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K SK, Rajan G, Marimuthu A. Challenges in the Diagnosis of Hepatic Dysfunction In Chronic Autoimmune Thyroiditis. J Assoc Physicians India 2020; 68:97. [PMID: 31979910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Sai Kiran K
- Government Stanley Medical College and Hospital
| | - G Rajan
- Government Stanley Medical College and Hospital
| | - A Marimuthu
- Government Stanley Medical College and Hospital
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Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Charles Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali G, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U. Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response. Mol Cell Proteomics 2017; 16:891-910. [PMID: 28331001 PMCID: PMC5417828 DOI: 10.1074/mcp.m117.067439] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/24/2017] [Indexed: 02/05/2023] Open
Abstract
Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence 747LREA750, are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations. However, 30-40% of patients with EGFR mutations exhibit primary resistance to these TKIs, underscoring the unmet need of identifying additional biomarkers of treatment response. Here, we sought to characterize the dynamics of tyrosine phosphorylation upon EGFR TKI treatment of mutant EGFR-driven human lung adenocarcinoma cell lines with varying sensitivity to EGFR TKIs, erlotinib and afatinib. We employed stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry to identify and quantify tyrosine phosphorylated peptides. The proportion of tyrosine phosphorylated sites that had reduced phosphorylation upon erlotinib or afatinib treatment correlated with the degree of TKI-sensitivity. Afatinib, an irreversible EGFR TKI, more effectively inhibited tyrosine phosphorylation of a majority of the substrates. The phosphosites with phosphorylation SILAC ratios that correlated with the TKI-sensitivity of the cell lines include sites on kinases, such as EGFR-Y1197 and MAPK7-Y221, and adaptor proteins, such as SHC1-Y349/350, ERRFI1-Y394, GAB1-Y689, STAT5A-Y694, DLG3-Y705, and DAPP1-Y139, suggesting these are potential biomarkers of TKI sensitivity. DAPP1, is a novel target of mutant EGFR signaling and Y-139 is the major site of DAPP1 tyrosine phosphorylation. We also uncovered several off-target effects of these TKIs, such as MST1R-Y1238/Y1239 and MET-Y1252/1253. This study provides unique insight into the TKI-mediated modulation of mutant EGFR signaling, which can be applied to the development of biomarkers of EGFR TKI response.
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Affiliation(s)
- Xu Zhang
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Tapan Maity
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Manoj K Kashyap
- §Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Mukesh Bansal
- ¶Department of System Biology, Columbia University, New York, New York, 10032
- ‖PsychoGenics Inc., Tarrytown, New York, 10591
| | - Abhilash Venugopalan
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Sahib Singh
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Shivangi Awasthi
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | | | | | - Natalya Belkina
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Stephanie Pitts
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Constance M Cultraro
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Shaojian Gao
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Guldal Kirkali
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Romi Biswas
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Raghothama Chaerkady
- §Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
- **Medimmune LLC, Gaithersburg, Maryland, 20878
| | - Andrea Califano
- ¶Department of System Biology, Columbia University, New York, New York, 10032
| | - Akhilesh Pandey
- §Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Udayan Guha
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892;
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Subbannayya Y, Syed N, Barbhuiya MA, Raja R, Marimuthu A, Sahasrabuddhe N, Pinto SM, Manda SS, Renuse S, Manju HC, Zameer MAL, Sharma J, Brait M, Srikumar K, Roa JC, Vijaya Kumar M, Kumar KVV, Prasad TSK, Ramaswamy G, Kumar RV, Pandey A, Gowda H, Chatterjee A. Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer Biol Ther 2015; 16:336-45. [PMID: 25756516 DOI: 10.4161/15384047.2014.972264] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer is one of the most common gastrointestinal malignancies and is associated with poor prognosis. Exploring alterations in the proteomic landscape of gastric cancer is likely to provide potential biomarkers for early detection and molecules for targeted therapeutic intervention. Using iTRAQ-based quantitative proteomic analysis, we identified 22 proteins that were overexpressed and 17 proteins that were downregulated in gastric tumor tissues as compared to the adjacent normal tissue. Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) was found to be 7-fold overexpressed in gastric tumor tissues. Immunohistochemical labeling of tumor tissue microarrays for validation of CAMKK2 overexpression revealed that it was indeed overexpressed in 94% (92 of 98) of gastric cancer cases. Silencing of CAMKK2 using siRNA significantly reduced cell proliferation, colony formation and invasion of gastric cancer cells. Our results demonstrate that CAMKK2 signals in gastric cancer through AMPK activation and suggest that CAMKK2 could be a novel therapeutic target in gastric cancer.
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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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5
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Wu X, Zahari MS, Ma B, Liu R, Renuse S, Sahasrabuddhe NA, Chen L, Chaerkady R, Kim MS, Zhong J, Jelinek C, Barbhuiya MA, Leal-Rojas P, Yang Y, Kashyap MK, Marimuthu A, Ling M, Fackler MJ, Merino V, Zhang Z, Zahnow CA, Gabrielson E, Stearns V, Roa JC, Sukumar S, Gill PS, Pandey A. Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways. Oncotarget 2015; 6:29143-60. [PMID: 26356563 PMCID: PMC4745717 DOI: 10.18632/oncotarget.5020] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is the most prevalent cancer in women worldwide. About 15-20% of all breast cancers are triple negative breast cancer (TNBC) and are often highly aggressive when compared to other subtypes of breast cancers. To better characterize the biology that underlies the TNBC phenotype, we profiled the phosphotyrosine proteome of a panel of twenty-six TNBC cell lines using quantitative high resolution Fourier transform mass spectrometry. A heterogeneous pattern of tyrosine kinase activation was observed based on 1,789 tyrosine-phosphorylated peptides identified from 969 proteins. One of the tyrosine kinases, AXL, was found to be activated in a majority of aggressive TNBC cell lines and was accompanied by a higher level of AXL expression. High levels of AXL expression are correlated with a significant decrease in patient survival. Treatment of cells bearing activated AXL with a humanized AXL antibody inhibited cell proliferation and migration in vitro, and tumor growth in mice. Overall, our global phosphoproteomic analysis provided new insights into the heterogeneity in the activation status of tyrosine kinase pathways in TNBCs. Our approach presents an effective means of identifying important novel biomarkers and targets for therapy such as AXL in TNBC.
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Affiliation(s)
- Xinyan Wu
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Muhammad Saddiq Zahari
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Binyun Ma
- 6 Department of Medicine, University of Southern California, Los Angeles, USA
| | - Ren Liu
- 6 Department of Medicine, University of Southern California, Los Angeles, USA
| | - Santosh Renuse
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Nandini A. Sahasrabuddhe
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Lily Chen
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Raghothama Chaerkady
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Min-Sik Kim
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Jun Zhong
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Christine Jelinek
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mustafa A. Barbhuiya
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Pamela Leal-Rojas
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 7 Department of Pathology, Center of Genetic and Immunological Studies (CEGIN) and Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Yi Yang
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Manoj Kumar Kashyap
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Arivusudar Marimuthu
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Min Ling
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mary Jo Fackler
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Vanessa Merino
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Zhen Zhang
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Cynthia A. Zahnow
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Edward Gabrielson
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
- 4 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Vered Stearns
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Juan Carlos Roa
- 8 Advanced Center for Chronic Diseases (ACCDiS), Department of Pathology Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Saraswati Sukumar
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Parkash S. Gill
- 6 Department of Medicine, University of Southern California, Los Angeles, USA
| | - Akhilesh Pandey
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
- 4 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
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6
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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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Rugo H, Sharma N, Reebel L, Rodal M, Peck A, West B, Marimuthu A, Karlin D, Dowlati A, Le M, Coussens L, Wesolowski R. Phase Ib Study of Plx3397, a Csf1R Inhibitor, and Paclitaxel in Patients with Advanced Solid Tumors. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu331.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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8
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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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9
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Kim MS, Zhong Y, Yachida S, Rajeshkumar NV, Abel ML, Marimuthu A, Mudgal K, Hruban RH, Poling JS, Tyner JW, Maitra A, Iacobuzio-Donahue CA, Pandey A. Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics. Mol Cell Proteomics 2014; 13:2803-11. [PMID: 24895378 DOI: 10.1074/mcp.m114.038547] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Many patients with pancreatic cancer have metastases to distant organs at the time of initial presentation. Recent studies examining the evolution of pancreatic cancer at the genetic level have shown that clonal complexity of metastatic pancreatic cancer is already initiated within primary tumors, and organ-specific metastases are derived from different subclones. However, we do not yet understand to what extent the evolution of pancreatic cancer contributes to proteomic and signaling alterations. We hypothesized that genetic heterogeneity of metastatic pancreatic cancer results in heterogeneity at the proteome level. To address this, we employed a model system in which cells isolated from three sites of metastasis (liver, lung, and peritoneum) from a single patient were compared. We used a SILAC-based accurate quantitative proteomic strategy combined with high-resolution mass spectrometry to analyze the total proteome and tyrosine phosphoproteome of each of the distal metastases. Our data revealed distinct patterns of both overall proteome expression and tyrosine kinase activities across the three different metastatic lesions. This heterogeneity was significant because it led to differential sensitivity of the neoplastic cells to small molecule inhibitors targeting various kinases and other pathways. For example, R428, a tyrosine kinase inhibitor that targets Axl receptor tyrosine kinase, was able to inhibit cells derived from lung and liver metastases much more effectively than cells from the peritoneal metastasis. Finally, we confirmed that administration of R428 in mice bearing xenografts of cells derived from the three different metastatic sites significantly diminished tumors formed from liver- and lung-metastasis-derived cell lines as compared with tumors derived from the peritoneal metastasis cell line. Overall, our data provide proof-of-principle support that personalized therapy of multiple organ metastases in a single patient should involve the administration of a combination of agents, with each agent targeted to the features of different subclones.
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Affiliation(s)
- Min-Sik Kim
- From the ‡McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Yi Zhong
- ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Shinichi Yachida
- ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - N V Rajeshkumar
- **Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Melissa L Abel
- §§Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Mailcode L592, Portland, Oregon 97239
| | - Arivusudar Marimuthu
- ¶¶Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Keshav Mudgal
- ‖‖School of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ralph H Hruban
- ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231; **Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Justin S Poling
- ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Jeffrey W Tyner
- §§Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Mailcode L592, Portland, Oregon 97239
| | - Anirban Maitra
- From the ‡McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231; **Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Christine A Iacobuzio-Donahue
- ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231; **Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231;
| | - Akhilesh Pandey
- From the ‡McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ‖Department of Pathology, the Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231;
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10
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Thomas JK, Kim MS, Balakrishnan L, Nanjappa V, Raju R, Marimuthu A, Radhakrishnan A, Muthusamy B, Khan AA, Sakamuri S, Tankala SG, Singal M, Nair B, Sirdeshmukh R, Chatterjee A, Prasad TSK, Maitra A, Gowda H, Hruban RH, Pandey A. Pancreatic Cancer Database: an integrative resource for pancreatic cancer. Cancer Biol Ther 2014; 15:963-7. [PMID: 24839966 DOI: 10.4161/cbt.29188] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 12/18/2022] Open
Abstract
Pancreatic cancer is the fourth leading cause of cancer-related death in the world. The etiology of pancreatic cancer is heterogeneous with a wide range of alterations that have already been reported at the level of the genome, transcriptome, and proteome. The past decade has witnessed a large number of experimental studies using high-throughput technology platforms to identify genes whose expression at the transcript or protein levels is altered in pancreatic cancer. Based on expression studies, a number of molecules have also been proposed as potential biomarkers for diagnosis and prognosis of this deadly cancer. Currently, there are no repositories which provide an integrative view of multiple Omics data sets from published research on pancreatic cancer. Here, we describe the development of a web-based resource, Pancreatic Cancer Database (http://www.pancreaticcancerdatabase.org), as a unified platform for pancreatic cancer research. PCD contains manually curated information pertaining to quantitative alterations in miRNA, mRNA, and proteins obtained from small-scale as well as high-throughput studies of pancreatic cancer tissues and cell lines. We believe that PCD will serve as an integrative platform for scientific community involved in pancreatic cancer research.
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Affiliation(s)
- Joji Kurian Thomas
- Institute of Bioinformatics; International Technology Park; Bangalore, India; Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, Kerala India
| | - Min-Sik Kim
- 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
| | | | - Vishalakshi Nanjappa
- Institute of Bioinformatics; International Technology Park; Bangalore, India; Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, Kerala India
| | - Rajesh Raju
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | | | - Aneesha Radhakrishnan
- Institute of Bioinformatics; International Technology Park; Bangalore, India; Department of Biochemistry and Molecular Biology; School of Life Sciences; Pondicherry University; Puducherry, India
| | - Babylakshmi Muthusamy
- Institute of Bioinformatics; International Technology Park; Bangalore, India; Bioinformatics Centre; School of Life Sciences; Pondicherry University; Puducherry, India
| | - Aafaque Ahmad Khan
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Sruthi Sakamuri
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | | | - Mukul Singal
- Government Medical College and Hospital; Chandigarh, India
| | - Bipin Nair
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, Kerala India
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Aditi Chatterjee
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - T S Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore, India; Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, Kerala India
| | - Anirban Maitra
- Departments of Pathology and Translational Molecular Pathology; Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research; UT MD Anderson Cancer Center; Houston, TX USA
| | - Harsha Gowda
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Ralph H Hruban
- Department of Pathology; Sol Goldman Pancreatic Cancer Research Center; Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Oncology; 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; Sol Goldman Pancreatic Cancer Research Center; Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Oncology; Johns Hopkins University School of Medicine; Baltimore, MD USA
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11
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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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12
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Nanjappa V, Thomas JK, Marimuthu A, Muthusamy B, Radhakrishnan A, Sharma R, Ahmad Khan A, Balakrishnan L, Sahasrabuddhe NA, Kumar S, Jhaveri BN, Sheth KV, Kumar Khatana R, Shaw PG, Srikanth SM, Mathur PP, Shankar S, Nagaraja D, Christopher R, Mathivanan S, Raju R, Sirdeshmukh R, Chatterjee A, Simpson RJ, Harsha HC, Pandey A, Prasad TSK. Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Res 2013; 42:D959-65. [PMID: 24304897 PMCID: PMC3965042 DOI: 10.1093/nar/gkt1251] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10,546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.
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Affiliation(s)
- Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, Karnataka, India, Amrita School of Biotechnology, Amrita University, Kollam 690 525, Kerala, India, Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India, Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India, Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bangalore 560 022, Karnataka, India, Department of Biotechnology, Kuvempu University, Shankaraghatta 577 451, Karnataka, India, Government Medical College, Bhavnagar 364 001, Gujarat, India, Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha 442 012, Maharashtra, India, The Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA, Department of Internal Medicine, Armed Forces Medical College, Pune 411 040, Maharashtra, India, Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore 560 022, Karnataka, India, Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3084, Australia, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA, Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA, Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA and Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA
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13
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Marimuthu A, Subbannayya Y, Sahasrabuddhe NA, Balakrishnan L, Syed N, Sekhar NR, Katte TV, Pinto SM, Srikanth SM, Kumar P, Pawar H, Kashyap MK, Maharudraiah J, Ashktorab H, Smoot DT, Ramaswamy G, Kumar RV, Cheng Y, Meltzer SJ, Roa JC, Chaerkady R, Prasad TK, Harsha HC, Chatterjee A, Pandey A. SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clin Appl 2013; 7:355-66. [PMID: 23161554 PMCID: PMC3804263 DOI: 10.1002/prca.201200069] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [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] [Received: 07/30/2012] [Revised: 09/24/2012] [Accepted: 10/25/2012] [Indexed: 02/05/2023]
Abstract
PURPOSE Gastric cancer is a commonly occurring cancer in Asia and one of the leading causes of cancer deaths. However, there is no reliable blood-based screening test for this cancer. Identifying proteins secreted from tumor cells could lead to the discovery of clinically useful biomarkers for early detection of gastric cancer. EXPERIMENTAL DESIGN A SILAC-based quantitative proteomic approach was employed to identify secreted proteins that were differentially expressed between neoplastic and non-neoplastic gastric epithelial cells. Proteins from the secretome were subjected to SDS-PAGE and SCX-based fractionation, followed by mass spectrometric analysis on an LTQ-Orbitrap Velos mass spectrometer. Immunohistochemical labeling was employed to validate a subset of candidates using tissue microarrays. RESULTS We identified 2205 proteins in the gastric cancer secretome of which 263 proteins were overexpressed greater than fourfold in gastric cancer-derived cell lines as compared to non-neoplastic gastric epithelial cells. Three candidate proteins, proprotein convertase subtilisin/kexin type 9 (PCSK9), lectin mannose binding 2 (LMAN2), and PDGFA-associated protein 1 (PDAP1) were validated by immunohistochemical labeling. CONCLUSIONS AND CLINICAL RELEVANCE We report here the largest cancer secretome described to date. The novel biomarkers identified in the current study are excellent candidates for further testing as early detection biomarkers for gastric adenocarcinoma.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Nandini A. Sahasrabuddhe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577 451, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India
| | - Nirujogi Raja Sekhar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Teesta V. Katte
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Srinivas M. Srikanth
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Manoj K. Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington DC 20060, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical College, Nashville 37208, Tennessee, USA
| | - Girija Ramaswamy
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Rekha V. Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen J Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- To whom correspondence should be addressed: Akhilesh Pandey M.D., Ph.D., McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205. Tel.: 410-502-6662; Fax: 410-502-7544;
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Marimuthu A, Zhang J, Linic S. Tuning Selectivity in Propylene Epoxidation by Plasmon Mediated Photo-Switching of Cu Oxidation State. Science 2013; 339:1590-3. [DOI: 10.1126/science.1231631] [Citation(s) in RCA: 470] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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15
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Kumar GSS, Venugopal AK, Kashyap MK, Raju R, Marimuthu A, Palapetta SM, Subbanayya Y, Goel R, Chawla A, Dikshit JB, Tata P, Harsha HC, Maharudraiah J, Ramachandra YL, Satishchandra P, Prasad TSK, Pandey A, Mahadevan A, Shankar SK. Gene Expression Profiling of Tuberculous Meningitis Co-infected with HIV. J Proteomics Bioinform 2012; 5:235-244. [PMID: 27053842 PMCID: PMC4820295 DOI: 10.4172/jpb.1000243] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tuberculous meningitis (TBM) is a fatal form of Mycobacterium tuberculosis infection of the central nervous system (CNS). The similarities in the clinical and radiological findings in TBM cases with or without HIV make the diagnosis very challenging. Identification of genes, which are differentially expressed in brain tissues of HIV positive and HIV negative TBM patients, would enable better understanding of the molecular aspects of the infection and would also serve as an initial platform to evaluate potential biomarkers. Here, we report the identification of 796 differentially regulated genes in brain tissues of TBM patients co-infected with HIV using oligonucleotide DNA microarrays. We also performed immunohistochemical validation and confirmed the abundance of four gene products-glial fibrillary acidic protein (GFAP), serpin peptidase inhibitor, clade A member 3 (SERPINA3), thymidine phosphorylase (TYMP/ECGF1) and heat shock 70 kDa protein 8 (HSPA8). Our study paves the way for understanding the mechanism of TBM in HIV positive patients and for further validation of potential disease biomarkers.
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Affiliation(s)
- Ghantasala S. Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
| | - Abhilash K. Venugopal
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Rajesh Raju
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Shyam Mohan Palapetta
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014, India
| | - Yashwanth Subbanayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
| | - Ankit Chawla
- Armed Forces Medical College, Pune-411040, India
| | | | - Pramila Tata
- Strand Life Sciences, Bangalore 560024, Karnataka, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Y. L. Ramachandra
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
| | | | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding authors: Akhilesh Pandey, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, USA, Tel: 410-502-6662; Fax: 410-502-7544; , S. K. Shankar, Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India, Tel: 91-080-26995001/5002; Fax: 91-080-26564830;
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - S. K. Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
- Corresponding authors: Akhilesh Pandey, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, USA, Tel: 410-502-6662; Fax: 410-502-7544; , S. K. Shankar, Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India, Tel: 91-080-26995001/5002; Fax: 91-080-26564830;
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Telikicherla D, Marimuthu A, Kashyap MK, Ramachandra YL, Mohan S, Roa JC, Maharudraiah J, Pandey A. Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer. Clin Proteomics 2012; 9:7. [PMID: 22709790 PMCID: PMC3439379 DOI: 10.1186/1559-0275-9-7] [Citation(s) in RCA: 21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/08/2012] [Indexed: 02/07/2023] Open
Abstract
The molecular events that lead to malignant transformation and subsequent metastasis of breast carcinoma include alterations in the cells at genome, transcriptome and proteome levels. In this study, we used publicly available gene expression databases to identify those candidate genes which are upregulated at the mRNA level in breast cancers but have not been systematically validated at the protein level. Based on an extensive literature search, we identified ribosome binding protein 1 (RRBP1) as a candidate that is upregulated at the mRNA level in five different studies but its protein expression had not been investigated. Immunohistochemical labeling of breast cancer tissue microarrays was carried out to determine the expression of RRBP1 in a large panel of breast cancers. We found that RRBP1 was overexpressed in 84% (177/219) of breast carcinoma cases tested. The subcellular localization of RRBP1 was mainly observed to be in the cytoplasm with intense staining in the perinuclear region. Our findings suggest that RRBP1 is an interesting molecule that can be further studied for its potential to serve as a breast cancer biomarker. This study also demonstrates how the integration of biological data from available resources in conjunction with systematic evaluation approaches can be successfully applied to clinical proteomics.
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Affiliation(s)
- Deepthi Telikicherla
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577451, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
| | - Y L Ramachandra
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577451, India
| | - Sujatha Mohan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
- Research Unit for Immunoinformatics, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
- Department of Pathology and Laboratory Medicine, Icon Hospitals, Bangalore 560027, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, USA
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Telikicherla D, Maharudraiah J, Pawar H, Marimuthu A, Kashyap MK, Ramachandra YL, Roa JC, Pandey A. Overexpression of Kinesin Associated Protein 3 (KIFAP3) in Breast Cancer. J Proteomics Bioinform 2012; 5:122-126. [PMID: 26843789 PMCID: PMC4734396 DOI: 10.4172/jpb.1000223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gene expression profiling studies on breast cancer have generated catalogs of differentially expressed genes. However, many of these genes have not been investigated for their expression at the protein level. It is possible to systematically evaluate such genes in a high-throughput fashion for their overexpression at the protein level using breast cancer tissue microarrays. Our strategy involved integration of information from publicly available repositories of gene expression to prepare a list of genes upregulated at the mRNA level in breast cancer followed by curation of the published literature to identify those genes that were not tested for overexpression at the protein level. We identified Kinesin Associated Protein 3 (KIFAP3) as one such molecule for further validation at the protein level. Immunohistochemical labeling of KIFAP3 using breast cancer tissue microarrays revealed overexpression of KIFAP3 protein in 84% (240/285) of breast cancers indicating the utility of our integrated approach of combining computational analysis with experimental biology.
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Affiliation(s)
- Deepthi Telikicherla
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta-577451, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
- Department of Pathology, Raja Rajeshwari Medical College and Hospital, Bangalore-560074, India
- Manipal University, Madhav Nagar, Manipal-576104, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
- Rajiv Gandhi University of Health Sciences, Bangalore-560041, India
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore-560029, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
| | - Y. L. Ramachandra
- Department of Biotechnology, Kuvempu University, Shankaraghatta-577451, India
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author: Akhilesh Pandey M.D., Ph.D., McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, USA, Tel: 410-502-6662; Fax: 410-502-7544;
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Wu X, Renuse S, Chen L, Chaerkady R, Kim MS, Zahari S, Sahasrabuddhe N, Zhong J, Yang Y, Kashyap M, Marimuthu A, Ling M, Fackler MJ, Merino V, Zhang Z, Sukumar S, Pandey A. Abstract 4797: Global phosphotyrosine survey reveals the evidence of activation of multiple tyrosine kinase signaling pathways in basal-like breast cancer cells. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
About 10-15% of all breast cancers are basal-like breast cancers (BLBCs) that are highly aggressive and lack effective targeted therapeutic options as they lack ER, PR and Her-2. Reversible phosphorylation of proteins is one the most important post-translational modifications and is involved in almost all kinds of cellular processes. Tyrosine phosphorylation (pY) accounts for a minority of total phosphorylation, less than 0.1% by overall abundance. However, pY plays a disproportionately large role in diseases especially in cancer. More than half of the 90 tyrosine kinases identified in the human proteome have been implicated in cancer through gain-of-function mutations, gene amplification, overexpression, or as tumor suppressors and become attractive therapeutic targets. To assess activated tyrosine kinase signaling pathways in TNBCs, we collected a panel of 28 publicly available triple-negative breast cancer cell lines and systematically analyzed the invasiveness and anchorage independent growth of this panel of cell lines. We carried out global quantitative phosphotyrosine profiling using high resolution Fourier transform mass spectrometry. In all, we identified 2,133 tyrosine-phosphorylated peptides from more than 800 proteins. A number of tyrosine kinases were found to be differentially phosphorylated in different sets of breast cancer cells. Pathway analysis revealed that phosphorylation level of certain oncogenic kinases including EGFR, MET, FAK1 and SRC was elevated in a majority of basal-like breast cancer cells. Notably, multiple members of EPH receptor family, EPHA1, EPHA2, EPHA3, EPHB3 and EPHB4, were hyper-phosphorylated in multiple basal-like breast cancer cells. Supervised clustering analysis of phosphorylated proteins identified specific phospho-signatures that correlated with invasiveness and anti-anoikis colony formation ability. One of these hyper-phosphorylated proteins was DYRK2, a dual specificity tyrosine kinase. We observed that DYRK2 had an effect on colony formation and invasive ability on a subset of TNBC cell lines. Overall, our global phosphoproteomic study confirms high heterogeneity in the activation status of tyrosine kinases across triple negative breast cancer cells and suggests that some of them are attractive candidates as therapeutic targets.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4797. doi:1538-7445.AM2012-4797
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Affiliation(s)
- Xinyan Wu
- 1Johns Hopkins University, Baltimore, MD
| | | | - Lily Chen
- 1Johns Hopkins University, Baltimore, MD
| | | | | | | | | | - Jun Zhong
- 1Johns Hopkins University, Baltimore, MD
| | - Yi Yang
- 1Johns Hopkins University, Baltimore, MD
| | | | | | - Min Ling
- 1Johns Hopkins University, Baltimore, MD
| | | | | | - Zhen Zhang
- 1Johns Hopkins University, Baltimore, MD
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Kim MS, Chaerkady R, Wu X, O'meally R, Kuppireddy SV, Zhong J, Jacob HKC, Marimuthu A, Kashyap MK, Cole R, Iacobuzio-Donahue C, Maitra A, Pandey A. Abstract 1269: Activation of diverse signaling pathways in pancreatic cancer revealed by phosphoproteomics. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-1269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic cancer is the fourth leading cause of cancer-related deaths in the United States. A number of genes that have somatic mutations including CDKN2A, SMAD4, TP53 and KRAS have been linked to pancreatic cancer. Recently, a comprehensive genomic analysis was performed in a panel of 14 primary pancreatic cancer cell lines and 10 xenografts, in which ∼1,500 somatic alterations were identified and a core set of 12 activated signaling pathways were defined. We decided to use a phosphoproteomics approach to identify tyrosine kinase signaling pathways that could serve as attractive therapeutic targets. Based on immunoblotting with anti-phosphotyrosine antibodies, we observed a heterogeneous pattern of tyrosine phosphorylation in the 14 primary pancreatic cancer cell lines whose genomes have been sequenced previously, which indicated that different tyrosine kinases were likely activated in different cells. To identify these kinases, phosphotyrosine-containing peptides were enriched by immunoprecipitation by anti-phosphotyrosine antibodies and analyzed on a high resolution Fourier transform mass spectrometer coupled to nanoflow reversed phase liquid chromatography. W employed the SILAC methodology to quantitate tyrosine phosphorylated peptides across the panel of cell lines. Our preliminary data indicates that the approach used in this study is suitable for global profiling of tyrosine kinase pathways that are abnormally activated in cancers. The differential alteration of tyrosine kinases was confirmed from the accurate quantitative tyrosine phosphoproteomic analysis. For example, HPNE, a normal pancreatic cell line showed the lowest level of phosphotyrosine levels, while each pancreatic cancer cell line could be differentiated based on its own set of activated tyrosine kinases. Interestingly, some of tyrosine kinases were activated in a small number of cell lines (e.g. AXL, SYK, DDR2, RON and RET), while other tyrosine kinases were found to be activated more broadly (e.g. YES1, TYK2, EPHA2 and EPHB4). Overall, we conclude that these aberrantly activated tyrosine kinases could be targeted to develop newer therapeutic regimens.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1269. doi:1538-7445.AM2012-1269
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Affiliation(s)
| | | | - Xinyan Wu
- 1Johns Hopkins University, Baltimore, MD
| | | | | | - Jun Zhong
- 1Johns Hopkins University, Baltimore, MD
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20
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Venugopal AK, Sameer Kumar GS, Mahadevan A, Selvan LDN, Marimuthu A, Dikshit JB, Tata P, Ramachandra Y, Chaerkady R, Sinha S, Chandramouli B, Arivazhagan A, Satishchandra P, Shankar S, Pandey A. Transcriptomic Profiling of Medial Temporal Lobe Epilepsy. ACTA ACUST UNITED AC 2012; 5. [PMID: 23483634 DOI: 10.4172/jpb.1000210] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [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: 11/09/2022]
Abstract
Epilepsy is one of the most prevalent neurological disorders affecting ~1% of the population. Medial temporal lobe epilepsy (MTLE) is the most frequent type of epilepsy observed in adults who do not respond to pharmacological treatment. The reason for intractability in these patients has not been systematically studied. Further, no markers are available that can predict the subset of patients who will not respond to pharmacotherapy. To identify potential biomarkers of epileptogenicity, we compared the mRNA profiles of surgically resected tissue from seizure zones with non-seizure zones from cases of intractable MTLE. We identified 413 genes that exhibited ≥2-fold change that were statistically significant across these two groups. Several of these differentially expressed genes have not been previously described in the context of MTLE including claudin 11 (CLDN11) and bone morphogenetic protein receptor, type IB (BMPR1B). In addition, we found significant downregulation of a subset of gamma-aminobutyric acid (GABA) associated genes. We also identified molecules such as BACH2 and ADAMTS15, which are already known to be associated with epilepsy. We validated one upregulated molecule, serine/threonine kinase 31 (STK31) and one downregulated molecule, SMARCA4, by immunohistochemical labeling of tissue sections. These molecules need to be further confirmed in large-scale studies to determine their potential use as diagnostic as well as prognostic markers in intractable MTLE.
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Affiliation(s)
- Abhilash K Venugopal
- Institute of Bioinformatics, International Technology Park, Bangalore, India ; Department of Biotechnology, Kuvempu University, Shimoga, India ; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA ; Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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21
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Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TSK, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics 2011; 10:M111.011627. [PMID: 22338125 PMCID: PMC3270104 DOI: 10.1074/mcp.m111.011445] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Mass spectrometric sequencing of low abundance, integral membrane proteins, particularly the transmembrane domains, presents challenges that span the multiple phases of sample preparation including solubilization, purification, enzymatic digestion, peptide extraction, and chromatographic separation. We describe a method through which we have obtained high peptide coverage for 12 γ-aminobutyric acid type A receptor (GABAA receptor) subunits from 2 picomoles of affinity-purified GABAA receptors from rat brain neocortex. Focusing on the α1 subunit, we identified peptides covering 96% of the protein sequence from fragmentation spectra (MS2) using a database searching algorithm and deduced 80% of the amino acid residues in the protein from de novo sequencing of Orbitrap spectra. The workflow combined microscale membrane protein solubilization, protein delipidation, in-solution multi-enzyme digestion, multiple stationary phases for peptide extraction, and acquisition of high-resolution full scan and fragmentation spectra. For de novo sequencing of peptides containing the transmembrane domains, timed digestions with chymotrypsin were utilized to generate peptides with overlapping sequences that were then recovered by sequential solid phase extraction using a C4 followed by a porous graphitic carbon stationary phase. The specificity of peptide identifications and amino acid residue sequences was increased by high mass accuracy and charge state assignment to parent and fragment ions. Analysis of three separate brain samples demonstrated that 78% of the sequence of the α1 subunit was observed in all three replicates with an additional 13% covered in two of the three replicates, indicating a high degree of sequence coverage reproducibility. Label-free quantitative analysis was applied to the three replicates to determine the relative abundances of 11 γ-aminobutyric acid type A receptor subunits. The deep sequence MS data also revealed two N-glycosylation sites on the α1 subunit, confirmed two splice variants of the γ2 subunit (γ2L and γ2S) and resolved a database discrepancy in the sequence of the α5 subunit.
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Affiliation(s)
- Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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22
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Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TSK, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics 2011. [PMID: 21969609 DOI: 10.1074/mcp.m111.011627] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ~250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes.
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Affiliation(s)
- Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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23
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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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24
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Pawar H, Kashyap MK, Sahasrabuddhe NA, Renuse S, Harsha HC, Kumar P, Sharma J, Kandasamy K, Marimuthu A, Nair B, Rajagopalan S, Maharudraiah J, Premalatha CS, Kumar KVV, Vijayakumar M, Chaerkady R, Prasad TSK, Kumar RV, Pandey A. Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biol Ther 2011; 12:510-22. [PMID: 21743296 PMCID: PMC3218592 DOI: 10.4161/cbt.12.6.16833] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [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] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is among the top ten most frequent malignancies worldwide. In this study, our objective was to identify potential biomarkers for ESCC through a quantitative proteomic approach using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. We compared the protein expression profiles of ESCC tumor tissues with the corresponding adjacent normal tissue from ten patients. LC-MS/MS analysis of strong cation exchange chromatography fractions was carried out on an Accurate Mass QTOF mass spectrometer, which led to the identification of 687 proteins. In all, 257 proteins were identified as differentially expressed in ESCC as compared to normal. We found several previously known protein biomarkers to be upregulated in ESCC including thrombospondin 1 (THBS1), periostin 1 (POSTN) and heat shock 70 kDa protein 9 (HSPA9) confirming the validity of our approach. In addition, several novel proteins that had not been reported previously were identified in our screen. These novel biomarker candidates included prosaposin (PSAP), plectin 1 (PLEC1) and protein disulfide isomerase A 4 (PDIA4) that were further validated to be overexpressed by immunohistochemical labeling using tissue microarrays. The success of our study shows that this mass spectrometric strategy can be applied to cancers in general to develop a panel of candidate biomarkers, which can then be validated by other techniques.
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Affiliation(s)
- Harsh Pawar
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Rajiv Gandhi University of Health Sciences; Bangalore, India
- Department of Pathology; Kidwai Memorial Institute of Oncology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Manoj Kumar Kashyap
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Nandini A Sahasrabuddhe
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
- 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
| | - Santosh Renuse
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Department of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, India
- 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
| | - HC Harsha
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Praveen Kumar
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Jyoti Sharma
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
| | - Kumaran Kandasamy
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Arivusudar Marimuthu
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
| | - Bipin Nair
- Department of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, India
| | | | - Jagadeesha Maharudraiah
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- RajaRajeswari Medical College; Bangalore, India
| | | | | | - M Vijayakumar
- Department of Surgical Oncology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Raghothama Chaerkady
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- 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
| | - Thotterthodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
- Centre of Excellence in Bioinformatics; School of Life Sciences; Pondicherry University; Pondicherry, India
| | - Rekha V Kumar
- Department of Pathology; Kidwai Memorial Institute of Oncology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - 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
- Oncology; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Pathology; Johns Hopkins University School of Medicine; Baltimore, MD USA
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25
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Marimuthu A, O'Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Goel R, Christopher R, Delanghe B, Cole RN, Harsha HC, Pandey A. A comprehensive map of the human urinary proteome. J Proteome Res 2011; 10:2734-43. [PMID: 21500864 DOI: 10.1021/pr2003038] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the human urinary proteome has the potential to offer significant insights into normal physiology as well as disease pathology. The information obtained from such studies could be applied to the diagnosis of various diseases. The high sensitivity, resolution, and mass accuracy of the latest generation of mass spectrometers provides an opportunity to accurately catalog the proteins present in human urine, including those present at low levels. To this end, we carried out a comprehensive analysis of human urinary proteome from healthy individuals using high-resolution Fourier transform mass spectrometry. Importantly, we used the Orbitrap for detecting ions in both MS (resolution 60 000) and MS/MS (resolution 15 000) modes. To increase the depth of our analysis, we characterized both unfractionated as well as lectin-enriched proteins in our experiments. In all, we identified 1,823 proteins with less than 1% false discovery rate, of which 671 proteins have not previously been reported as constituents of human urine. This data set should serve as a comprehensive reference list for future studies aimed at identification and characterization of urinary biomarkers for various diseases.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
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Marimuthu A, Jacob HK, Jakharia A, Subbannayya Y, Keerthikumar S, Kashyap MK, Goel R, Balakrishnan L, Dwivedi S, Pathare S, Dikshit JB, Maharudraiah J, Singh S, Sameer Kumar GS, Vijayakumar M, Veerendra Kumar KV, Premalatha CS, Tata P, Hariharan R, Roa JC, Prasad T, Chaerkady R, Kumar RV, Pandey A. Gene Expression Profiling of Gastric Cancer. J Proteomics Bioinform 2011; 4:74-82. [PMID: 27030788 PMCID: PMC4809432 DOI: pmid/27030788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent's whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in which SPOCK1 was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Harrys K.C. Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
| | - Aniruddha Jakharia
- Department of Zoology, Gauhati University, Guwahati 781014, Assam, India
- Imgenex India, Bhubaneswar 751024, Orissa, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore, 560041, Karnataka, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Sutopa Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam 690525, Kerala, India
| | | | | | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- RajaRajeswari Medical college, Bangalore, 560074, India
| | - Sujay Singh
- Imgenex India, Bhubaneswar 751024, Orissa, India
- Imgenex Corporation, San Diego 92121, California, USA
| | - Ghantasala S Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - M. Vijayakumar
- Departments of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India
| | | | | | - Pramila Tata
- Strand Life Sciences, Bangalore 560024, Karnataka, India
| | | | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - T.S.K Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India
- Corresponding authors: Akhilesh Pandey MD, PhD, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, Tel: 410-502-6662; Fax: 410-502-7544; , Rekha V. Kumar, MD, Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029; India. Tel: 091-080-6560708; Fax: 091-080-6560723;
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Corresponding authors: Akhilesh Pandey MD, PhD, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, Tel: 410-502-6662; Fax: 410-502-7544; , Rekha V. Kumar, MD, Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029; India. Tel: 091-080-6560708; Fax: 091-080-6560723;
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Hector A, Montgomery EA, Karikari C, Canto M, Dunbar KB, Wang JS, Feldmann G, Hong SM, Haffner MC, Meeker AK, Holland SJ, Yu J, Heckrodt TJ, Zhang J, Ding P, Goff D, Singh R, Roa JC, Marimuthu A, Riggins GJ, Eshleman JR, Nelkin BD, Pandey A, Maitra A. The Axl receptor tyrosine kinase is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer Biol Ther 2010; 10:1009-18. [PMID: 20818175 DOI: 10.4161/cbt.10.10.13248] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) arises in the backdrop of reflux-induced metaplastic phenomenon known as Barrett esophagus. The prognosis of advanced EAC is dismal, and there is an urgent need for identifying molecular targets for therapy. Serial Analysis of Gene Expression (SAGE) was performed on metachronous mucosal biopsies from a patient who underwent progression to EAC during endoscopic surveillance. SAGE confirmed significant upregulation of Axl "tags" during the multistep progression of Barrett esophagus to EAC. In a cohort of 92 surgically resected EACs, Axl overexpression was associated with shortened median survival on both univariate (p < 0.004) and multivariate (p < 0.036) analysis. Genetic knockdown of Axl receptor tyrosine kinase (RTK) function was enabled in two EAC lines (OE33 and JH-EsoAd1) using lentiviral short hairpin RNA (shRNA). Genetic knockdown of Axl in EAC cell lines inhibited invasion, migration, and in vivo engraftment, which was accompanied by downregulation in the activity of the Ral GTPase proteins (RalA and RalB). Restoration of Ral activation rescued the transformed phenotype of EAC cell lines, suggesting a novel effector mechanism for Axl in cancer cells. Pharmacological inhibition of Axl was enabled using a small molecule antagonist, R428 (Rigel Pharmaceuticals). Pharmacological inhibition of Axl with R428 in EAC cell lines significantly reduced anchorage-independent growth, invasion and migration. Blockade of Axl function abrogated phosphorylation of ERBB2 (Her-2/neu) at the Tyr877 residue, indicative of receptor crosstalk. Axl RTK is an adverse prognostic factor in EAC. The availability of small molecule inhibitors of Axl function provides a tractable strategy for molecular therapy of established EAC.
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Affiliation(s)
- Alvarez Hector
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TSK, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biol Ther 2010; 10:796-810. [PMID: 20686364 PMCID: PMC3093916 DOI: 10.4161/cbt.10.8.12914] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [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] Open
Abstract
The identification of secreted proteins that are differentially expressed between non-neoplastic and esophageal squamous cell carcinoma (ESCC) cells can provide potential biomarkers of ESCC. We used a SILAC-based quantitative proteomic approach to compare the secretome of ESCC cells with that of non-neoplastic esophageal squamous epithelial cells. Proteins were resolved by SDS-PAGE, and tandem mass spectrometry analysis (LC-MS/MS) of in-gel trypsin-digested peptides was carried out on a high-accuracy qTOF mass spectrometer. In total, we identified 441 proteins in the combined secretomes, including 120 proteins with > 2-fold upregulation in the ESCC secretome vs. that of non-neoplastic esophageal squamous epithelial cells. In this study, several potential protein biomarkers previously known to be increased in ESCC including matrix metalloproteinase 1, transferrin receptor, and transforming growth factor beta-induced 68 kDa were identified as overexpressed in the ESCC-derived secretome. In addition, we identified several novel proteins that have not been previously reported to be associated with ESCC. Among the novel candidate proteins identified, protein disulfide isomerase family a member 3 (PDIA3), GDP dissociation inhibitor 2 (GDI2), and lectin galactoside binding soluble 3 binding protein (LGALS3BP) were further validated by immunoblot analysis and immunohistochemical labeling using tissue microarrays. This tissue microarray analysis showed overexpression of protein disulfide isomerase family a member 3, GDP dissociation inhibitor 2, and lectin galactoside binding soluble 3 binding protein in 93%, 93% and 87% of 137 ESCC cases, respectively. Hence, we conclude that these potential biomarkers are excellent candidates for further evaluation to test their role and efficacy in the early detection of ESCC.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- 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 Biotechnology; Kuvempu University; Shimoga, India
| | - HC Harsha
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Department of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Rajiv Gandhi University of Health Sciences; Bangalore, India
| | - Nandini A Sahasrabuddhe
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Manipal University; Manipal, Karnataka India
| | - Min-Sik Kim
- 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
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- 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
- Manipal University; Manipal, Karnataka India
| | | | | | - Kumaran Kandasamy
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- 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 Biotechnology; Kuvempu University; Shimoga, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Rajiv Gandhi University of Health Sciences; Bangalore, India
| | | | - Riaz Mahmood
- Department of Biotechnology; Kuvempu University; Shimoga, India
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- 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
| | - Stephen J Meltzer
- Department of Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Oncology; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Rekha V Kumar
- Department of Pathology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Anil K Rustgi
- Division of Gastroenterology; Department of Medicine and Genetics; Abramson Cancer Center; University of Pennsylvania; Philadelphia, Pennsylvania 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
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Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics Clin Appl 2010. [DOI: 10.1002/prca.201090040] [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: 11/08/2022]
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Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics 2010; 10:1359-73. [PMID: 20104618 DOI: 10.1002/pmic.200900483] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pluripotent human embryonic stem cells (ESCs) can be differentiated in vitro into a variety of cells which hold promise for transplantation therapy. Human embryonal carcinoma cells (ECCs), stem cells of human teratocarcinomas, are considered a close but malignant counterpart to human ESCs. In this study, a comprehensive quantitative proteomic analysis of ESCs and ECCs was carried out using the iTRAQ method. Using two-dimensional LC and MS/MS analyses, we identified and quantitated approximately 1800 proteins. Among these are proteins associated with pluripotency and development as well as tight junction signaling and TGFbeta receptor pathway. Nearly approximately 200 proteins exhibit more than twofold difference in abundance between ESCs and ECCs. Examples of early developmental markers high in ESCs include beta-galactoside-binding lectin, undifferentiated embryonic cell transcription factor-1, DNA cytosine methyltransferase 3beta isoform-B, melanoma antigen family-A4, and interferon-induced transmembrane protein-1. In contrast, CD99-antigen (CD99), growth differentiation factor-3, cellular retinoic acid binding protein-2, and developmental pluripotency associated-4 were among the highly expressed proteins in ECCs. Several proteins that were highly expressed in ECCs such as heat shock 27 kDa protein-1, mitogen-activated protein kinase kinase-1, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor like-2, and S100 calcium-binding protein-A4 have also been attributed to malignancy in other systems. Importantly, immunocytochemistry was used to validate the proteomic analyses for a subset of the proteins. In summary, this is the first large-scale quantitative proteomic study of human ESCs and ECCs, which provides critical information about the regulators of these two closely related, but developmentally distinct, stem cells.
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Kashyap MK, Marimuthu A, Peri S, Kumar GSS, Jacob HK, Prasad TSK, Mahmood R, Kumar KVV, Kumar MV, Meltzer SJ, Montgomery EA, Kumar RV, Pandey A. Overexpression of periostin and lumican in esophageal squamous cell carcinoma. Cancers (Basel) 2010; 2:133-42. [PMID: 24281036 PMCID: PMC3827595 DOI: 10.3390/cancers2010133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/08/2010] [Accepted: 02/20/2010] [Indexed: 02/07/2023] Open
Abstract
To identify biomarkers for early detection for esophageal squamous cell carcinoma (ESCC), we previously carried out a genome-wide gene expression profiling study using an oligonucleotide microarray platform. This analysis led to identification of several transcripts that were significantly upregulated in ESCC compared to the adjacent normal epithelium. In the current study, we performed immunohistochemical analyses of protein products for two candidates genes identified from the DNA microarray analysis, periostin (POSTN) and lumican (LUM), using tissue microarrays. Increased expression of both periostin and lumican was observed in 100% of 137 different ESCC samples arrayed on tissue microarrays. Increased expression of periostin and lumican was observed in carcinoma as well as in stromal cell in the large majority of cases. These findings suggest that these candidates can be investigated in the sera of ESCC patients using ELISA or multiple reaction monitoring (MRM) type assays to further explore their utility as biomarkers.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biotechnology, Kuvempu University, Shimoga District, Karnataka 577451, India; E-Mail: (R.M.)
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Suraj Peri
- Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA; E-Mail: (S.P.)
| | - Ghantasala S. Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- Department of Biotechnology, Kuvempu University, Shimoga District, Karnataka 577451, India; E-Mail: (R.M.)
| | - Harrys K.C. Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Riaz Mahmood
- Department of Biotechnology, Kuvempu University, Shimoga District, Karnataka 577451, India; E-Mail: (R.M.)
| | - K. V. Veerendra Kumar
- Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029, India; E-Mails: (K.V.V.K.); (M.V.)
| | - M. Vijaya Kumar
- Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029, India; E-Mails: (K.V.V.K.); (M.V.)
| | - Stephen J. Meltzer
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (S.J.M.)
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elizabeth A. Montgomery
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (E.A.M.)
| | - Rekha V. Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029, India
- Authors to whom correspondence should be addressed; E-Mail: (A.P.) ; (R.V.K.); Tel.: +1-410-502-6662; Fax: +1-410-502-7544 (A.P.); Tel.: +91-80-656-708; Fax: +91-80-6560723 (R.V.K.).
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (E.A.M.)
- Authors to whom correspondence should be addressed; E-Mail: (A.P.) ; (R.V.K.); Tel.: +1-410-502-6662; Fax: +1-410-502-7544 (A.P.); Tel.: +91-80-656-708; Fax: +91-80-6560723 (R.V.K.).
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Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LDN, Goel R, Mathivanan S, Marimuthu A, Kashyap M, Vizza RF, Mayer RJ, DeCaprio JA, Srivastava S, Hanash SM, Hruban RH, Pandey A. A compendium of potential biomarkers of pancreatic cancer. PLoS Med 2009; 6:e1000046. [PMID: 19360088 PMCID: PMC2661257 DOI: 10.1371/journal.pmed.1000046] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Akhilesh Pandey and colleagues describe a compendium of potential biomarkers that can be systematically validated by the pancreatic cancer community.
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Affiliation(s)
- H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Manipal University, Manipal, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kumaran Kandasamy
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Prathibha Ranganathan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Sandhya Rani
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Subhashri Ramabadran
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Sashikanth Gollapudi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Sutopa B. Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Deepthi Telikicherla
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | | | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Suresh Mathivanan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Manipal University, Manipal, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Manoj Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Robert F. Vizza
- The Lustgarten Foundation for Pancreatic Cancer Research, Bethpage, New York, United States of America
| | - Robert J. Mayer
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - James A. DeCaprio
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samir M. Hanash
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ralph H. Hruban
- Departments of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
- Departments of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
- * E-mail:
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Kashyap MK, Marimuthu A, Kishore CJH, Peri S, Ranganathan P, Sanjeeviah RC, Mahmood R, Kumar KVV, Vijayakumar M, Montgomery E, Kumar RV, Pandey A. A panel of biomarkers for esophageal squamous cell carcinoma. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.925.11] [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: 11/11/2022]
Affiliation(s)
- Manoj K Kashyap
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins School of MedicineBaltimoreMD
- Institute of BioinformaticsBangaloreIndia
| | - Arivusudar Marimuthu
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins School of MedicineBaltimoreMD
- Institute of BioinformaticsBangaloreIndia
| | | | - Suraj Peri
- Biostatistics and BioinformaticsFox Chase Cancer CenterPhiladelphiaPA
| | | | | | | | | | - M. Vijayakumar
- Surgical OncologyKidwai Memorial Institute of OncologyBangaloreIndia
| | | | - Rekha V. Kumar
- PathologyKidwai Memorial Institute of OncologyBangaloreIndia
| | - Akhilesh Pandey
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins School of MedicineBaltimoreMD
- PathologyJohns Hopkins University School of MedicineBaltimoreMD
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Chaerkady R, Kerr CL, Marimuthu A, Kelkar DS, Kashyap MK, Gucek M, Gearhart JD, Pandey A. Temporal analysis of neural differentiation using quantitative proteomics. J Proteome Res 2009; 8:1315-26. [PMID: 19173612 PMCID: PMC2693473 DOI: 10.1021/pr8006667] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [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
The ability to derive neural progenitors, differentiated neurons and glial cells from human embryonic stem cells (hESCs) with high efficiency holds promise for a number of clinical applications. However, investigating the temporal events is crucial for defining the underlying mechanisms that drive this process of differentiation along different lineages. We carried out quantitative proteomic profiling using a multiplexed approach capable of analyzing eight different samples simultaneously to monitor the temporal dynamics of protein abundance as human embryonic stem cells differentiate into motor neurons or astrocytes. With this approach, a catalog of approximately 1200 proteins along with their relative quantitative expression patterns was generated. The differential expression of the large majority of these proteins has not previously been reported or studied in the context of neural differentiation. As expected, two of the widely used markers of pluripotency, alkaline phosphatase (ALPL) and LIN28, were found to be downregulated during differentiation, while S-100 and tenascin C were upregulated in astrocytes. Neurofilament 3 protein, doublecortin and CAM kinase-like 1 and nestin proteins were upregulated during motor neuron differentiation. We identified a number of proteins whose expression was largely confined to specific cell types, embryonic stem cells, embryoid bodies and differentiating motor neurons. For example, glycogen phosphorylase (PYGL) and fatty acid binding protein 5 (FABP5) were enriched in ESCs, while beta spectrin (SPTBN5) was highly expressed in embryoid bodies. Karyopherin, heat shock 27 kDa protein 1 and cellular retinoic acid binding protein 2 (CRABP2) were upregulated in differentiating motor neurons but were downregulated in mature motor neurons. We validated some of the novel markers of the differentiation process using immunoblotting and immunocytochemical labeling. To our knowledge, this is the first large-scale temporal proteomic profiling of human stem cell differentiation into neural cell types highlighting proteins with limited or undefined roles in neural fate.
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Affiliation(s)
- Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
- To whom correspondence should be addressed. E-mail: and E-mail:
| | - Candace L. Kerr
- Institute for Cell Engineering, Department of Obstetrics and Gynecology, Baltimore, MD, 21205, USA
- To whom correspondence should be addressed. E-mail: and E-mail:
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
| | - Dhanashree S. Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
| | - Marjan Gucek
- Institute of Basic Biomedical Sciences, Baltimore, MD, 21205, USA
| | - John D. Gearhart
- Institute for Cell Engineering, Department of Obstetrics and Gynecology, Baltimore, MD, 21205, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
- Department of Pathology and Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
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Kashyap MK, Marimuthu A, Kishore CJH, Peri S, Keerthikumar S, Prasad TSK, Mahmood R, Rao S, Ranganathan P, Sanjeeviah RC, Vijayakumar M, Kumar KVV, Montgomery EA, Kumar RV, Pandey A. Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biol Ther 2009; 8:36-46. [PMID: 18981721 DOI: 10.4161/cbt.8.1.7090] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer of the esophagus is of two main types, each with distinct etiological and pathological characteristics. Esophageal squamous cell carcinoma (ESCC) is predominant type of esophageal cancers worldwide comprising almost 95% of cases. While ESCC is prevalent in the developing world, esophageal adenocarcinoma is commonly seen in the developed country, usually in association with Barrett's esophagus. In spite of its higher prevalence, ESCC has not been studied as intensively as esophageal adenocarcinoma. ESCC and esophageal adenocarcinoma are common cancers worldwide with poor survival rate among patients mainly because both of these cancers lack early biomarkers of identification. Molecular mechanisms contributing to initiation and progression of esophageal squamous cell carcinoma are still poorly understood. Development of DNA microarray technology allows high-throughput identification of gene expression profiles in cancers. In order to identify molecules as candidates for early diagnosis and/or as therapeutic targets, we analyzed the mRNA expression profiles of 20 cases of ESCC using whole genome DNA microarrays. A total of 2,235 genes were differentially regulated in the tumors as compared to the corresponding adjacent normal epithelium of which 881 were significantly upregulated. We validated two molecules that were not previously reported to be overexpressed in ESCC, oral cancer overexpressed 2 (ORAOV2) and fibroblast activation protein (FAP), by immunohistochemical labeling of tissue microarrays and archival tissue sections and found that they were overexpressed in 98% (116/118) and 68% (79/116) of cases, respectively. By gene enrichment analysis, we identified significant downregulation of several genes in the arachidonic acid metabolic pathway. Overall, using this approach we have identified a number of promising novel candidates that can be validated further for their potential to serve as biomarkers for ESCC.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic Acids Res 2009; 37:D767-72. [PMID: 18988627 PMCID: PMC2686490 DOI: 10.1093/nar/gkn892] [Citation(s) in RCA: 2223] [Impact Index Per Article: 148.2] [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] [Indexed: 02/07/2023] Open
Abstract
Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.
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Affiliation(s)
- T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Renu Goel
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kumaran Kandasamy
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Shivakumar Keerthikumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sameer Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Suresh Mathivanan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Deepthi Telikicherla
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rajesh Raju
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Beema Shafreen
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Abhilash Venugopal
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sutopa Banerjee
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Devi S. Somanathan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Aimy Sebastian
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sandhya Rani
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Somak Ray
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - C. J. Harrys Kishore
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sashi Kanth
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mukhtar Ahmed
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Manoj K. Kashyap
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Riaz Mohmood
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Y. L. Ramachandra
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - V. Krishna
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - B. Abdul Rahiman
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sujatha Mohan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Prathibha Ranganathan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Subhashri Ramabadran
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
- *To whom correspondence should be addressed. Tel: +410 502 6662; Fax: +410 502 7544;
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Roy S, Marimuthu A, Deshpande PA, Hegde MS, Madras G. Selective Catalytic Reduction of NOx: Mechanistic Perspectives on the Role of Base Metal and Noble Metal Ion Substitution. Ind Eng Chem Res 2008. [DOI: 10.1021/ie8010879] [Citation(s) in RCA: 17] [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: 11/30/2022]
Affiliation(s)
- Sounak Roy
- Solid State and Structural Chemistry Unit and Chemical Engineering Department, Indian Institute of Science, Bangalore 560012, India
| | - A. Marimuthu
- Solid State and Structural Chemistry Unit and Chemical Engineering Department, Indian Institute of Science, Bangalore 560012, India
| | - Parag A. Deshpande
- Solid State and Structural Chemistry Unit and Chemical Engineering Department, Indian Institute of Science, Bangalore 560012, India
| | - M. S. Hegde
- Solid State and Structural Chemistry Unit and Chemical Engineering Department, Indian Institute of Science, Bangalore 560012, India
| | - Giridhar Madras
- Solid State and Structural Chemistry Unit and Chemical Engineering Department, Indian Institute of Science, Bangalore 560012, India
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Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE. Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci U S A 2008; 105:14112-7. [PMID: 18776048 PMCID: PMC2531065 DOI: 10.1073/pnas.0806158105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [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] Open
Abstract
We have used unbiased phosphoproteomic approaches, based on quantitative mass spectrometry using stable isotope labeling with amino acids in cell culture (SILAC), to identify tyrosine phosphorylated proteins in isogenic human bronchial epithelial cells (HBECs) and human lung adenocarcinoma cell lines, expressing either of the two mutant alleles of EGFR (L858R and Del E746-A750), or a mutant KRAS allele, which are common in human lung adenocarcinomas. Tyrosine phosphorylation of signaling molecules was greater in HBECs expressing the mutant EGFRs than in cells expressing WT EGFR or mutant KRAS. Receptor tyrosine kinases (such as EGFR, ERBB2, MET, and IGF1R), and Mig-6, an inhibitor of EGFR signaling, were more phosphorylated in HBECs expressing mutant EGFR than in cells expressing WT EGFR or mutant RAS. Phosphorylation of some proteins differed in the two EGFR mutant-expressing cells; for example, some cell junction proteins (beta-catenin, plakoglobin, and E-cadherin) were more phosphorylated in HBECs expressing L858R EGFR than in cells expressing Del EGFR. There were also differences in degree of phosphorylation at individual tyrosine sites within a protein; for example, a previously uncharacterized phosphorylation site in the nucleotide-binding loop of the kinase domains of EGFR (Y727), ERBB2 (Y735), or ERBB4 (Y733), is phosphorylated significantly more in HBECs expressing the deletion mutant than in cells expressing the wild type or L858R EGFR. Signaling molecules not previously implicated in ERBB signaling, such as polymerase transcript release factor (PTRF), were also phosphorylated in cells expressing mutant EGFR. Bayesian network analysis of these and other datasets revealed that PTRF might be a potentially important component of the ERBB signaling network.
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Affiliation(s)
- Udayan Guha
- *Programs in Cancer Biology and Genetics, and
- †To whom correspondence may be addressed. E-mail: or
| | - Raghothama Chaerkady
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - Arivusudar Marimuthu
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - A. Scott Patterson
- ‖Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
| | - Manoj K. Kashyap
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - H. C. Harsha
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - Mitsuo Sato
- **Department of Clinical Oncology and Chemotherapy, Nagoya University School of Medicine, Nagoya, Japan 466-8550; and
| | - Joel S. Bader
- ‖Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
| | - Alex E. Lash
- ††Comptational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065;
| | - John D. Minna
- ‡‡Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Akhilesh Pandey
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
| | - Harold E. Varmus
- *Programs in Cancer Biology and Genetics, and
- †To whom correspondence may be addressed. E-mail: or
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Affiliation(s)
- A. Marimuthu
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-12, India
| | - Giridhar Madras
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-12, India
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Affiliation(s)
- A. Marimuthu
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Giridhar Madras
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
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44
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Affiliation(s)
- A. Marimuthu
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-12, India
| | - Giridhar Madras
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-12, India
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Webb P, Anderson CM, Valentine C, Nguyen P, Marimuthu A, West BL, Baxter JD, Kushner PJ. The nuclear receptor corepressor (N-CoR) contains three isoleucine motifs (I/LXXII) that serve as receptor interaction domains (IDs). Mol Endocrinol 2000; 14:1976-85. [PMID: 11117528 DOI: 10.1210/mend.14.12.0566] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Unliganded thyroid hormone receptors (TRs) repress transcription through recruitment of corepressors, including nuclear receptor corepressor (N-CoR). We find that N-CoR contains three interaction domains (IDs) that bind to TR, rather than the previously reported two. The hitherto unrecognized ID (ID3) serves as a fully functional TR binding site, both in vivo and in vitro, and may be the most important for TR binding. Each ID motif contains a conserved hydrophobic core (I/LXXII) that resembles the hydrophobic core of nuclear receptor boxes (LXXLL), which mediates p160 coactivator binding to liganded nuclear receptors. Although the integrity of the I/LXXII motif is required for ID function, substitution of ID isoleucines with leucines did not allow ID peptides to bind to liganded TR, and substitution of NR box leucines with isoleucines did not allow NR box peptides to bind unliganded TR. This indicates that the binding preferences of N-CoR for unliganded TR and p160s for liganded TR are not dictated solely by the identity of conserved hydrophobic residues within their TR binding motifs. Examination of sequence conservation between IDs, and mutational analysis of individual IDs, suggests that they are comprised of the central hydrophobic core and distinct adjacent sequences that may make unique contacts with the TR surface. Accordingly, a hybrid peptide that contains distinct adjacent sequences from ID3 and ID1 shows enhanced binding to TR.
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Affiliation(s)
- P Webb
- Metabolic Research Unit, University of California School of Medicine, San Francisco 94143-0540, USA
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