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Selvan LDN, Danda R, Madugundu AK, Puttamallesh VN, Sathe GJ, Krishnan UM, Khetan V, Rishi P, Prasad TSK, Pandey A, Krishnakumar S, Gowda H, Elchuri SV. Phosphoproteomics of Retinoblastoma: A Pilot Study Identifies Aberrant Kinases. Molecules 2018; 23:molecules23061454. [PMID: 29914080 PMCID: PMC6100359 DOI: 10.3390/molecules23061454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 01/09/2023] Open
Abstract
Retinoblastoma is a malignant tumour of the retina which most often occurs in children. Earlier studies on retinoblastoma have concentrated on the identification of key players in the disease and have not provided information on activated/inhibited signalling pathways. The dysregulation of protein phosphorylation in cancer provides clues about the affected signalling cascades in cancer. Phosphoproteomics is an ideal tool for the study of phosphorylation changes in proteins. Hence, global phosphoproteomics of retinoblastoma (RB) was carried out to identify signalling events associated with this cancer. Over 350 proteins showed differential phosphorylation in RB compared to control retina. Our study identified stress response proteins to be hyperphosphorylated in RB which included H2A histone family member X (H2AFX) and sirtuin 1. In particular, Ser140 of H2AFX also known as gamma-H2AX was found to be hyperphosphorylated in retinoblastoma, which indicated the activation of DNA damage response pathways. We also observed the activation of anti-apoptosis in retinoblastoma compared to control. These observations showed the activation of survival pathways in retinoblastoma. The identification of hyperphosphorylated protein kinases including Bromodomain containing 4 (BRD4), Lysine deficient protein kinase 1 (WNK1), and Cyclin-dependent kinase 1 (CDK1) in RB opens new avenues for the treatment of RB. These kinases can be considered as probable therapeutic targets for RB, as small-molecule inhibitors for some of these kinases are already in clinical trials for the treatment other cancers.
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Affiliation(s)
| | - Ravikanth Danda
- L&T Opthalmic Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
- Centre for Nanotechnology and Advanced Biomaterials, Shanmugha Arts, Science, Technology and Research Academy University, Tanjore, Tamil Nadu 613 401, India.
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576 104, India.
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology and Advanced Biomaterials, Shanmugha Arts, Science, Technology and Research Academy University, Tanjore, Tamil Nadu 613 401, India.
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575 108, India.
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Subramanian Krishnakumar
- L&T Opthalmic Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
| | - Sailaja V Elchuri
- Department of Nanotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
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Tiwari R, Sahu I, Soni BL, Sathe GJ, Thapa P, Patel P, Sinha S, Vadivel CK, Patel S, Jamghare SN, Oak S, Thorat R, Gowda H, Vaidya MM. Depletion of keratin 8/18 modulates oncogenic potential by governing multiple signaling pathways. FEBS J 2018; 285:1251-1276. [DOI: 10.1111/febs.14401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/21/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Richa Tiwari
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
- Homi Bhabha National Institute Mumbai India
| | - Indrajit Sahu
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
- Homi Bhabha National Institute Mumbai India
- Department of Biology Technion – Israel Institute of Technology Haifa Israel
| | - Bihari Lal Soni
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
- Homi Bhabha National Institute Mumbai India
| | | | - Pankaj Thapa
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
- Homi Bhabha National Institute Mumbai India
| | - Pavan Patel
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | - Shruti Sinha
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | | | - Shweta Patel
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | - Sayli Nitin Jamghare
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | - Swapnil Oak
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | - Rahul Thorat
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | | | - Milind M. Vaidya
- Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
- Homi Bhabha National Institute Mumbai India
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Nanjappa V, Sathe GJ, Jain AP, Rajagopalan P, Raja R, Subbannayya T, Patil AH, Kumar P, Prasad TSK, Mathur PP, Sidransky D, Gowda H, Chatterjee A. Investigation of curcumin-mediated signalling pathways in head and neck squamous cell carcinoma. Translational Research in Oral Oncology 2017. [DOI: 10.1177/2057178x17743142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Gajanan J. Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, India
| | - Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - Arun H. Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - T. S. 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 Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
| | - Premendu Prakash Mathur
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
- Department of Biochemistry & Molecular Biology, Pondicherry University, Pondicherry, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
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Tiwari R, Sahu I, Soni BL, Sathe GJ, Datta KK, Thapa P, Sinha S, Vadivel CK, Dhaka B, Gowda H, Vaidya MM. Quantitative phosphoproteomic analysis reveals system-wide signaling pathways regulated by site-specific phosphorylation of Keratin-8 in skin squamous cell carcinoma derived cell line. Proteomics 2017; 17. [PMID: 28176443 DOI: 10.1002/pmic.201600254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 01/14/2017] [Accepted: 02/01/2017] [Indexed: 12/20/2022]
Abstract
Keratin 8/18, a simple epithelia specific keratin pair, is often aberrantly expressed in squamous cell carcinomas (SCC) where its expression is correlated with increased invasion and poor prognosis. Majority of Keratin 8 (K8) functions are governed by its phosphorylation at Serine73 (head-domain) and Serine431 (tail-domain) residues. Although, deregulation of K8 phosphorylation is associated with progression of different carcinomas, its role in skin-SCC and the underlying mechanism is obscure. In this direction, we performed tandem mass tag-based quantitative phosphoproteomics by expressing K8 wild type, phosphodead, and phosphomimetic mutants in K8-deficient A431 cells. Further analysis of our phosphoproteomics data showed a significant proportion of total phosphoproteome associated with migratory, proliferative, and invasive potential of these cells to be differentially phosphorylated. Differential phosphorylation of CDK1T14,Y15 , EIF4EBP1T46,T50 , EIF4BS422 , AKT1S1T246,S247 , CTTN1T401,S405,Y421 , and CAP1S307/309 in K8-S73A/D mutant and CTTN1T401,S405,Y421 , BUB1BS1043 , and CARHSP1S30,S32 in K8-S431A/D mutants as well as some anonymous phosphosites including MYCS176 , ZYXS344 , and PNNS692 could be potential candidates associated with K8 phosphorylation mediated tumorigenicity. Biochemical validation followed by phenotypic analysis further confirmed our quantitative phosphoproteomics data. In conclusion, our study provides the first global picture of K8 site-specific phosphorylation function in neoplastic progression of A431 cells and suggests various potential starting points for further mechanistic studies.
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Affiliation(s)
- Richa Tiwari
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Indrajit Sahu
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India.,Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Bihari Lal Soni
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India.,Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | - Pankaj Thapa
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Shruti Sinha
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | | | | | | | - Milind M Vaidya
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
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5
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Tiwari R, Sahu I, Soni BL, Sathe GJ, Datta KK, Thapa P, Sinha S, Vadivel CK, Dhaka B, Gowda H, Vaidya MM. Inside Front Cover: Quantitative phosphoproteomic analysis reveals system-wide signaling pathways regulated by site-specific phosphorylation of Keratin-8 in skin squamous cell carcinoma derived cell-line. Proteomics 2017. [DOI: 10.1002/pmic.201770056] [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: 11/05/2022]
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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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7
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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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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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9
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Rajagopalan P, Nanjappa V, Raja R, Jain AP, Mangalaparthi KK, Sathe GJ, Babu N, Patel K, Cavusoglu N, Soeur J, Pandey A, Roy N, Breton L, Chatterjee A, Misra N, Gowda H. How Does Chronic Cigarette Smoke Exposure Affect Human Skin? A Global Proteomics Study in Primary Human Keratinocytes. OMICS 2016; 20:615-626. [PMID: 27828771 DOI: 10.1089/omi.2016.0123] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cigarette smoking has been associated with multiple negative effects on human skin. Long-term physiological effects of cigarette smoke are through chronic and not acute exposure. Molecular alterations due to chronic exposure to cigarette smoke remain unclear. Primary human skin keratinocytes chronically exposed to cigarette smoke condensate (CSC) showed a decreased wound-healing capacity with an increased expression of NRF2 and MMP9. Using quantitative proteomics, we identified 4728 proteins, of which 105 proteins were overexpressed (≥2-fold) and 41 proteins were downregulated (≤2-fold) in primary skin keratinocytes chronically exposed to CSC. We observed an alteration in the expression of several proteins involved in maintenance of epithelial barrier integrity, including keratin 80 (5.3 fold, p value 2.5 × 10-7), cystatin A (3.6-fold, p value 3.2 × 10-3), and periplakin (2.4-fold, p value 1.2 × 10-8). Increased expression of proteins associated with skin hydration, including caspase 14 (2.2-fold, p value 4.7 × 10-2) and filaggrin (3.6-fold, p value 5.4 × 10-7), was also observed. In addition, we report differential expression of several proteins, including adipogenesis regulatory factor (2.5-fold, p value 1.3 × 10-3) and histone H1.0 (2.5-fold, p value 6.3 × 10-3) that have not been reported earlier. Bioinformatics analyses demonstrated that proteins differentially expressed in response to CSC are largely related to oxidative stress, maintenance of skin integrity, and anti-inflammatory responses. Importantly, treatment with vitamin E, a widely used antioxidant, could partially rescue adverse effects of CSC exposure in primary skin keratinocytes. The utility of antioxidant-based new dermatological formulations in delaying or preventing skin aging and oxidative damages caused by chronic cigarette smoke exposure warrants further clinical investigations and multi-omics research.
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Affiliation(s)
- Pavithra Rajagopalan
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
- 2 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Vishalakshi Nanjappa
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
- 3 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Remya Raja
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
| | - Ankit P Jain
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
- 2 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Kiran K Mangalaparthi
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
- 3 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Gajanan J Sathe
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
- 4 Manipal University , Manipal, India
| | - Niraj Babu
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
| | - Krishna Patel
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
- 3 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | | | - Jeremie Soeur
- 5 L'Oréal Research and Innovation , Aulnay Sous Bois, France
| | - Akhilesh Pandey
- 6 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland
- 7 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland
- 8 Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, Maryland
- 9 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Nita Roy
- 10 L'Oréal India, Bangalore, India
| | - Lionel Breton
- 5 L'Oréal Research and Innovation , Aulnay Sous Bois, France
| | - Aditi Chatterjee
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
| | | | - Harsha Gowda
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India
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10
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Nanjappa V, Renuse S, Sathe GJ, Raja R, Syed N, Radhakrishnan A, Subbannayya T, Patil A, Marimuthu A, Sahasrabuddhe NA, Guerrero-Preston R, Somani BL, Nair B, Kundu GC, Prasad TK, Califano JA, Gowda H, Sidransky D, Pandey A, Chatterjee A. Chronic exposure to chewing tobacco selects for overexpression of stearoyl-CoA desaturase in normal oral keratinocytes. Cancer Biol Ther 2015; 16:1593-603. [PMID: 26391970 PMCID: PMC4846103 DOI: 10.1080/15384047.2015.1078022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/24/2015] [Accepted: 07/26/2015] [Indexed: 01/10/2023] Open
Abstract
Chewing tobacco is a common practice in certain socio-economic sections of southern Asia, particularly in the Indian subcontinent and has been well associated with head and neck squamous cell carcinoma. The molecular mechanisms of chewing tobacco which leads to malignancy remains unclear. In large majority of studies, short-term exposure to tobacco has been evaluated. From a biological perspective, however, long-term (chronic) exposure to tobacco mimics the pathogenesis of oral cancer more closely. We developed a cell line model to investigate the chronic effects of chewing tobacco. Chronic exposure to tobacco resulted in higher cellular proliferation and invasive ability of the normal oral keratinocytes (OKF6/TERT1). We carried out quantitative proteomic analysis of OKF6/TERT1 cells chronically treated with chewing tobacco compared to the untreated cells. We identified a total of 3,636 proteins among which expression of 408 proteins were found to be significantly altered. Among the overexpressed proteins, stearoyl-CoA desaturase (SCD) was found to be 2.6-fold overexpressed in the tobacco treated cells. Silencing/inhibition of SCD using its specific siRNA or inhibitor led to a decrease in cellular proliferation, invasion and colony forming ability of not only the tobacco treated cells but also in a panel of head and neck cancer cell lines. These findings suggest that chronic exposure to chewing tobacco induced carcinogenesis in non-malignant oral epithelial cells and SCD plays an essential role in this process. The current study provides evidence that SCD can act as a potential therapeutic target in head and neck squamous cell carcinoma, especially in patients who are users of tobacco.
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Affiliation(s)
- Vishalakshi Nanjappa
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Amrita School of Biotechnology; Amrita University; Kollam, India
| | - Santosh Renuse
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Amrita School of Biotechnology; Amrita University; Kollam, India
| | - Gajanan J Sathe
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Madhav Nagar; Manipal, India
| | - Remya Raja
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Nazia Syed
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Department of Biochemistry and Molecular Biology; Pondicherry University; Puducherry, India
| | - Aneesha Radhakrishnan
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Department of Biochemistry and Molecular Biology; Pondicherry University; Puducherry, India
| | - Tejaswini Subbannayya
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Amrita School of Biotechnology; Amrita University; Kollam, India
| | - Arun Patil
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- School of Biotechnology; KIIT University; Bhubaneswar, India
| | | | | | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Babu L Somani
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Bipin Nair
- Amrita School of Biotechnology; Amrita University; Kollam, India
| | - Gopal C Kundu
- National Center for Cell Science (NCCS); NCCS Complex; Pune, India
| | - T Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Amrita School of Biotechnology; Amrita University; Kollam, India
- YU-IOB Center for Systems Biology and Molecular Medicine; Yenepoya University; Mangalore, India
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Milton J. Dance Head and Neck Center; Greater Baltimore Medical Center; Baltimore, MD USA
| | - Harsha Gowda
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine; Yenepoya University; Mangalore, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery; 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
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Pathology; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Aditi Chatterjee
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine; Yenepoya University; Mangalore, India
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11
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Reddy PJ, Ray S, Sathe GJ, Prasad TSK, Rapole S, Panda D, Srivastava S. Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone. OMICS 2015; 19:12-23. [PMID: 25562197 DOI: 10.1089/omi.2014.0099] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infectious diseases and increasing antibiotic resistance among diverse classes of microbes are global health concerns and a prime focus of omics systems science applications in novel drug discovery. Plumbagin is a plant-derived naphthoquinone, a natural product that exhibits antibacterial activity against gram-positive bacteria. In the present study, we investigated the antimicrobial effects of plumbagin against Bacillus subtilis using two complementary proteomics techniques: two-dimensional electrophoresis (2-DE) and isobaric tag for relative and absolute quantification (iTRAQ). Comparative quantitative proteomics analysis of plumbagin treated and untreated control samples identified differential expression of 230 proteins (1% FDR, 1.5 fold-change and ≥2 peptides) in B. subtilis after plumbagin treatment. Pathway analysis involving the differentially expressed proteins suggested that plumbagin effectively increases heme and protein biosynthesis, whereas fatty acid synthesis was significantly reduced. Gene expression and metabolic activity assays further corroborated the proteomics findings. We anticipate that plumbagin blocks the cell division by altering the membrane permeability required for energy generation. This is the first report, to the best of our knowledge, offering new insights, at proteome level, for the putative mode(s) of action of plumbagin and attendant cellular targets in B. subtilis. The findings also suggest new ways forward for the modern omics-guided drug target discovery, building on traditional plant medicine.
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Affiliation(s)
- Panga Jaipal Reddy
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Powai, Mumbai, India
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12
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Sivadasan P, Kumar Gupta M, Sathe GJ, Balakrishnan L, Palit P, Gowda H, Suresh A, Abraham Kuriakose M, Sirdeshmukh R. Data from human salivary proteome - A resource of potential biomarkers for oral cancer. Data Brief 2015. [PMID: 26217819 PMCID: PMC4510580 DOI: 10.1016/j.dib.2015.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Salivary proteins are an important source for developing marker-based assays for oral cancers. To get an insight into the proteins present in human saliva, we applied multiple strategies involving affinity-based depletion of abundant proteins, fractionation of the resulting proteins or their tryptic peptides followed by LC–MS/MS analysis, using high resolution mass spectrometry. By integrating the protein identifications observed by us with those from similar workflows employed in earlier investigations, we compiled an updated salivary proteome. We have mapped the salivary proteome to the published data on differentially expressed proteins from oral cancer tissues and also for their secretory features using prediction tools, SignalP 4.1, TMHMM 2c and Exocarta. Proteotypic peptides for the subset of proteins implicated in oral cancer and mapped to any two of the prediction tools for secretory potential have been listed. The data here are related to the research article “Human saliva proteome – a resource of potential biomarkers for oral cancer” in the Journal of Proteomics [1].
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Affiliation(s)
- Priya Sivadasan
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India ; Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | | | - Priyanka Palit
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Amritha Suresh
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India ; Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore 560099, India
| | - Moni Abraham Kuriakose
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India ; Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore 560099, India
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India ; Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore 560099, India
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13
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Sivadasan P, Gupta MK, Sathe GJ, Balakrishnan L, Palit P, Gowda H, Suresh A, Kuriakose MA, Sirdeshmukh R. Human salivary proteome--a resource of potential biomarkers for oral cancer. J Proteomics 2015; 127:89-95. [PMID: 26073025 DOI: 10.1016/j.jprot.2015.05.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [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: 02/02/2015] [Revised: 05/09/2015] [Accepted: 05/26/2015] [Indexed: 12/16/2022]
Abstract
Proteins present in human saliva offer an immense potential for clinical applications. However, exploring salivary proteome is technically challenged due to the presence of amylase and albumin in high abundance. In this study, we used four workflows to analyze human saliva from healthy individuals which involved depletion of abundant proteins using affinity-based separation methods followed by protein or peptide fractionation and high resolution mass spectrometry analysis. We identified a total of 1256 human salivary proteins, 292 of them being reported for the first time. All identifications were verified for any shared proteins/peptides from the salivary microbiome that may conflict with the human protein identifications. On integration of our results with the analyses reported earlier, we arrived at an updated human salivary proteome containing 3449 proteins, 808 of them have been reported as differentially expressed proteins in oral cancer tissues. The secretory nature of 598 of the 808 proteins has also been supported on the basis of the presence of signal sequence, transmembrane domain or association with exosomes. From this subset, we provide a priority list of 139 proteins along with their proteotypic peptides, which may serve as a reference for targeted investigations as secretory markers for clinical applications in oral malignancies. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Priya Sivadasan
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India; Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | | | - Priyanka Palit
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Amritha Suresh
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India; Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore 560099, India
| | - Moni Abraham Kuriakose
- Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health, Bangalore 560099, India; Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore 560099, India.
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore 560099, India.
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14
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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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15
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Reddy PJ, Sinha S, Ray S, Sathe GJ, Chatterjee A, Prasad TSK, Dhali S, Srikanth R, Panda D, Srivastava S. Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment. PLoS One 2015; 10:e0120620. [PMID: 25874956 PMCID: PMC4397091 DOI: 10.1371/journal.pone.0120620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
Curcumin is a natural dietary compound with antimicrobial activity against various gram positive and negative bacteria. This study aims to investigate the proteome level alterations in Bacillus subtilis due to curcumin treatment and identification of its molecular/cellular targets to understand the mechanism of action. We have performed a comprehensive proteomic analysis of B. subtilis AH75 strain at different time intervals of curcumin treatment (20, 60 and 120 min after the drug exposure, three replicates) to compare the protein expression profiles using two complementary quantitative proteomic techniques, 2D-DIGE and iTRAQ. To the best of our knowledge, this is the first comprehensive longitudinal investigation describing the effect of curcumin treatment on B. subtilis proteome. The proteomics analysis revealed several interesting targets such UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1, putative septation protein SpoVG and ATP-dependent Clp protease proteolytic subunit. Further, in silico pathway analysis using DAVID and KOBAS has revealed modulation of pathways related to the fatty acid metabolism and cell wall synthesis, which are crucial for cell viability. Our findings revealed that curcumin treatment lead to inhibition of the cell wall and fatty acid synthesis in addition to differential expression of many crucial proteins involved in modulation of bacterial metabolism. Findings obtained from proteomics analysis were further validated using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) assay for respiratory activity, resazurin assay for metabolic activity and membrane integrity assay by potassium and inorganic phosphate leakage measurement. The gene expression analysis of selected cell wall biosynthesis enzymes has strengthened the proteomics findings and indicated the major effect of curcumin on cell division.
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Affiliation(s)
- Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sneha Sinha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gajanan J. Sathe
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
- Manipal University, Madhav Nagar,Manipal, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
- Manipal University, Madhav Nagar,Manipal, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
| | - Snigdha Dhali
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Rapole Srikanth
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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16
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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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Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Kumar GSS, Marimuthu A, Prasad TSK, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A. NetSlim: high-confidence curated signaling maps. Database (Oxford) 2011; 2011:bar032. [PMID: 21959865 PMCID: PMC3263596 DOI: 10.1093/database/bar032] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We previously developed NetPath as a resource for comprehensive manually curated signal transduction pathways. The pathways in NetPath contain a large number of molecules and reactions which can sometimes be difficult to visualize or interpret given their complexity. To overcome this potential limitation, we have developed a set of more stringent curation and inclusion criteria for pathway reactions to generate high-confidence signaling maps. NetSlim is a new resource that contains this ‘core’ subset of reactions for each pathway for easy visualization and manipulation. The pathways in NetSlim are freely available at http://www.netpath.org/netslim. Database URL:www.netpath.org/netslim
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Affiliation(s)
- Rajesh Raju
- Institute of Bioinformatics, International Tech Park, Bangalore, India
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