK3 in GBC have not been studied. We found that DKK3 expression levels were low in GBC patients and cell lines. Treatment of GBC cell lines with demethylating agent 5-Aza- 2'-deoxycytidine enhances its expression, establishing impact of methylation on DKK3 expression. We observed low expression of DKK3 in gallbladder adenocarcinoma tumors and highly invasive GBC cell lines. We showed that overexpression of DKK3 can decrease cell invasion, proliferation, and colony forming ability of GBC cells. Our data thus demonstrated the DKK3 gene is a potential tumor suppressor gene in GBC and aberrant promoter methylation could be involved in its downregulation, which may play a role in the tumorigenesis and aggressiveness of GBC.
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Affiliation(s)
- Kirti Gondkar
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Krishna Patel
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Geeta V Patil Okaly
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education, Manipal, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India.,Manipal Academy of Higher Education, Manipal, India
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15
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Deb B, Patel K, Sathe G, Kumar P. N-Glycoproteomic Profiling Reveals Alteration In Extracellular Matrix Organization In Non-Type Bladder Carcinoma. J Clin Med 2019; 8:jcm8091303. [PMID: 31450586 PMCID: PMC6780497 DOI: 10.3390/jcm8091303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/03/2023] Open
Abstract
Treatment of advanced and metastatic bladder carcinoma is often ineffective and displays variable clinical outcomes. Studying this aggressive molecular subtype of bladder carcinoma will lead to better understanding of the pathogenesis which may lead to the identification of new therapeutic strategies. The non-type bladder subtype is phenotypically mesenchymal and has mesenchymal features with a high metastatic ability. Post-translational addition of oligosaccharide residues is an important modification that influences cellular functions and contributes to disease pathology. Here, we report the comparative analysis of N-linked glycosylation across bladder cancer subtypes. To analyze the glycosite-containing peptides, we carried out LC-MS/MS-based quantitative proteomic and glycoproteomic profiling. We identified 1299 unique N-linked glycopeptides corresponding to 460 proteins. Additionally, we identified 118 unique N-linked glycopeptides corresponding to 84 proteins to be differentially glycosylated only in non-type subtypes as compared to luminal/basal subtypes. Most of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 55 differentially expressed glycoproteins showed no significant change at the protein abundance level, representing that the glycosylation site occupancy was changed between the non-type subtype and luminal/basal subtypes. Importantly, the extracellular matrix organization pathway was dysregulated in the non-type subtype of bladder carcinoma. N-glycosylation modifications in the extracellular matrix organization proteins may be a contributing factor for the mesenchymal aggressive phenotype in non-type subtype. These aberrant protein glycosylation would provide additional avenues to employ glycan-based therapies and may lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.
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