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Armstrong LA, Lange SM, Cesare VD, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y. Correction: Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One 2024; 19:e0302418. [PMID: 38626090 PMCID: PMC11020524 DOI: 10.1371/journal.pone.0302418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0253364.].
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Armstrong LA, Lange SM, Dee Cesare V, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y. Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One 2021; 16:e0253364. [PMID: 34270554 PMCID: PMC8284666 DOI: 10.1371/journal.pone.0253364] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease domain (PLpro) that cleaves not only the viral polypeptide but also K48-linked polyubiquitin and the ubiquitin-like modifier, ISG15, from host cell proteins. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal catalytic domain of PLpro. Using a MALDI-TOF based assay, we screen 1971 approved clinical compounds and identify five compounds that inhibit PLpro with IC50s in the low micromolar range but showed cross reactivity with other human deubiquitinases and had no significant antiviral activity in cellular SARS-CoV-2 infection assays. We therefore looked for alternative methods to block PLpro activity and engineered competitive nanobodies that bind to PLpro at the substrate binding site with nanomolar affinity thus inhibiting the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology during the viral infection cycle.
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Affiliation(s)
- Lee A. Armstrong
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Sven M. Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Virginia Dee Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Stephen P. Matthews
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Raja Sekhar Nirujogi
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Isobel Cole
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Anthony Hope
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Fraser Cunningham
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Rachel Toth
- MRC Reagents and Services, University of Dundee, Dundee, Scotland, United Kingdom
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Goethe University Frankfurt Medical Faculty, University Hospital, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Denisa Bojkova
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Franz Gruber
- National Phenotypic Screening Centre, University of Dundee, Dundee, Scotland, United Kingdom
| | - David Gray
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Paul G. Wyatt
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Jindrich Cinatl
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Frankfurt Medical Faculty, University Hospital, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
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Ma SX, Seo BA, Kim D, Xiong Y, Kwon SH, Brahmachari S, Kim S, Kam TI, Nirujogi RS, Kwon SH, Dawson VL, Dawson TM, Pandey A, Na CH, Ko HS. Complement and Coagulation Cascades are Potentially Involved in Dopaminergic Neurodegeneration in α-Synuclein-Based Mouse Models of Parkinson's Disease. J Proteome Res 2021; 20:3428-3443. [PMID: 34061533 PMCID: PMC8628316 DOI: 10.1021/acs.jproteome.0c01002] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder that results in motor dysfunction and, eventually, cognitive impairment. α-Synuclein protein is known as a central protein to the pathophysiology of PD, but the underlying pathological mechanism still remains to be elucidated. In an effort to understand how α-synuclein underlies the pathology of PD, various PD mouse models with α-synuclein overexpression have been developed. However, systemic analysis of the brain proteome of those mouse models is lacking. In this study, we established two mouse models of PD by injecting α-synuclein preformed fibrils (PFF) or by inducing overexpression of human A53T α-synuclein to investigate common pathways in the two different types of the PD mouse models. For more accurate quantification of mouse brain proteome, the proteins were quantified using the method of stable isotope labeling with amino acids in mammals . We identified a total of 8355 proteins from the two mouse models; ∼6800 and ∼7200 proteins from α-synuclein PFF-injected mice and human A53T α-synuclein transgenic mice, respectively. Through pathway analysis of the differentially expressed proteins common to both PD mouse models, it was discovered that the complement and coagulation cascade pathways were enriched in the PD mice compared to control animals. Notably, a validation study demonstrated that complement component 3 (C3)-positive astrocytes were increased in the ventral midbrain of the intrastriatal α-synuclein PFF-injected mice and C3 secreted from astrocytes could induce the degeneration of dopaminergic neurons. This is the first study that highlights the significance of the complement and coagulation pathways in the pathogenesis of PD through proteome analyses with two sophisticated mouse models of PD.
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Affiliation(s)
- Shi-Xun Ma
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Bo Am Seo
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Donghoon Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Pharmacology, Peripheral Neuropathy Research Center, Dong-A University College of Medicine, Busan 49201, South Korea
| | - Yulan Xiong
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Seung-Hwan Kwon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Saurav Brahmachari
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Sangjune Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Tae-In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Sang Ho Kwon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Adrienne Helis Malvin Medical Research Foundation, New Orleans 70130, Louisiana, United States
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Adrienne Helis Malvin Medical Research Foundation, New Orleans 70130, Louisiana, United States
- Diana Helis Henry Medical Research Foundation, New Orleans 70130, Louisiana, United States
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chan Hyun Na
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore 21205-2105, Maryland, United States
- Adrienne Helis Malvin Medical Research Foundation, New Orleans 70130, Louisiana, United States
- Diana Helis Henry Medical Research Foundation, New Orleans 70130, Louisiana, United States
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Kolar EA, Shi X, Clay EM, Moser AB, Lal B, Nirujogi RS, Pandey A, Bandaru VVR, Laterra J, Pei Z, Watkins PA. Very long-chain acyl-CoA synthetase 3 mediates onco-sphingolipid metabolism in malignant glioma. ACTA ACUST UNITED AC 2021; 9. [PMID: 34395855 DOI: 10.18103/mra.v9i5.2433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Gliomas are the largest category of primary malignant brain tumors in adults, and glioblastomas account for nearly half of malignant gliomas. Glioblastomas are notoriously aggressive and drug-resistant, with a very poor 5 year survival rate of about 5%. New approaches to treatment are thus urgently needed. We previously identified an enzyme of fatty acid metabolism, very long-chain acyl-CoA synthetase 3 (ACSVL3), as a potential therapeutic target in glioblastoma. Using the glioblastoma cell line U87MG, we created a cell line with genomic deletion of ACSVL3 (U87-KO) and investigated potential mechanisms to explain how this enzyme supports the malignant properties of glioblastoma cells. Compared to U87MG cells, U87-KO cells grew slower and assumed a more normal morphology. They produced fewer, and far smaller, subcutaneous xenografts in nude mice. Acyl-CoA synthetases, including ACSVL3, convert fatty acids to their acyl-CoA derivatives, allowing participation in diverse downstream lipid pathways. We examined the effect of ACSVL3 depletion on several such pathways. Fatty acid degradation for energy production was not affected in U87-KO cells. Fatty acid synthesis, and incorporation of de novo synthesized fatty acids into membrane phospholipids needed for rapid tumor cell growth, was not significantly affected by lack of ACSVL3. In contrast, U87-KO cells exhibited evidence of altered sphingolipid metabolism. Levels of ceramides containing 18-22 carbon fatty acids were significantly lower in U87-KO cells. This paralleled the fatty acid substrate specificity profile of ACSVL3. The rate of incorporation of stearate, an 18-carbon saturated fatty acid, into ceramides was reduced in U87-KO cells, and proteomics revealed lower abundance of ceramide synthesis pathway enzymes. Sphingolipids, including gangliosides, are functional constituents of lipid rafts, membrane microdomains thought to be organizing centers for receptor-mediated signaling. Both raft morphology and ganglioside composition were altered by deficiency of ACSVL3. Finally, levels of sphingosine-1-phosphate, a sphingolipid signaling molecule, were reduced in U87-KO cells. We conclude that ACSVL3 supports the malignant behavior of U87MG cells, at least in part, by altering cellular sphingolipid metabolism.
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Affiliation(s)
- Elizabeth A Kolar
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205
| | - Xiaohai Shi
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205
| | - Emily M Clay
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205
| | - Ann B Moser
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bachchu Lal
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Zhengtong Pei
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Paul A Watkins
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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Martinez M, Renuse S, Kreimer S, O'Meally R, Natov P, Madugundu AK, Nirujogi RS, Tahir R, Cole R, Pandey A, Zachara NE. Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress. Mol Cell Proteomics 2021; 20:100069. [PMID: 33716169 PMCID: PMC8079276 DOI: 10.1016/j.mcpro.2021.100069] [Citation(s) in RCA: 18] [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: 07/31/2020] [Revised: 01/26/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
The dynamic modification of specific serine and threonine residues of intracellular proteins by O-linked N-acetyl-β-D-glucosamine (O-GlcNAc) mitigates injury and promotes cytoprotection in a variety of stress models. The O-GlcNAc transferase (OGT) and the O-GlcNAcase are the sole enzymes that add and remove O-GlcNAc, respectively, from thousands of substrates. It remains unclear how just two enzymes can be specifically controlled to affect glycosylation of target proteins and signaling pathways both basally and in response to stress. Several lines of evidence suggest that protein interactors regulate these responses by affecting OGT and O-GlcNAcase activity, localization, and substrate specificity. To provide insight into the mechanisms by which OGT function is controlled, we have used quantitative proteomics to define OGT’s basal and stress-induced interactomes. OGT and its interaction partners were immunoprecipitated from OGT WT, null, and hydrogen peroxide–treated cell lysates that had been isotopically labeled with light, medium, and heavy lysine and arginine (stable isotopic labeling of amino acids in cell culture). In total, more than 130 proteins were found to interact with OGT, many of which change their association upon hydrogen peroxide stress. These proteins include the major OGT cleavage and glycosylation substrate, host cell factor 1, which demonstrated a time-dependent dissociation after stress. To validate less well-characterized interactors, such as glyceraldehyde 3-phosphate dehydrogenase and histone deacetylase 1, we turned to parallel reaction monitoring, which recapitulated our discovery-based stable isotopic labeling of amino acids in cell culture approach. Although the majority of proteins identified are novel OGT interactors, 64% of them are previously characterized glycosylation targets that contain varied domain architecture and function. Together these data demonstrate that OGT interacts with unique and specific interactors in a stress-responsive manner. O-GlcNAc levels change dynamically in response to injury. Injury does not induce changes in activity of the enzymes that cycle O-GlcNAc. Quantitative proteomics identified and validated interactors of OGT. The interactome of OGT changes significantly in response to oxidative stress.
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Affiliation(s)
- Marissa Martinez
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at Foghorn Therapeutics, Cambridge, Massachusetts, United States
| | - Santosh Renuse
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at the Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States; Currently at the Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Simion Kreimer
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; The Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Currently at the Advanced Clinical Biosystems Institute, Smidt Heart institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Robert O'Meally
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; The Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter Natov
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at the Department of Internal Medicine, Yale New Haven Hospital, Yale School of Medicine, New Haven, Connecticut, USA
| | - Anil K Madugundu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at the Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Raja Sekhar Nirujogi
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at the Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Raiha Tahir
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at Ginkgo Bioworks, Massachusetts, United States
| | - Robert Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; The Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Currently at the Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States; Currently at the Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States; Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Natasha E Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.
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6
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Tahir R, Renuse S, Udainiya S, Madugundu AK, Cutler JA, Nirujogi RS, Na CH, Xu Y, Wu X, Pandey A. Mutation-Specific and Common Phosphotyrosine Signatures of KRAS G12D and G13D Alleles. J Proteome Res 2020; 20:670-683. [PMID: 32986951 DOI: 10.1021/acs.jproteome.0c00587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
KRAS is one of the most frequently mutated genes across all cancer subtypes. Two of the most frequent oncogenic KRAS mutations observed in patients result in glycine to aspartic acid substitution at either codon 12 (G12D) or 13 (G13D). Although the biochemical differences between these two predominant mutations are not fully understood, distinct clinical features of the resulting tumors suggest involvement of disparate signaling mechanisms. When we compared the global phosphotyrosine proteomic profiles of isogenic colorectal cancer cell lines bearing either G12D or G13D KRAS mutation, we observed both shared as well as unique signaling events induced by the two KRAS mutations. Remarkably, while the G12D mutation led to an increase in membrane proximal and adherens junction signaling, the G13D mutation led to activation of signaling molecules such as nonreceptor tyrosine kinases, MAPK kinases, and regulators of metabolic processes. The importance of one of the cell surface molecules, MPZL1, which was found to be hyperphosphorylated in G12D cells, was confirmed by cellular assays as its knockdown led to a decrease in proliferation of G12D but not G13D expressing cells. Overall, our study reveals important signaling differences across two common KRAS mutations and highlights the utility of our approach to systematically dissect subtle differences between related oncogenic mutants and potentially lead to individualized treatments.
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Affiliation(s)
- Raiha Tahir
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Savita Udainiya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.,Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Chan Hyun Na
- Department of Neurology, Institute of Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Yaoyu Xu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Xinyan Wu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.,Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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7
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Mun DG, Renuse S, Saraswat M, Madugundu A, Udainiya S, Kim H, Park SKR, Zhao H, Nirujogi RS, Na CH, Kannan N, Yates JR, Lee SW, Pandey A. PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies. Anal Chem 2020; 92:14466-14475. [PMID: 33079518 DOI: 10.1021/acs.analchem.0c02513] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A data-independent acquisition (DIA) approach is being increasingly adopted as a promising strategy for identification and quantitation of proteomes. As most DIA data sets are acquired with wide isolation windows, highly complex MS/MS spectra are generated, which negatively impacts obtaining peptide information through classical protein database searches. Therefore, the analysis of DIA data mainly relies on the evidence of the existence of peptides from prebuilt spectral libraries. Consequently, one major weakness of this method is that it does not account for peptides that are not included in the spectral library, precluding the use of DIA for discovery studies. Here, we present a strategy termed Precursor ion And Small Slice-DIA (PASS-DIA) in which MS/MS spectra are acquired with small isolation windows (slices) and MS/MS spectra are interpreted with accurately determined precursor ion masses. This method enables the direct application of conventional spectrum-centric analysis pipelines for peptide identification and precursor ion-based quantitation. The performance of PASS-DIA was observed to be superior to both data-dependent acquisition (DDA) and conventional DIA experiments with 69 and 48% additional protein identifications, respectively. Application of PASS-DIA for the analysis of post-translationally modified peptides again highlighted its superior performance in characterizing phosphopeptides (77% more), N-terminal acetylated peptides (56% more), and N-glycopeptides (83% more) as compared to DDA alone. Finally, the use of PASS-DIA to characterize a rare proteome of human fallopian tube organoids enabled 34% additional protein identifications than DDA alone and revealed biologically relevant pathways including low abundance proteins. Overall, PASS-DIA is a novel DIA approach for use as a discovery tool that outperforms both conventional DDA and DIA experiments to provide additional protein information. We believe that the PASS-DIA method is an important strategy for discovery-type studies when deeper proteome characterization is required.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Santosh Renuse
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104 Karnataka, India
| | - Anil Madugundu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104 Karnataka, India
| | - Savita Udainiya
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
| | - Hokeun Kim
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Sung-Kyu Robin Park
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hui Zhao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Raja Sekhar Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sang-Won Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104 Karnataka, India
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8
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Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado‐Torres L, Halushka MK, Kim M, Pandey A. Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics 2019; 19:e1800315. [PMID: 30983154 PMCID: PMC6812510 DOI: 10.1002/pmic.201800315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/17/2019] [Indexed: 01/11/2023]
Abstract
Understanding the molecular profile of every human cell type is essential for understanding its role in normal physiology and disease. Technological advancements in DNA sequencing, mass spectrometry, and computational methods allow us to carry out multiomics analyses although such approaches are not routine yet. Human umbilical vein endothelial cells (HUVECs) are a widely used model system to study pathological and physiological processes associated with the cardiovascular system. In this study, next-generation sequencing and high-resolution mass spectrometry to profile the transcriptome and proteome of primary HUVECs is employed. Analysis of 145 million paired-end reads from next-generation sequencing confirmed expression of 12 186 protein-coding genes (FPKM ≥0.1), 439 novel long non-coding RNAs, and revealed 6089 novel isoforms that were not annotated in GENCODE. Proteomics analysis identifies 6477 proteins including confirmation of N-termini for 1091 proteins, isoforms for 149 proteins, and 1034 phosphosites. A database search to specifically identify other post-translational modifications provide evidence for a number of modification sites on 117 proteins which include ubiquitylation, lysine acetylation, and mono-, di- and tri-methylation events. Evidence for 11 "missing proteins," which are proteins for which there was insufficient or no protein level evidence, is provided. Peptides supporting missing protein and novel events are validated by comparison of MS/MS fragmentation patterns with synthetic peptides. Finally, 245 variant peptides derived from 207 expressed proteins in addition to alternate translational start sites for seven proteins and evidence for novel proteoforms for five proteins resulting from alternative splicing are identified. Overall, it is believed that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.
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Affiliation(s)
- Anil K. Madugundu
- Center for Molecular MedicineNational Institute of Mental Health and NeurosciencesHosur RoadBangalore560029KarnatakaIndia
- Institute of BioinformaticsInternational Technology ParkBangalore560066KarnatakaIndia
- Manipal Academy of Higher EducationManipal576104KarnatakaIndia
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
| | - Chan Hyun Na
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- NeurologyInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Raja Sekhar Nirujogi
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Santosh Renuse
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
| | - Kwang Pyo Kim
- Department of Applied ChemistryKyung Hee UniversityYonginGyeonggi17104Republic of Korea
| | - Kathleen H. Burns
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMD21205USA
- High Throughput Biology CenterJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Christopher Wilks
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
| | - Ben Langmead
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
| | - Shannon E. Ellis
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMD21205USA
| | - Leonardo Collado‐Torres
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
- Lieber Institute for Brain DevelopmentJohns Hopkins Medical CampusBaltimoreMD21205USA
| | - Marc K. Halushka
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Min‐Sik Kim
- Department of Applied ChemistryKyung Hee UniversityYonginGyeonggi17104Republic of Korea
- Department of New BiologyDGISTDaegu42988Republic of Korea
| | - Akhilesh Pandey
- Center for Molecular MedicineNational Institute of Mental Health and NeurosciencesHosur RoadBangalore560029KarnatakaIndia
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
- NeurologyInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of Biological ChemistryJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of OncologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
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9
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Shears MJ, Sekhar Nirujogi R, Swearingen KE, Renuse S, Mishra S, Jaipal Reddy P, Moritz RL, Pandey A, Sinnis P. Proteomic Analysis of Plasmodium Merosomes: The Link between Liver and Blood Stages in Malaria. J Proteome Res 2019; 18:3404-3418. [PMID: 31335145 DOI: 10.1021/acs.jproteome.9b00324] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/29/2022]
Abstract
The pre-erythrocytic liver stage of the malaria parasite, comprising sporozoites and the liver stages into which they develop, remains one of the least understood parts of the lifecycle, in part owing to the low numbers of parasites. Nonetheless, it is recognized as an important target for antimalarial drugs and vaccines. Here we provide the first proteomic analysis of merosomes, which define the final phase of the liver stage and are responsible for initiating the blood stage of infection. We identify a total of 1879 parasite proteins, and a core set of 1188 proteins quantitatively detected in every biological replicate, providing an extensive picture of the protein repertoire of this stage. This unique data set will allow us to explore key questions about the biology of merosomes and hepatic merozoites.
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Affiliation(s)
- Melanie J Shears
- Department of Molecular Microbiology & Immunology , Johns Hopkins Bloomberg School of Public Health , 615 North Wolfe Street , Baltimore , Maryland 21205 , United States
| | - Raja Sekhar Nirujogi
- Department of Biological Chemistry , Johns Hopkins School of Medicine , 733 N. Broadway , Baltimore , Maryland 21205 , United States.,Institute of Bioinformatics , International Tech Park , Bangalore 560 066 , India
| | - Kristian E Swearingen
- Institute for Systems Biology , 401 Terry Avenue , North Seattle , Washington 98109 , United States
| | - Santosh Renuse
- Department of Biological Chemistry , Johns Hopkins School of Medicine , 733 N. Broadway , Baltimore , Maryland 21205 , United States
| | - Satish Mishra
- Department of Molecular Microbiology & Immunology , Johns Hopkins Bloomberg School of Public Health , 615 North Wolfe Street , Baltimore , Maryland 21205 , United States
| | - Panga Jaipal Reddy
- Institute for Systems Biology , 401 Terry Avenue , North Seattle , Washington 98109 , United States
| | - Robert L Moritz
- Institute for Systems Biology , 401 Terry Avenue , North Seattle , Washington 98109 , United States
| | - Akhilesh Pandey
- Department of Biological Chemistry , Johns Hopkins School of Medicine , 733 N. Broadway , Baltimore , Maryland 21205 , United States
| | - Photini Sinnis
- Department of Molecular Microbiology & Immunology , Johns Hopkins Bloomberg School of Public Health , 615 North Wolfe Street , Baltimore , Maryland 21205 , United States
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10
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Nirujogi RS, Muthusamy B, Kim MS, Sathe GJ, Lakshmi PTV, Kovbasnjuk ON, Prasad TSK, Wade M, Jabbour RE. Secretome analysis of diarrhea-inducing strains of Escherichia coli. Proteomics 2017; 17. [PMID: 28070933 DOI: 10.1002/pmic.201600299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 07/15/2016] [Revised: 12/19/2016] [Accepted: 01/05/2017] [Indexed: 01/05/2023]
Abstract
Secreted proteins constitute a major part of virulence factors that are responsible for pathogenesis caused by Gram-negative bacteria. Enterohemorrhagic Escherichia coli, O157:H7, is the major pathogen often causing outbreaks. However, studies have reported that the significant outbreaks caused by non-O157:H7 E. coli strains, also known as "Big-Six" serogroup strains, are increasing. There is no systematic study describing differential secreted proteins from these non-O157:H7 E. coli strains. In this study, we carried out MS-based differential secretome analysis using tandem mass tags labeling strategy of non-O157:H7 E. coli strains, O103, O111, O121, O145, O26, and O45. We identified 1241 proteins, of which 565 proteins were predicted to be secreted. We also found that 68 proteins were enriched in type III secretion system and several of them were differentially expressed across the strains. Additionally, we identified several strain-specific secreted proteins that could be used for developing potential markers for the identification and strain-level differentiation. To our knowledge, this study is the first comparative proteomic study on secretome of E. coli Big-Six serogroup and the several of these strain-specific secreted proteins can be further studied to develop potential markers for identification and strain-level differentiation. Moreover, the results of this study can be utilized in several applications, including food safety, diagnostics of E. coli outbreaks, and detection and identification of bio threats in biodefense.
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Bioinformatics, Pondicherry University, Puducherry, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal University, Madhav Nagar, Manipal, India
| | - P T V Lakshmi
- Centre for Bioinformatics, Pondicherry University, Puducherry, India
| | - Olga N Kovbasnjuk
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Bioinformatics, Pondicherry University, Puducherry, India.,Manipal University, Madhav Nagar, Manipal, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | - Mary Wade
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Rabih E Jabbour
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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11
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Nirujogi RS, Muthusamy B, Kim MS, Sathe GJ, Lakshmi P, Kovbasnjuk ON, Prasad TK, Wade M, Jabbour RE. Front Cover: Secretome analysis of diarrhea-inducing strains of Escherichia coli. Proteomics 2017. [DOI: 10.1002/pmic.201770040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A. Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis. Leukemia 2017; 31:1513-1524. [DOI: 10.1038/leu.2017.61] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/04/2017] [Accepted: 01/11/2017] [Indexed: 12/15/2022]
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13
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Dammalli M, Murthy KR, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Nair B, Gowda H, Keshava Prasad TS. Toward Postgenomics Ophthalmology: A Proteomic Map of the Human Choroid–Retinal Pigment Epithelium Tissue. ACTA ACUST UNITED AC 2017; 21:114-122. [DOI: 10.1089/omi.2016.0170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Krishna R. Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Manipal University, Manipal, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
- NIMHANS-IOB Bioinformatics and Proteomics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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14
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Ugolino J, Ji YJ, Conchina K, Chu J, Nirujogi RS, Pandey A, Brady NR, Hamacher-Brady A, Wang J. Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling. PLoS Genet 2016; 12:e1006443. [PMID: 27875531 PMCID: PMC5119725 DOI: 10.1371/journal.pgen.1006443] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/21/2016] [Indexed: 12/13/2022] Open
Abstract
The most common cause of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal dementia is a hexanucleotide repeat expansion in C9orf72. Here we report a study of the C9orf72 protein by examining the consequences of loss of C9orf72 functions. Deletion of one or both alleles of the C9orf72 gene in mice causes age-dependent lethality phenotypes. We demonstrate that C9orf72 regulates nutrient sensing as the loss of C9orf72 decreases phosphorylation of the mTOR substrate S6K1. The transcription factor EB (TFEB), a master regulator of lysosomal and autophagy genes, which is negatively regulated by mTOR, is substantially up-regulated in C9orf72 loss-of-function animal and cellular models. Consistent with reduced mTOR activity and increased TFEB levels, loss of C9orf72 enhances autophagic flux, suggesting that C9orf72 is a negative regulator of autophagy. We identified a protein complex consisting of C9orf72 and SMCR8, both of which are homologous to DENN-like proteins. The depletion of C9orf72 or SMCR8 leads to significant down-regulation of each other’s protein level. Loss of SMCR8 alters mTOR signaling and autophagy. These results demonstrate that the C9orf72-SMCR8 protein complex functions in the regulation of metabolism and provide evidence that loss of C9orf72 function may contribute to the pathogenesis of relevant diseases. C9orf72 is one of many uncharacterized genes in the human genome. The presence of repeated nucleotides in the non-coding region of the C9orf72 gene (GGGGCC) has been linked to the neurodegenerative diseases Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD). However, how the presence of these repeats in the gene leads to neurodegeneration is unknown. One possible explanation is that the repeats lead to a reduced expression of the C9orf72 gene and loss of function of the C9orf72 protein. Although C9orf72 is well-conserved among multi-cellular organisms, its protein function remains to be determined. In this study, we demonstrated that loss of C9orf72 reduces mTOR signaling and enhances autophagy. mTOR signaling and autophagy are important for the cellular maintenance of metabolic balances, especially under stress conditions. C9orf72 protein exists in a complex with another DENN-like protein, SMCR8, which also regulates mTOR signaling and autophagy. We generated mice lacking C9orf72, which died prematurely and showed dramatic upregulation of TFEB, a crucial transcriptional regulator of autophagy and lysosomal genes, that integrates mTOR activity state and autophagic capacity. We propose that C9orf72 function is important for metabolic control and its deficiency can contribute to the development of neurodegenerative diseases.
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Affiliation(s)
- Janet Ugolino
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yon Ju Ji
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Karen Conchina
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Justin Chu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Nathan R. Brady
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Maryland, United States of America
| | - Anne Hamacher-Brady
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Maryland, United States of America
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, and Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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15
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Prasad TSK, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res 2016; 27:133-144. [PMID: 28003436 PMCID: PMC5204337 DOI: 10.1101/gr.201368.115] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [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: 10/28/2015] [Accepted: 11/10/2016] [Indexed: 01/05/2023]
Abstract
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.
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Affiliation(s)
- T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Ajeet Kumar Mohanty
- National Institute of Malaria Research, Field Station, Goa 403001, India.,Department of Zoology, Goa University, Taleigao Plateau, Goa 403206, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Srikanth S Manda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sutopa B Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Brantley Hall
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Xiaofang Jiang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Hitendra S Solanki
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Krishna M Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Keshava K Datta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Aafaque Ahmed Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka 572103, India
| | - Savita Jayaram
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chan-Hyun Na
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Nirbhay Kumar
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA
| | - Photini Sinnis
- Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Charles Wang
- Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Zhijian Tu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashwani Kumar
- National Institute of Malaria Research, Field Station, Goa 403001, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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16
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Murthy KR, Dammalli M, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Subbannayya Y, Mishra UK, Nair B, Gowda H, Prasad TK. A Comprehensive Proteomics Analysis of the Human Iris Tissue: Ready to Embrace Postgenomics Precision Medicine in Ophthalmology? OMICS: A Journal of Integrative Biology 2016; 20:510-9. [DOI: 10.1089/omi.2016.0100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Manipal, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
- NIMHANS-IOB Bioinformatics and Proteomics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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17
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Sathe G, Pinto SM, Syed N, Nanjappa V, Solanki HS, Renuse S, Chavan S, Khan AA, Patil AH, Nirujogi RS, Nair B, Mathur PP, Prasad TSK, Gowda H, Chatterjee A. Phosphotyrosine profiling of curcumin-induced signaling. Clin Proteomics 2016; 13:13. [PMID: 27307780 PMCID: PMC4908701 DOI: 10.1186/s12014-016-9114-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 01/01/2016] [Accepted: 05/04/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Curcumin, derived from the rhizome Curcuma longa, is a natural anti-cancer agent and has been shown to inhibit proliferation and survival of tumor cells. Although the anti-cancer effects of curcumin are well established, detailed understanding of the signaling pathways altered by curcumin is still lacking. In this study, we carried out SILAC-based quantitative proteomic analysis of a HNSCC cell line (CAL 27) to investigate tyrosine signaling in response to curcumin. RESULTS Using high resolution Orbitrap Fusion Tribrid Fourier transform mass spectrometer, we identified 627 phosphotyrosine sites mapping to 359 proteins. We observed alterations in the level of phosphorylation of 304 sites corresponding to 197 proteins upon curcumin treatment. We report here for the first time, curcumin-induced alterations in the phosphorylation of several kinases including TNK2, FRK, AXL, MAPK12 and phosphatases such as PTPN6, PTPRK, and INPPL1 among others. Pathway analysis revealed that the proteins differentially phosphorylated in response to curcumin are known to be involved in focal adhesion kinase signaling and actin cytoskeleton reorganization. CONCLUSIONS The study indicates that curcumin may regulate cellular processes such as proliferation and migration through perturbation of the focal adhesion kinase pathway. This is the first quantitative phosphoproteomics-based study demonstrating the signaling events that are altered in response to curcumin. Considering the importance of curcumin as an anti-cancer agent, this study will significantly improve the current knowledge of curcumin-mediated signaling in cancer.
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Affiliation(s)
- Gajanan Sathe
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Sneha M Pinto
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India
| | - Nazia Syed
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, 605014 India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Hitendra S Solanki
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Santosh Renuse
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Sandip Chavan
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Aafaque Ahmad Khan
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Arun H Patil
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014 India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | | | - T S Keshava Prasad
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| | - Harsha Gowda
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India
| | - Aditi Chatterjee
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India
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18
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Mitchell CJ, Kim MS, Zhong J, Nirujogi RS, Bose AK, Pandey A. Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. Mol Oncol 2016; 10:910-20. [PMID: 27067626 DOI: 10.1016/j.molonc.2016.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 11/25/2015] [Revised: 02/26/2016] [Accepted: 03/15/2016] [Indexed: 01/11/2023] Open
Abstract
The leukocyte antigen related (LAR) family of receptor-like protein tyrosine phosphatases has three members in humans - PTPRF, PTPRD and PTPRS - that have been implicated in diverse processes including embryonic development, inhibition of cell growth and axonal guidance. Mutations in the LAR family are associated with developmental defects such as cleft palate as well as various cancers including breast, neck, lung, colon and brain. Although this family of tyrosine phosphatases is important for many developmental processes, little is known of their substrates. This is partially due to functional redundancy within the LAR family, as deletion of a single gene in the LAR family does not have an appreciable phenotype, but a dual knockout is embryonically lethal in mouse models. To circumvent the inability to knockout multiple members of the LAR family in mouse models, we used a knockout of ptp-3, which is the only known ortholog of the LAR family in Caenorhabditis elegans and allows for the study of the LAR family at the organismal level. Using SILAC-based quantitative phosphoproteomics, we identified 255 putative substrates of ptp-3, which included four of the nine known annotated substrates of the LAR family. A motif analysis of the identified phosphopeptides allowed for the determination of sequences that appear to be preferentially dephosphorylated. Finally, we discovered that kinases were overrepresented in the list of identified putative substrates and tyrosine residues whose phosphorylation is known to increase kinase activity were dephosphorylated by ptp-3. These data are suggestive of ptp-3 as a potential negative regulator of several kinase families, such as the mitogen activated kinases (MAPKs), and multiple tyrosine kinases including FER, MET, and NTRK2.
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Affiliation(s)
- Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute of Bioinformatics, Bangalore, India
| | - Anjun K Bose
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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19
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Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Chavan S, Nirujogi RS, Patil AH, Solanki H, Renuse S, Sahasrabuddhe NA, Mathur PP, Prasad TSK, Kumar P, Califano JA, Sidransky D, Pandey A, Gowda H, Chatterjee A. Dysregulation of splicing proteins in head and neck squamous cell carcinoma. Cancer Biol Ther 2016; 17:219-29. [PMID: 26853621 DOI: 10.1080/15384047.2016.1139234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 01/23/2023] Open
Abstract
Signaling plays an important role in regulating all cellular pathways. Altered signaling is one of the hallmarks of cancers. Phosphoproteomics enables interrogation of kinase mediated signaling pathways in biological systems. In cancers, this approach can be utilized to identify aberrantly activated pathways that potentially drive proliferation and tumorigenesis. To identify signaling alterations in head and neck squamous cell carcinoma (HNSCC), we carried out proteomic and phosphoproteomic analysis of HNSCC cell lines using a combination of tandem mass tag (TMT) labeling approach and titanium dioxide-based enrichment. We identified 4,920 phosphosites corresponding to 2,212 proteins in six HNSCC cell lines compared to a normal oral cell line. Our data indicated significant enrichment of proteins associated with splicing. We observed hyperphosphorylation of SRSF protein kinase 2 (SRPK2) and its downstream substrates in HNSCC cell lines. SRPK2 is a splicing kinase, known to phosphorylate serine/arginine (SR) rich domain proteins and regulate splicing process in eukaryotes. Although genome-wide studies have reported the contribution of alternative splicing events of several genes in the progression of cancer, the involvement of splicing kinases in HNSCC is not known. In this study, we studied the role of SRPK2 in HNSCC. Inhibition of SRPK2 resulted in significant decrease in colony forming and invasive ability in a panel of HNSCC cell lines. Our results indicate that phosphorylation of SRPK2 plays a crucial role in the regulation of splicing process in HNSCC and that splicing kinases can be developed as a new class of therapeutic target in HNSCC.
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Affiliation(s)
- Aneesha Radhakrishnan
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,b Department of Biochemistry and Molecular Biology , Pondicherry University , Puducherry , India
| | - Vishalakshi Nanjappa
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,c Amrita School of Biotechnology, Amrita University , Kollam , India
| | - Remya Raja
- a Institute of Bioinformatics, International Technology Park , Bangalore , India
| | - Gajanan Sathe
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,d Manipal University , Madhav Nagar, Manipal , India
| | - Sandip Chavan
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,d Manipal University , Madhav Nagar, Manipal , India
| | - Raja Sekhar Nirujogi
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,e Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry , India
| | - Arun H Patil
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,f School of Biotechnology, KIIT University , Bhubaneswar , India
| | - Hitendra Solanki
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,f School of Biotechnology, KIIT University , Bhubaneswar , India
| | - Santosh Renuse
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,c Amrita School of Biotechnology, Amrita University , Kollam , India
| | | | - Premendu P Mathur
- b Department of Biochemistry and Molecular Biology , Pondicherry University , Puducherry , India.,f School of Biotechnology, KIIT University , Bhubaneswar , India
| | - T S Keshava Prasad
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,c Amrita School of Biotechnology, Amrita University , Kollam , India.,e Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry , India.,g YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore , India
| | - Prashant Kumar
- a Institute of Bioinformatics, International Technology Park , Bangalore , India
| | - Joseph A Califano
- h Milton J Dance Head and Neck Center, Greater Baltimore Medical Center , Baltimore , MD , USA.,i Department of Otolaryngology-Head and Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - David Sidransky
- i Department of Otolaryngology-Head and Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Akhilesh Pandey
- j McKusick-Nathans Institute of Genetic Medicine , Baltimore , MD , USA.,k Departments of Biological Chemistry , Baltimore , MD , USA.,l Oncology and Pathology, Johns Hopkins University School of Medicine , Baltimore , MD , USA.,m Pathology, Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Harsha Gowda
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,g YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore , India
| | - Aditi Chatterjee
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,g YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore , India
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20
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Li R, Liao G, Nirujogi RS, Pinto SM, Shaw PG, Huang TC, Wan J, Qian J, Gowda H, Wu X, Lv DW, Zhang K, Manda SS, Pandey A, Hayward SD. Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling. PLoS Pathog 2015; 11:e1005346. [PMID: 26714015 PMCID: PMC4699913 DOI: 10.1371/journal.ppat.1005346] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/28/2015] [Indexed: 12/21/2022] Open
Abstract
Epstein-Barr virus (EBV) is etiologically linked to infectious mononucleosis and several human cancers. EBV encodes a conserved protein kinase BGLF4 that plays a key role in the viral life cycle. To provide new insight into the host proteins regulated by BGLF4, we utilized stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics to compare site-specific phosphorylation in BGLF4-expressing Akata B cells. Our analysis revealed BGLF4-mediated hyperphosphorylation of 3,046 unique sites corresponding to 1,328 proteins. Frequency analysis of these phosphosites revealed a proline-rich motif signature downstream of BGLF4, indicating a broader substrate recognition for BGLF4 than its cellular ortholog cyclin-dependent kinase 1 (CDK1). Further, motif analysis of the hyperphosphorylated sites revealed enrichment in ATM, ATR and Aurora kinase substrates while functional analyses revealed significant enrichment of pathways related to the DNA damage response (DDR), mitosis and cell cycle. Phosphorylation of proteins associated with the mitotic spindle assembly checkpoint (SAC) indicated checkpoint activation, an event that inactivates the anaphase promoting complex/cyclosome, APC/C. Furthermore, we demonstrated that BGLF4 binds to and directly phosphorylates the key cellular proteins PP1, MPS1 and CDC20 that lie upstream of SAC activation and APC/C inhibition. Consistent with APC/C inactivation, we found that BGLF4 stabilizes the expression of many known APC/C substrates. We also noted hyperphosphorylation of 22 proteins associated the nuclear pore complex, which may contribute to nuclear pore disassembly and SAC activation. A drug that inhibits mitotic checkpoint activation also suppressed the accumulation of extracellular EBV virus. Taken together, our data reveal that, in addition to the DDR, manipulation of mitotic kinase signaling and SAC activation are mechanisms associated with lytic EBV replication. All MS data have been deposited in the ProteomeXchange with identifier PXD002411 (http://proteomecentral.proteomexchange.org/dataset/PXD002411). Epstein-Barr virus (EBV) is a herpesvirus that is associated with B cell and epithelial human cancers. Herpesviruses encode a protein kinase which is an important regulator of lytic virus replication and is consequently a target for anti-viral drug development. The EBV genome encodes for a serine/threonine protein kinase called BGLF4. Previous work on BGLF4 has largely focused on its cyclin-dependent kinase 1 (CDK1)-like activity. The range of BGLF4 cellular substrates and the full impact of BGLF4 on the intracellular microenvironment still remain to be elucidated. Here, we utilized unbiased quantitative phosphoproteomic approach to dissect the changes in the cellular phosphoproteome that are mediated by BGLF4. Our MS analyses revealed extensive hyperphosphorylation of substrates that are normally targeted by CDK1, Ataxia telangiectasia mutated (ATM), Ataxia telangiectasia and Rad3-related (ATR) proteins and Aurora kinases. The up-regulated phosphoproteins were functionally linked to the DNA damage response, mitosis and cell cycle pathways. Our data demonstrate widespread changes in the cellular phosphoproteome that occur upon BGLF4 expression and suggest that manipulation of the DNA damage and mitotic kinase signaling pathways are central to efficient EBV lytic replication.
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Affiliation(s)
- Renfeng Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Philips Institute for Oral Health Research, VCU School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail: (RL); (AP); (SDH)
| | - Gangling Liao
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Raja Sekhar Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Patrick G. Shaw
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tai-Chung Huang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jun Wan
- Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jiang Qian
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dong-Wen Lv
- Philips Institute for Oral Health Research, VCU School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kun Zhang
- Philips Institute for Oral Health Research, VCU School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Srikanth S. Manda
- Philips Institute for Oral Health Research, VCU School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- Philips Institute for Oral Health Research, VCU School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana, United States of America
- * E-mail: (RL); (AP); (SDH)
| | - S. Diane Hayward
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (RL); (AP); (SDH)
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21
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Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TSK, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. A multi-omic analysis of human naïve CD4+ T cells. BMC Syst Biol 2015; 9:75. [PMID: 26542228 PMCID: PMC4636073 DOI: 10.1186/s12918-015-0225-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 10/28/2015] [Indexed: 12/21/2022]
Abstract
Background Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome and proteome of a single human cell type to obtain a coherent view of the complex interplay between various biomolecules has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells isolated from a single individual. Results Integrating multi-omics datasets allowed us to investigate genome-wide methylation and its effect on mRNA/protein expression patterns, extent of RNA editing under normal physiological conditions and allele specific expression in naïve CD4+ T cells. In addition, we carried out a multi-omic comparative analysis of naïve with primary resting memory CD4+ T cells to identify molecular changes underlying T cell differentiation. This analysis provided mechanistic insights into how several molecules involved in T cell receptor signaling are regulated at the DNA, RNA and protein levels. Phosphoproteomics revealed downstream signaling events that regulate these two cellular states. Availability of multi-omics data from an identical genetic background also allowed us to employ novel proteogenomics approaches to identify individual-specific variants and putative novel protein coding regions in the human genome. Conclusions We utilized multiple high-throughput technologies to derive a comprehensive profile of two primary human cell types, naïve CD4+ T cells and memory CD4+ T cells, from a single donor. Through vertical as well as horizontal integration of whole genome sequencing, methylation arrays, RNA-Seq, miRNA-Seq, proteomics, and phosphoproteomics, we derived an integrated and comparative map of these two closely related immune cells and identified potential molecular effectors of immune cell differentiation following antigen encounter. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0225-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Derese Getnet
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Srikanth S Manda
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Praveen Kumar
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Tai-Chung Huang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Sneha M Pinto
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Mio Iwasaki
- Department of Molecular & Cellular BioAnalysis, Kyoto University, Kyoto, Japan.
| | - Patrick G Shaw
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Raghothama Chaerkady
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | | | | | - Rajesh Raju
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Caitlyn Bowman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ludmila Danilova
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jevon Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Charles G Drake
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Luigi Marchionni
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Peter N Murakami
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
| | - Alan F Scott
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Leming Shi
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA.
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
| | - Rafael Irizarry
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA.
| | - Leslie Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Kyoto University, Kyoto, Japan.
| | - Charles Wang
- Center for Genomics and Division of Microbiology & Molecular Genetics, Loma Linda University, Loma Linda, CA, USA.
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India. .,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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22
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Nirujogi RS, Wright JD, Manda SS, Zhong J, Na CH, Meyerhoff J, Benton B, Jabbour R, Willis K, Kim MS, Pandey A, Sekowski JW. Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats. Proteomics 2015; 15:487-99. [PMID: 25403869 DOI: 10.1002/pmic.201400371] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 08/01/2014] [Revised: 10/01/2014] [Accepted: 11/12/2014] [Indexed: 01/15/2023]
Abstract
To gain insights into the toxicity induced by the nerve agent VX, an MS-based phosphoproteomic analysis was carried out on the piriform cortex region of brains from VX-treated rats. Using isobaric tag based TMT labeling followed by titanium dioxide enrichment strategy, we identified 9975 unique phosphosites derived from 3287 phosphoproteins. Temporal changes in the phosphorylation status of peptides were observed over a time period of 24 h in rats exposed to a 1× LD50, intravenous (i.v.) dose with the most notable changes occurring at the 1 h postexposure time point. Five major functional classes of proteins exhibited changes in their phosphorylation status: (i) ion channels/transporters, including ATPases, (ii) kinases/phosphatases, (iii) GTPases, (iv) structural proteins, and (v) transcriptional regulatory proteins. This study is the first quantitative phosphoproteomic analysis of VX toxicity in the brain. Understanding the toxicity and compensatory signaling mechanisms will improve the understanding of the complex toxicity of VX in the brain and aid in the elucidation of novel molecular targets that would be important for development of improved countermeasures. All MS data have been deposited in the ProteomeXchange with identifier PXD001184 (http://proteomecentral.proteomexchange.org/dataset/PXD001184).
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India; School of Life Sciences, Centre for Bioinformatics, Pondicherry University, Puducherry, India; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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23
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Pinto SM, Nirujogi RS, Rojas PL, Patil AH, Manda SS, Subbannayya Y, Roa JC, Chatterjee A, Prasad TSK, Pandey A. Quantitative phosphoproteomic analysis of IL-33-mediated signaling. Proteomics 2015; 15:532-44. [PMID: 25367039 DOI: 10.1002/pmic.201400303] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/25/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022]
Abstract
Interleukin-33 (IL-33) is a novel member of the IL-1 family of cytokines that plays diverse roles in the regulation of immune responses. IL-33 exerts its effects through a heterodimeric receptor complex resulting in the production and release of proinflammatory cytokines. A detailed understanding of the signaling pathways activated by IL-33 is still unclear. To gain insights into the IL-33-mediated signaling mechanisms, we carried out a SILAC-based global quantitative phosphoproteomic analysis that resulted in the identification of 7191 phosphorylation sites derived from 2746 proteins. We observed alterations in the level of phosphorylation in 1050 sites corresponding to 672 proteins upon IL-33 stimulation. We report, for the first time, phosphorylation of multiple protein kinases, including mitogen-activated protein kinase activated protein kinase 2 (Mapkapk2), receptor (TNFRSF) interacting serine-threonine kinase 1 (Ripk1), and NAD kinase (Nadk) that are induced by IL-33. In addition, we observed IL-33-induced phosphorylation of several protein phosphatases including protein tyrosine phosphatase, nonreceptor-type 12 (Ptpn12), and inositol polyphosphate-5-phosphatase D (Inpp5d), which have not been reported previously. Network analysis revealed an enrichment of actin binding and cytoskeleton reorganization that could be important in macrophage activation induced by IL-33. Our study is the first quantitative analysis of IL-33-regulated phosphoproteome. Our findings significantly expand the understanding of IL-33-mediated signaling events and have the potential to provide novel therapeutic targets pertaining to immune-related diseases such as asthma where dysregulation of IL-33 is observed. All MS data have been deposited in the ProteomeXchange with identifier PXD000984 (http://proteomecentral.proteomexchange.org/dataset/PXD000984).
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Affiliation(s)
- Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, India; Manipal University, Madhava Nagar, Manipal, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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24
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Syed N, Barbhuiya MA, Pinto SM, Nirujogi RS, Renuse S, Datta KK, Khan AA, Srikumar K, Prasad TSK, Kumar MV, Kumar RV, Chatterjee A, Pandey A, Gowda H. Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous-cell carcinoma. Proteomics 2015; 15:374-82. [PMID: 25366905 PMCID: PMC4309511 DOI: 10.1002/pmic.201400379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 08/08/2014] [Revised: 10/01/2014] [Accepted: 10/28/2014] [Indexed: 01/17/2023]
Abstract
Esophageal squamous‐cell carcinoma (ESCC) is one of the most common malignancies in Asia. Currently, surgical resection of early‐stage tumor is the best available treatment. However, most patients present late when surgery is not an option. Data suggest that chemotherapy regimens are inadequate for clinical management of advanced cancer. Targeted therapy has emerged as one of the most promising approaches to treat several malignancies. A prerequisite for developing targeted therapy is prior knowledge of proteins and pathways that drive proliferation in malignancies. We carried out phosphotyrosine profiling across four different ESCC cell lines and compared it to non‐neoplastic Het‐1A cell line to identify activated tyrosine kinase signaling pathways in ESCC. A total of 278 unique phosphopeptides were identified across these cell lines. This included several tyrosine kinases and their substrates that were hyperphosphorylated in ESCC. Ephrin receptor A2 (EPHA2), a receptor tyrosine kinase, was hyperphosphorylated in all the ESCC cell lines used in the study. EPHA2 is reported to be oncogenic in several cancers and is also known to promote metastasis. Immunohistochemistry‐based studies have revealed EPHA2 is overexpressed in nearly 50% of ESCC. We demonstrated EPHA2 as a potential therapeutic target in ESCC by carrying out siRNA‐based knockdown studies. Knockdown of EPHA2 in ESCC cell line TE8 resulted in significant decrease in cell proliferation and invasion, suggesting it is a promising therapeutic target in ESCC that warrants further evaluation.
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Affiliation(s)
- Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, India; Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India
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25
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Zahari MS, Wu X, Pinto SM, Nirujogi RS, Kim MS, Fetics B, Philip M, Barnes SR, Godfrey B, Gabrielson E, Nevo E, Pandey A. Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Sci Rep 2015; 5:13660. [PMID: 26329039 PMCID: PMC4557083 DOI: 10.1038/srep13660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 03/27/2015] [Accepted: 07/27/2015] [Indexed: 01/06/2023] Open
Abstract
Delays between tissue collection and tissue fixation result in ischemia and ischemia-associated changes in protein phosphorylation levels, which can misguide the examination of signaling pathway status. To identify a biomarker that serves as a reliable indicator of ischemic changes that tumor tissues undergo, we subjected harvested xenograft tumors to room temperature for 0, 2, 10 and 30 minutes before freezing in liquid nitrogen. Multiplex TMT-labeling was conducted to achieve precise quantitation, followed by TiO2 phosphopeptide enrichment and high resolution mass spectrometry profiling. LC-MS/MS analyses revealed phosphorylation level changes of a number of phosphosites in the ischemic samples. The phosphorylation of one of these sites, S82 of the heat shock protein 27 kDa (HSP27), was especially abundant and consistently upregulated in tissues with delays in freezing as short as 2 minutes. In order to eliminate effects of ischemia, we employed a novel cryogenic biopsy device which begins freezing tissues in situ before they are excised. Using this device, we showed that the upregulation of phosphorylation of S82 on HSP27 was abrogated. We thus demonstrate that our cryogenic biopsy device can eliminate ischemia-induced phosphoproteome alterations, and measurements of S82 on HSP27 can be used as a robust marker of ischemia in tissues.
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Affiliation(s)
- Muhammad Saddiq Zahari
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sneha M Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066 India
| | | | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Barry Fetics
- Robin Medical, Inc., P.O. Box 2414, Baltimore, MD 21203, USA
| | - Mathew Philip
- Robin Medical, Inc., P.O. Box 2414, Baltimore, MD 21203, USA
| | - Sheri R Barnes
- Charles River Discovery Research Services, 3300 Gateway Centre Boulevard, Morrisville NC 27560
| | - Beverly Godfrey
- Charles River Discovery Research Services, 3300 Gateway Centre Boulevard, Morrisville NC 27560
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Erez Nevo
- Robin Medical, Inc., P.O. Box 2414, Baltimore, MD 21203, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
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26
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Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A. Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer. Mol Cell Proteomics 2015; 14:2887-900. [PMID: 26330541 DOI: 10.1074/mcp.m115.050484] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 01/13/2023] Open
Abstract
Tamoxifen, an estrogen receptor-α (ER) antagonist, is an important agent for the treatment of breast cancer. However, this therapy is complicated by the fact that a substantial number of patients exhibit either de novo or acquired resistance. To characterize the signaling mechanisms underlying this resistance, we treated the MCF7 breast cancer cell line with tamoxifen for over six months and showed that this cell line acquired resistance to tamoxifen in vitro and in vivo. We performed SILAC-based quantitative phosphoproteomic profiling on the tamoxifen resistant and vehicle-treated sensitive cell lines to quantify the phosphorylation alterations associated with tamoxifen resistance. From >5600 unique phosphopeptides identified, 1529 peptides exhibited hyperphosphorylation and 409 peptides showed hypophosphorylation in the tamoxifen resistant cells. Gene set enrichment analysis revealed that focal adhesion pathway was one of the most enriched signaling pathways activated in tamoxifen resistant cells. Significantly, we showed that the focal adhesion kinase FAK2 was not only hyperphosphorylated but also transcriptionally up-regulated in tamoxifen resistant cells. FAK2 suppression by specific siRNA knockdown or a small molecule inhibitor repressed cellular proliferation in vitro and tumor formation in vivo. More importantly, our survival analysis revealed that high expression of FAK2 is significantly associated with shorter metastasis-free survival in estrogen receptor-positive breast cancer patients treated with tamoxifen. Our studies suggest that FAK2 is a potential therapeutic target for the management of hormone-refractory breast cancers.
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Affiliation(s)
- Xinyan Wu
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Muhammad Saddiq Zahari
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Santosh Renuse
- §Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | - Raja Sekhar Nirujogi
- §Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | - Min-Sik Kim
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Srikanth S Manda
- §Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | | | - Edward Gabrielson
- ‖Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | | | - Akhilesh Pandey
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ¶Department of Oncology; ‖Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
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27
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Murthy KR, Rajagopalan P, Pinto SM, Advani J, Murthy PR, Goel R, Subbannayya Y, Balakrishnan L, Dash M, Anil AK, Manda SS, Nirujogi RS, Kelkar DS, Sathe GJ, Dey G, Chatterjee A, Gowda H, Chakravarti S, Shankar S, Sahasrabuddhe NA, Nair B, Somani BL, Prasad TSK, Pandey A. Proteomics of Human Aqueous Humor. OMICS: A Journal of Integrative Biology 2015; 19:283-93. [DOI: 10.1089/omi.2015.0029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | | | - Renu Goel
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta, India
| | - Mahashweta Dash
- Department of Internal Medicine, Armed Forces Medical College, Pune, India
| | - Abhijith K. Anil
- Department of Internal Medicine, Armed Forces Medical College, Pune, India
| | - Srikanth S. Manda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Gajanan J. Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Shukti Chakravarti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Subramanian Shankar
- Department of Rheumatology, Medical Division, Command Hospital (Air Force), Bangalore, India
| | | | - Bipin Nair
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Babu Lal Somani
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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28
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Marimuthu A, Huang TC, Selvan LDN, Renuse S, Nirujogi RS, Kumar P, Pinto SM, Rajagopalan S, Pandey A, Harsha H, Chatterjee A. Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach. EuPA Open Proteomics 2014. [DOI: 10.1016/j.euprot.2014.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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29
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Manda SS, Nirujogi RS, Pinto SM, Kim MS, Datta KK, Sirdeshmukh R, Prasad TSK, Thongboonkerd V, Pandey A, Gowda H. Identification and Characterization of Proteins Encoded by Chromosome 12 as Part of Chromosome-centric Human Proteome Project. J Proteome Res 2014; 13:3166-77. [DOI: 10.1021/pr401123v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Srikanth Srinivas Manda
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre
of Excellence in Bioinformatics, Bioinformatics Centre, School of
Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Raja Sekhar Nirujogi
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre
of Excellence in Bioinformatics, Bioinformatics Centre, School of
Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Sneha Maria Pinto
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | | | - Keshava K. Datta
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
- School of
Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Ravi Sirdeshmukh
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - T. S. Keshava Prasad
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Visith Thongboonkerd
- Medical
Proteomics Unit, Office for Research and Development, Faculty of Medicine
Siriraj Hospital, and Center for Research in Complex Systems Science, Mahidol University, Bangkok 10700, Thailand
| | - Akhilesh Pandey
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Harsha Gowda
- Institute
of Bioinformatics, International Technology Park, Bangalore 560066, India
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30
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Dwivedi SB, Muthusamy B, Kumar P, Kim MS, Nirujogi RS, Getnet D, Ahiakonu P, De G, Nair B, Gowda H, Prasad TSK, Kumar N, Pandey A, Okulate M. Brain proteomics of Anopheles gambiae. OMICS 2014; 18:421-37. [PMID: 24937107 DOI: 10.1089/omi.2014.0007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Anopheles gambiae has a well-adapted system for host localization, feeding, and mating behavior, which are all governed by neuronal processes in the brain. However, there are no published reports characterizing the brain proteome to elucidate neuronal signaling mechanisms in the vector. To this end, a large-scale mapping of the brain proteome of An. gambiae was carried out using high resolution tandem mass spectrometry, revealing a repertoire of >1800 proteins, of which 15% could not be assigned any function. A large proportion of the identified proteins were predicted to be involved in diverse biological processes including metabolism, transport, protein synthesis, and olfaction. This study also led to the identification of 10 GPCR classes of proteins, which could govern sensory pathways in mosquitoes. Proteins involved in metabolic and neural processes, chromatin modeling, and synaptic vesicle transport associated with neuronal transmission were predominantly expressed in the brain. Proteogenomic analysis expanded our findings with the identification of 15 novel genes and 71 cases of gene refinements, a subset of which were validated by RT-PCR and sequencing. Overall, our study offers valuable insights into the brain physiology of the vector that could possibly open avenues for intervention strategies for malaria in the future.
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Affiliation(s)
- Sutopa B Dwivedi
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India
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31
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Balakrishnan L, Nirujogi RS, Ahmad S, Bhattacharjee M, Manda SS, Renuse S, Kelkar DS, Subbannayya Y, Raju R, Goel R, Thomas JK, Kaur N, Dhillon M, Tankala SG, Jois R, Vasdev V, Ramachandra Y, Sahasrabuddhe NA, Prasad TK, Mohan S, Gowda H, Shankar S, Pandey A. Proteomic analysis of human osteoarthritis synovial fluid. Clin Proteomics 2014; 11:6. [PMID: 24533825 PMCID: PMC3942106 DOI: 10.1186/1559-0275-11-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [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: 08/06/2013] [Accepted: 01/06/2014] [Indexed: 12/30/2022] Open
Abstract
Background Osteoarthritis is a chronic musculoskeletal disorder characterized mainly by progressive degradation of the hyaline cartilage. Patients with osteoarthritis often postpone seeking medical help, which results in the diagnosis being made at an advanced stage of cartilage destruction. Sustained efforts are needed to identify specific markers that might help in early diagnosis, monitoring disease progression and in improving therapeutic outcomes. We employed a multipronged proteomic approach, which included multiple fractionation strategies followed by high resolution mass spectrometry analysis to explore the proteome of synovial fluid obtained from osteoarthritis patients. In addition to the total proteome, we also enriched glycoproteins from synovial fluid using lectin affinity chromatography. Results We identified 677 proteins from synovial fluid of patients with osteoarthritis of which 545 proteins have not been previously reported. These novel proteins included ADAM-like decysin 1 (ADAMDEC1), alanyl (membrane) aminopeptidase (ANPEP), CD84, fibulin 1 (FBLN1), matrix remodelling associated 5 (MXRA5), secreted phosphoprotein 2 (SPP2) and spondin 2 (SPON2). We identified 300 proteins using lectin affinity chromatography, including the glycoproteins afamin (AFM), attractin (ATRN), fibrillin 1 (FBN1), transferrin (TF), tissue inhibitor of metalloproteinase 1 (TIMP1) and vasorin (VSN). Gene ontology analysis confirmed that a majority of the identified proteins were extracellular and are mostly involved in cell communication and signaling. We also confirmed the expression of ANPEP, dickkopf WNT signaling pathway inhibitor 3 (DKK3) and osteoglycin (OGN) by multiple reaction monitoring (MRM) analysis of osteoarthritis synovial fluid samples. Conclusions We present an in-depth analysis of the synovial fluid proteome from patients with osteoarthritis. We believe that the catalog of proteins generated in this study will further enhance our knowledge regarding the pathophysiology of osteoarthritis and should assist in identifying better biomarkers for early diagnosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Subramanian Shankar
- Department of Internal Medicine, Armed Forces Medical College, Pune, Maharashtra 411040, India.
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Nagarajha Selvan LD, Kaviyil JE, Nirujogi RS, Muthusamy B, Puttamallesh VN, Subbannayya T, Syed N, Radhakrishnan A, Kelkar DS, Ahmad S, Pinto SM, Kumar P, Madugundu AK, Nair B, Chatterjee A, Pandey A, Ravikumar R, Gowda H, Prasad TSK. Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clin Proteomics 2014; 11:5. [PMID: 24484775 PMCID: PMC3915034 DOI: 10.1186/1559-0275-11-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 04/30/2013] [Accepted: 12/17/2013] [Indexed: 12/30/2022] Open
Abstract
Background Cryptococcus neoformans, a basidiomycetous fungus of universal occurrence, is a significant opportunistic human pathogen causing meningitis. Owing to an increase in the number of immunosuppressed individuals along with emergence of drug-resistant strains, C. neoformans is gaining importance as a pathogen. Although, whole genome sequencing of three varieties of C. neoformans has been completed recently, no global proteomic studies have yet been reported. Results We performed a comprehensive proteomic analysis of C. neoformans var. grubii (Serotype A), which is the most virulent variety, in order to provide protein-level evidence for computationally predicted gene models and to refine the existing annotations. We confirmed the protein-coding potential of 3,674 genes from a total of 6,980 predicted protein-coding genes. We also identified 4 novel genes and corrected 104 predicted gene models. In addition, our studies led to the correction of translational start site, splice junctions and reading frame used for translation in a number of proteins. Finally, we validated a subset of our novel findings by RT-PCR and sequencing. Conclusions Proteogenomic investigation described here facilitated the validation and refinement of computationally derived gene models in the intron-rich genome of C. neoformans, an important fungal pathogen in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.
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Balakrishnan L, Bhattacharjee M, Ahmad S, Nirujogi RS, Renuse S, Subbannayya Y, Marimuthu A, Srikanth SM, Raju R, Dhillon M, Kaur N, Jois R, Vasudev V, Ramachandra Y, Sahasrabuddhe NA, Prasad TK, Mohan S, Gowda H, Shankar S, Pandey A. Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. Clin Proteomics 2014; 11:1. [PMID: 24393543 PMCID: PMC3918105 DOI: 10.1186/1559-0275-11-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [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: 04/30/2013] [Accepted: 12/10/2013] [Indexed: 01/09/2023] Open
Abstract
Background Rheumatoid arthritis and osteoarthritis are two common musculoskeletal disorders that affect the joints. Despite high prevalence rates, etiological factors involved in these disorders remain largely unknown. Dissecting the molecular aspects of these disorders will significantly contribute to improving their diagnosis and clinical management. In order to identify proteins that are differentially expressed between these two conditions, a quantitative proteomic profiling of synovial fluid obtained from rheumatoid arthritis and osteoarthritis patients was carried out by using iTRAQ labeling followed by high resolution mass spectrometry analysis. Results We have identified 575 proteins out of which 135 proteins were found to be differentially expressed by ≥3-fold in the synovial fluid of rheumatoid arthritis and osteoarthritis patients. Proteins not previously reported to be associated with rheumatoid arthritis including, coronin-1A (CORO1A), fibrinogen like-2 (FGL2), and macrophage capping protein (CAPG) were found to be upregulated in rheumatoid arthritis. Proteins such as CD5 molecule-like protein (CD5L), soluble scavenger receptor cysteine-rich domain-containing protein (SSC5D), and TTK protein kinase (TTK) were found to be upregulated in the synovial fluid of osteoarthritis patients. We confirmed the upregulation of CAPG in rheumatoid arthritis synovial fluid by multiple reaction monitoring assay as well as by Western blot. Pathway analysis of differentially expressed proteins revealed a significant enrichment of genes involved in glycolytic pathway in rheumatoid arthritis. Conclusions We report here the largest identification of proteins from the synovial fluid of rheumatoid arthritis and osteoarthritis patients using a quantitative proteomics approach. The novel proteins identified from our study needs to be explored further for their role in the disease pathogenesis of rheumatoid arthritis and osteoarthritis. Sartaj Ahmad and Raja Sekhar Nirujogi contributed equally to this article.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Subramanian Shankar
- Department of Internal Medicine, Armed Forces Medical College, Pune 411040, India.
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Prasad TSK, Verma R, Kumar S, Nirujogi RS, Sathe GJ, Madugundu AK, Sharma J, Puttamallesh VN, Ganjiwale A, Myneedu VP, Chatterjee A, Pandey A, Harsha H, Narayana J. Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis. Clin Proteomics 2013; 10:8. [PMID: 23870090 PMCID: PMC3729367 DOI: 10.1186/1559-0275-10-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 03/28/2013] [Accepted: 07/16/2013] [Indexed: 12/02/2022] Open
Abstract
Background Purified protein derivative (PPD) has been used for more than half a century as an antigen for the diagnosis of tuberculosis infection based on delayed type hypersensitivity. Although designated as “purified,” in reality, the composition of PPD is highly complex and remains ill-defined. In this report, high resolution mass spectrometry was applied to understand the complexity of its constituent components. A comparative proteomic analysis of various PPD preparations and their functional characterization is likely to help in short-listing the relevant antigens required to prepare a less complex and more potent reagent for diagnostic purposes. Results Proteomic analysis of Connaught Tuberculin 68 (PPD-CT68), a tuberculin preparation generated from M. tuberculosis, was carried out in this study. PPD-CT68 is the protein component of a commercially available tuberculin preparation, Tubersol, which is used for tuberculin skin testing. Using a high resolution LTQ-Orbitrap Velos mass spectrometer, we identified 265 different proteins. The identified proteins were compared with those identified from PPD M. bovis, PPD M. avium and PPD-S2 from previous mass spectrometry-based studies. In all, 142 proteins were found to be shared between PPD-CT68 and PPD-S2 preparations. Out of the 354 proteins from M. tuberculosis–derived PPDs (i.e. proteins in either PPD-CT68 or PPD-S2), 37 proteins were found to be shared with M. avium PPD and 80 were shared with M. bovis PPD. Alignment of PPD-CT68 proteins with proteins encoded by 24 lung infecting bacteria revealed a number of similar proteins (206 bacterial proteins shared epitopes with 47 PPD-CT68 proteins), which could potentially be involved in causing cross-reactivity. The data have been deposited to the ProteomeXchange with identifier PXD000377. Conclusions Proteomic and bioinformatics analysis of different PPD preparations revealed commonly and differentially represented proteins. This information could help in delineating the relevant antigens represented in various PPDs, which could further lead to development of a lesser complex and better defined skin test antigen with a higher specificity and sensitivity.
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Nirujogi RS, Pawar H, Renuse S, Kumar P, Chavan S, Sathe G, Sharma J, Khobragade S, Pande J, Modak B, Prasad TSK, Harsha HC, Patole MS, Pandey A. Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. J Proteomics 2013; 97:48-61. [PMID: 23665000 DOI: 10.1016/j.jprot.2013.04.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 12/29/2012] [Revised: 04/02/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
UNLABELLED The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani. BIOLOGICAL SIGNIFICANCE Leishmania donovani genome sequencing was recently completed, which permitted us to use a proteogenomic approach to map its proteome and to carry out annotation of it genome. This resulted in mapping of 50% (3999 proteins) of L. donovani proteome. Our study identified 20 novel genes previously not predicted from the L. donovani genome in addition to correcting annotations of 40 existing gene models. The identified proteins may help in better understanding of stage-specific protein expression profiles in L. donovani and to identify novel stage-specific drug targets in L. donovani which could be used in the treatment of leishmaniasis. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | | | | | - Bhakti Modak
- National Centre for Cell Sciences, Pune 411007, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | | | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA.
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