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Aziz RA, Ramesh P, Suchithra KV, Stothard P, Narayana VK, Raghu SV, Shen FT, Young CC, Prasad TSK, Hameed A. Comprehensive insights into the impact of bacterial indole-3-acetic acid on sensory preferences in Drosophila melanogaster. Sci Rep 2024; 14:8311. [PMID: 38594449 PMCID: PMC11003987 DOI: 10.1038/s41598-024-58829-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Several bacteria of environmental and clinical origins, including some human-associated strains secrete a cross-kingdom signaling molecule indole-3-acetic acid (IAA). IAA is a tryptophan (trp) derivative mainly known for regulating plant growth and development as a hormone. However, the nutritional sources that boost IAA secretion in bacteria and the impact of secreted IAA on non-plant eukaryotic hosts remained less explored. Here, we demonstrate significant trp-dependent IAA production in Pseudomonas juntendi NEEL19 when provided with ethanol as a carbon source in liquid cultures. IAA was further characterized to modulate the odor discrimination, motility and survivability in Drosophila melanogaster. A detailed analysis of IAA-fed fly brain proteome using high-resolution mass spectrometry showed significant (fold change, ± 2; p ≤ 0.05) alteration in the proteins governing neuromuscular features, audio-visual perception and energy metabolism as compared to IAA-unfed controls. Sex-wise variations in differentially regulated proteins were witnessed despite having similar visible changes in chemo perception and psychomotor responses in IAA-fed flies. This study not only revealed ethanol-specific enhancement in trp-dependent IAA production in P. juntendi, but also showed marked behavioral alterations in flies for which variations in an array of proteins governing odor discrimination, psychomotor responses, and energy metabolism are held responsible. Our study provided novel insights into disruptive attributes of bacterial IAA that can potentially influence the eukaryotic gut-brain axis having broad environmental and clinical implications.
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Affiliation(s)
- Raifa Abdul Aziz
- Neurogenetics Lab, Department of Applied Zoology, Mangalore University, Mangalagangothri, Konaje, Mangalore, 574199, India
| | - Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575018, India
| | - Kokkarambath Vannadil Suchithra
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Vanya Kadla Narayana
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575018, India
| | - Shamprasad Varija Raghu
- Neurogenetics Lab, Department of Applied Zoology, Mangalore University, Mangalagangothri, Konaje, Mangalore, 574199, India
- Division of Neuroscience, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India
| | - Fo-Ting Shen
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Chiu-Chung Young
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 402, Taiwan
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575018, India.
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India.
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
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2
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Singh I, Hoti SL, Chauhan N, Joshi RK, Prasad TSK, Sarikhani M, Kaushik M, Unger BS, Jadhav P, Modi PK. Immunomodulation of streptozotocin induced Type 1 diabetes mellitus in mouse model by Macrophage migration inhibitory factor-2 (MIF-2) homologue of human lymphatic filarial parasite, Wuchereria bancrofti. Acta Trop 2024; 252:107142. [PMID: 38331083 DOI: 10.1016/j.actatropica.2024.107142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Helminth parasites modulate the host immune system to ensure a long-lasting asymptomatic form of infection generally, mediated by the secretion of immunomodulatory molecules and one such molecule is a homologue of human host cytokine, Macrophage migratory Inhibitory Factor (hMIF). In this study, we sought to understand the role of homologue of hMIF from the lymphatic filarial parasite, Wuchereria bancrofti (Wba-MIF2), in the immunomodulation of the Streptozotocin (STZ)-induced Type1 Diabetes Mellitus (T1DM) animal model. Full-length recombinant Wba-MIF2 was expressed and found to have both oxidoreductase and tautomerase activities. Wba-MIF2 recombinant protein was treated to STZ induced T1DM animals, and after 5 weeks pro-inflammatory (IL-1, IL-2, IL-6, TNF-α, IFN-γ) and anti-inflammatory (IL-4, IL-10) cytokines and gene expressions were determined in sera samples and spleen respectively. Pro-inflammatory and anti-inflammatory cytokine levels were significantly (p<0.05) up-regulated and down-regulated respectively, in the STZ-T1DM animals, as compared to treated groups. Histopathology showed macrophage infiltration and greater damage of islets of beta cells in the pancreatic tissue of STZ-T1DM animals, than Wba-MIF2 treated STZ-T1DM animals. The present study clearly showed the potential of Wba-MIF2 as an immunomodulatory molecule, which could modulate the host immune system in the STZ-T1DM mice model from a pro-inflammatory to anti-inflammatory milieu.
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Affiliation(s)
- Ishwar Singh
- ICMR-National Institute of Traditional Medicine, Belagavi 590010, India Karnataka, India; KLE Academy of Higher Education and Research, Belagavi 590010, India Karnataka, India
| | - S L Hoti
- ICMR-National Institute of Traditional Medicine, Belagavi 590010, India Karnataka, India.
| | - Nikhil Chauhan
- ICMR-National Institute of Traditional Medicine, Belagavi 590010, India Karnataka, India
| | - R K Joshi
- ICMR-National Institute of Traditional Medicine, Belagavi 590010, India Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575007, Karnataka, India
| | | | - Meenakshi Kaushik
- ICMR-National Institute of Traditional Medicine, Belagavi 590010, India Karnataka, India
| | - Banappa S Unger
- ICMR-National Institute of Traditional Medicine, Belagavi 590010, India Karnataka, India
| | - Pankaj Jadhav
- Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575007, Karnataka, India
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3
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Gupta P, Goswami SG, Kumari G, Saravanakumar V, Bhargava N, Rai AB, Singh P, Bhoyar RC, Arvinden VR, Gunda P, Jain S, Narayana VK, Deolankar SC, Prasad TSK, Natarajan VT, Scaria V, Singh S, Ramalingam S. Development of pathophysiologically relevant models of sickle cell disease and β-thalassemia for therapeutic studies. Nat Commun 2024; 15:1794. [PMID: 38413594 PMCID: PMC10899644 DOI: 10.1038/s41467-024-46036-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/12/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Ex vivo cellular system that accurately replicates sickle cell disease and β-thalassemia characteristics is a highly sought-after goal in the field of erythroid biology. In this study, we present the generation of erythroid progenitor lines with sickle cell disease and β-thalassemia mutation using CRISPR/Cas9. The disease cellular models exhibit similar differentiation profiles, globin expression and proteome dynamics as patient-derived hematopoietic stem/progenitor cells. Additionally, these cellular models recapitulate pathological conditions associated with both the diseases. Hydroxyurea and pomalidomide treatment enhanced fetal hemoglobin levels. Notably, we introduce a therapeutic strategy for the above diseases by recapitulating the HPFH3 genotype, which reactivates fetal hemoglobin levels and rescues the disease phenotypes, thus making these lines a valuable platform for studying and developing new therapeutic strategies. Altogether, we demonstrate our disease cellular systems are physiologically relevant and could prove to be indispensable tools for disease modeling, drug screenings and cell and gene therapy-based applications.
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Affiliation(s)
- Pragya Gupta
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sangam Giri Goswami
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geeta Kumari
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vinodh Saravanakumar
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - Nupur Bhargava
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Praveen Singh
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rahul C Bhoyar
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - V R Arvinden
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Padma Gunda
- Thalassemia and Sickle Cell Society- Kamala Hospital and Research Centre, Shivarampally, Hyderabad, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society- Kamala Hospital and Research Centre, Shivarampally, Hyderabad, India
| | - Vanya Kadla Narayana
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Sayali C Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Vivek T Natarajan
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinod Scaria
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shailja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
| | - Sivaprakash Ramalingam
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Rawat RS, Gupta A, Antil N, Bhatnagar S, Singh M, Rawat A, Prasad TSK, Sharma P. Protein kinase PfPK2 mediated signalling is critical for host erythrocyte invasion by malaria parasite. PLoS Pathog 2023; 19:e1011770. [PMID: 37988347 PMCID: PMC10662742 DOI: 10.1371/journal.ppat.1011770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
Signalling pathways in malaria parasite remain poorly defined and major reason for this is the lack of understanding of the function of majority of parasite protein kinases and phosphatases in parasite signalling and its biology. In the present study, we have elucidated the function of Protein Kinase 2 (PfPK2), which is known to be indispensable for the survival of human malaria parasite Plasmodium falciparum. We demonstrate that it is involved in the invasion of host erythrocytes, which is critical for establishing infection. In addition, PfPK2 may also be involved in the maturation of the parasite post-invasion. PfPK2 regulates the release of microneme proteins like Apical Membrane Antigen 1 (AMA1), which facilitates the formation of Tight Junction between the merozoite and host erythrocyte- a key step in the process of invasion. Comparative phosphoproteomics studies revealed that PfPK2 may be involved in regulation of several key proteins involved in invasion and signalling. Furthermore, PfPK2 regulates the generation of cGMP and the release of calcium in the parasite, which are key second messengers for the process of invasion. These and other studies have shed light on a novel signalling pathway in which PfPK2 acts as an upstream regulator of important cGMP-calcium signalling, which plays an important role in parasite invasion.
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Affiliation(s)
- Rahul Singh Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Ankit Gupta
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Neelam Antil
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sonika Bhatnagar
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Monika Singh
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - Akanksha Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Pushkar Sharma
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
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5
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Suchitha GP, Balaya RDA, Raju R, Keshava Prasad TS, Dagamajalu S. A network map of cytoskeleton-associated protein 4 (CKAP4) mediated signaling pathway in cancer. J Cell Commun Signal 2023; 17:1097-1104. [PMID: 36944905 PMCID: PMC10409693 DOI: 10.1007/s12079-023-00739-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 03/23/2023] Open
Abstract
Cytoskeleton-associated protein 4 (CKAP4) is a non-glycosylated type II transmembrane protein that serves as a cell surface-activated receptor. It is expressed primarily in the plasma membranes of bladder epithelial cells, type II alveolar pneumocytes, and vascular smooth muscle cells. CKAP4 is involved in various biological activities including cell proliferation, cell migration, keratinocyte differentiation, glycogenesis, fibrosis, thymic development, cardiogenesis, neuronal apoptosis, and cancer. CKAP4 has been described as a pro-tumor molecule that regulates the progression of various cancers, including lung cancer, breast cancer, esophageal squamous cell carcinoma, hepatocellular carcinoma, cervical cancer, oral cancer, bladder cancer, cholangiocarcinoma, pancreatic cancer, myeloma, renal cell carcinoma, melanoma, squamous cell carcinoma, colorectal cancer, and osteosarcoma. CKAP4 and its isoform bind to DKK1 or DKK3 (Dickkopf proteins) or antiproliferative factor (APF) and regulates several downstream signaling cascades. The CKAP4 complex plays a crucial role in regulating the signaling pathways including PI3K/AKT and MAPK1/3. Recently, CKAP4 has been recognized as a potential target for cancer therapy. Due to its biomedical importance, we integrated a network map of CKAP4. The available literature on CKAP4 signaling was manually curated according to the NetPath annotation criteria. The consolidated pathway map comprises 41 activation/inhibition events, 21 catalysis events, 35 molecular associations, 134 gene regulation events, 83 types of protein expression, and six protein translocation events. CKAP4 signaling pathway map data is freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5322 ). Generation of CKAP4 signaling pathway map.
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Affiliation(s)
- G. P. Suchitha
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
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6
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Sanjeev D, Dagamajalu S, Shaji V, George M, Subbannayya Y, Prasad TSK, Raju R, Devasahayam Arokia Balaya R. A network map of macrophage-stimulating protein (MSP) signaling. J Cell Commun Signal 2023; 17:1113-1120. [PMID: 37142846 PMCID: PMC10409925 DOI: 10.1007/s12079-023-00755-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
Macrophage-stimulating protein (MSP), a serum-derived growth factor belonging to the plasminogen-related kringle domain family, is mainly produced by the liver and released into the blood. MSP is the only known ligand for RON ("Recepteur d'Origine Nantais", also known as MST1R), which is a member of the receptor tyrosine kinase (RTK) family. MSP is associated with many pathological conditions, including cancer, inflammation, and fibrosis. Activation of the MSP/RON system regulates main downstream signaling pathways, including phosphatidylinositol 3-kinase/ AKT serine/threonine kinase/ (PI3-K/AKT), mitogen-activated protein kinases (MAPK), c-Jun N-terminal kinase (JNK) & Focal adhesion kinase (FAK). These pathways are mainly involved in cell proliferation, survival, migration, invasion, angiogenesis & chemoresistance. In this work, we created a pathway resource of signaling events mediated by MSP/RON considering its contribution to diseases. We provide an integrated pathway reaction map of MSP/RON that is composed of 113 proteins and 26 reactions based on the curation of data from the published literature. The consolidated pathway map of MSP/RON mediated signaling events contains seven molecular associations, 44 enzyme catalysis, 24 activation/inhibition, six translocation events, 38 gene regulation events, and forty-two protein expression events. The MSP/RON signaling pathway map can be freely accessible through the WikiPathways Database URL: https://classic.wikipathways.org/index.php/Pathway:WP5353 .
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Affiliation(s)
- Diya Sanjeev
- Centre for Integrative OmicsData Science (CIODS), Yenepoya (Deemed to be University), Derlakatte, Mangalore, Karnataka 575018 India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Vineetha Shaji
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Mejo George
- Centre for Integrative OmicsData Science (CIODS), Yenepoya (Deemed to be University), Derlakatte, Mangalore, Karnataka 575018 India
| | - Yashwanth Subbannayya
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH UK
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Rajesh Raju
- Centre for Integrative OmicsData Science (CIODS), Yenepoya (Deemed to be University), Derlakatte, Mangalore, Karnataka 575018 India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Rex Devasahayam Arokia Balaya
- Centre for Integrative OmicsData Science (CIODS), Yenepoya (Deemed to be University), Derlakatte, Mangalore, Karnataka 575018 India
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Dagamajalu S, Rex DAB, Suchitha GP, Rai AB, Kumar S, Joshi S, Raju R, Prasad TSK. A network map of discoidin domain receptor 1(DDR1)-mediated signaling in pathological conditions. J Cell Commun Signal 2023; 17:1081-1088. [PMID: 36454444 PMCID: PMC10409954 DOI: 10.1007/s12079-022-00714-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
Discoidin domain receptor 1 (DDR1) is one of the receptors that belong to a family of non-integrin collagen receptors. In common, DDR1 is predominantly found in epithelial and smooth muscle cells and its mainly involved in organogenesis during embryonic development. However, it's also overexpressed in several pathological conditions, including cancer and inflammation. The DDR1 is reported in numerous cancers, including breast, prostate, pancreatic, bladder, lung, liver, pituitary, colorectal, skin, gastric, glioblastoma, and inflammation. DDR1 activates through the collagen I, IV, IGF-1/IGF1R, and IGF2/IR, regulating downstream signaling molecules such as MAPKs, PI3K/Akt, and NF-kB in diseases. Despite its biomedical importance, there is a lack of consolidated network map of the DDR1 signaling pathway, which prompted us for curation of literature data pertaining to the DDR1 system following the NetPath criteria. We present here the compiled pathway map comprises 39 activation/inhibition events, 17 catalysis events, 22 molecular associations, 65 gene regulation events, 35 types of protein expression, and two protein translocation events. The detailed DDR1 signaling pathway map is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/ Pathway: https://www.wikipathways.org/index.php/Pathway:WP5288 ).
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Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - D. A. B. Rex
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - G. P. Suchitha
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - Akhila B. Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - Shreya Kumar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - Shreya Joshi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka 575018 India
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8
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Upadhyay SS, Devasahayam Arokia Balaya R, Parate SS, Dagamajalu S, Keshava Prasad TS, Shetty R, Raju R. An assembly of TROP2-mediated signaling events. J Cell Commun Signal 2023; 17:1105-1111. [PMID: 37014471 PMCID: PMC10409939 DOI: 10.1007/s12079-023-00742-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/15/2023] [Indexed: 04/05/2023] Open
Abstract
Trophoblast cell surface antigen 2 (TROP2) is a calcium-transducing transmembrane protein mainly involved in embryo development. The aberrant expression of TROP2 is observed in numerous cancers, including triple-negative breast cancer, gastric, colorectal, pancreatic, squamous cell carcinoma of the oral cavity, and prostate cancers. The main signaling pathways mediated by TROP2 are calcium signaling, PI3K/AKT, JAK/STAT, MAPKs, and β-catenin signaling. However, collective information about the TROP2-mediated signaling pathway is not available for visualization or analysis. In this study, we constructed a TROP2 signaling map with respect to its role in different cancers. The data curation was done manually by following the NetPath annotation criteria. The described map consists of different molecular events, including 8 activation/inhibition, 16 enzyme catalysis, 19 gene regulations, 12 molecular associations, 39 induced-protein expressions, and 2 protein translocation. The data of the TROP2 pathway map is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5300 ). Development of TROP2 signaling pathway map.
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Affiliation(s)
- Shubham Sukerndeo Upadhyay
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | | | - Sakshi Sanjay Parate
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College Hospital, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018 India
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Ramesh P, Behera SK, Kotimoole CN, Mohanty V, Raju R, Prasad TSK, Codi JAK. Mining proteomics data to extract post-translational modifications associated with gastric cancer. Amino Acids 2023; 55:993-1001. [PMID: 37311859 DOI: 10.1007/s00726-023-03287-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023]
Abstract
Gastric cancers are highly heterogeneous, deep-seated tumours associated with late diagnosis and poor prognosis. Post-translational modifications (PTMs) of proteins are known to be well-associated with oncogenesis and metastasis in most cancers. Several enzymes which drive PTMs have also been used as theranostics in cancers of the breast, ovary, prostate and bladder. However, there is limited data on PTMs in gastric cancers. Considering that experimental protocols for simultaneous analysis of multiple PTMs are being explored, a data-driven approach involving reanalysis of mass spectrometry-derived data is useful in cataloguing altered PTMs. We subjected publicly available mass spectrometry data on gastric cancer to an iterative searching strategy for fetching PTMs including phosphorylation, acetylation, citrullination, methylation and crotonylation. These PTMs were catalogued and further analyzed for their functional enrichment through motif analysis. This value-added approach delivered identification of 21,710 unique modification sites on 16,364 modified peptides. Interestingly, we observed 278 peptides corresponding to 184 proteins to be differentially abundant. Using bioinformatics approaches, we observed that majority of these altered PTMs/proteins belonged to cytoskeletal and extracellular matrix proteins, which are known to be perturbed in gastric cancer. The dataset derived by this mutiPTM investigation can provide leads to further investigate the potential role of altered PTMs in gastric cancer management.
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Affiliation(s)
- Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India.
| | - Jalaluddin Akbar Kandel Codi
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University), Mangalore, 575018, India.
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Fernandes LB, D'Souza JS, Prasad TSK, Ghag SB. Isolation and characterization of extracellular vesicles from Fusarium oxysporum f. sp. cubense, a banana wilt pathogen. Biochim Biophys Acta Gen Subj 2023; 1867:130382. [PMID: 37207907 DOI: 10.1016/j.bbagen.2023.130382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Fusarium wilt of banana is a destructive widespread disease caused by Fusarium oxysporum f. sp. cubense (Foc) that ravaged banana plantations globally, incurring huge economic losses. Current knowledge demonstrates the involvement of several transcription factors, effector proteins, and small RNAs in the Foc-banana interaction. However, the precise mode of communication at the interface remains elusive. Cutting-edge research has emphasized the significance of extracellular vesicles (EVs) in trafficking the virulent factors modulating the host physiology and defence system. EVs are ubiquitous inter- and intra-cellular communicators across kingdoms. This study focuses on the isolation and characterization of Foc EVs from methods that make use of sodium acetate, polyethylene glycol, ethyl acetate, and high-speed centrifugation. Isolated EVs were microscopically visualized using Nile red staining. Further, the EVs were characterized using transmission electron microscopy, which revealed the presence of spherical, double-membrane, vesicular structures ranging in size from 50 to 200 nm (diameter). The size was also determined using the principle based on Dynamic Light Scattering. The Foc EVs contained proteins that were separated using SDS-PAGE and ranged between 10 and 315 kDa. Mass spectrometry analysis revealed the presence of EV-specific marker proteins, toxic peptides, and effectors. The Foc EVs were found to be cytotoxic, whose toxicity increased with EVs isolated from the co-culture preparation. Taken together, a better understanding of Foc EVs and their cargo will aid in deciphering the molecular crosstalk between banana and Foc.
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Affiliation(s)
- Lizelle B Fernandes
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai campus, Kalina, Santacruz (East), Mumbai 400098, India
| | - Jacinta S D'Souza
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai campus, Kalina, Santacruz (East), Mumbai 400098, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore 575018, India
| | - Siddhesh B Ghag
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai campus, Kalina, Santacruz (East), Mumbai 400098, India.
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Devasahayam Arokia Balaya R, Chandrasekaran J, Kanekar S, Kumar Modi P, Dagamajalu S, Gopinathan K, Raju R, Prasad TSK. Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) inhibitors: a novel approach in small molecule discovery. J Biomol Struct Dyn 2023; 41:15196-15206. [PMID: 37029757 DOI: 10.1080/07391102.2023.2193999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/25/2023] [Indexed: 04/09/2023]
Abstract
The calcium/calmodulin dependent protein kinase kinase 2 (CAMKK2) plays a key role in regulation of intracellular calcium levels and signaling pathways. It is involved in activation of downstream signaling pathways that regulate various cellular processes. Dysregulation of CAMKK2 activity has been linked to various diseases including cancer, suggesting that CAMKK2 inhibitors might be beneficial in oncological, metabolic and inflammatory indications. The most pressing issues in small molecule discovery are synthesis feasibility, novel chemical structure and desired biological characteristics. To circumvent this constraint, we employed 'DrugspaceX' for rapid lead identification, followed by repositioning seven FDA-approved drugs for CAMKK2 inhibition. Further, first-level transformation (Set1 analogues) was performed in 'DrugspaceX', followed by virtual screening. The t-SNE visualization revealed that the transformations surrounding Rucaparib, Treprostinil and Canagliflozin are more promising for developing CAMKK2 inhibitors. Second, using the top-ranked Set1 analogues, Set2 analogues were generated, and virtual screening revealed the top-ranked five analogues. Among the top five Set2 analogues, DE273038_5 had the lowest docking score of -11.034 kcal/mol and SA score of 2.59, retaining the essential interactions with Hotspot residues LYS194 and VAL270 across 250 ns simulation period. When compared to the other four compounds, the ligand effectiveness score was 0.409, and the number of rotatable penalties was only three. Further, DE273038_5 after two rounds of transformations was discovered to be novel and had not been previously described in other databases. These data suggest that the new candidate DE273038_5 is likely to have inhibitory activity at the CAMKK2 active site, implying potential therapeutic use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Jaikanth Chandrasekaran
- Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher education and Research (Deemed to be University), Chennai, India
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Kirthika Gopinathan
- Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher education and Research (Deemed to be University), Chennai, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
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12
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Rex DAB, Dagamajalu S, Gouda MM, Suchitha GP, Chanderasekaran J, Raju R, Prasad TSK, Bhandary YP. A comprehensive network map of IL-17A signaling pathway. J Cell Commun Signal 2023; 17:209-215. [PMID: 35838944 PMCID: PMC9284958 DOI: 10.1007/s12079-022-00686-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 10/28/2022] Open
Abstract
Interleukin-17A (IL-17A) is one of the member of IL-17 family consisting of other five members (IL-17B to IL-17F). The Gamma delta (γδ) T cells and T helper 17 (Th17) cells are the major producers of IL-17A. Aberrant signaling by IL-17A has been implicated in the pathogenesis of several autoimmune diseases including idiopathic pulmonary fibrosis, acute lung injury, chronic airway diseases, and cancer. Activation of the IL-17A/IL-17 receptor A (IL-17RA) system regulates phosphoinositide 3-kinase/AKT serine/threonine kinase/mammalian target of rapamycin (PI3K/AKT/mTOR), mitogen-activated protein kinases (MAPKs) and activation of nuclear factor-κB (NF-κB) mediated signaling pathways. The IL-17RA activation orchestrates multiple downstream signaling cascades resulting in the release of pro-inflammatory cytokines such as interleukins (IL)-1β, IL-6, and IL-8, chemokines (C-X-C motif) and promotes neutrophil-mediated immune response. Considering the biomedical importance of IL-17A, we developed a pathway resource of signaling events mediated by IL-17A/IL-17RA in this study. The curation of literature data pertaining to the IL-17A system was performed manually by the NetPath criteria. Using data mined from the published literature, we describe an integrated pathway reaction map of IL-17A/IL-17RA consisting of 114 proteins and 68 reactions. That includes detailed information on IL-17A/IL-17RA mediated signaling events of 9 activation/inhibition events, 17 catalysis events, 3 molecular association events, 68 gene regulation events, 109 protein expression events, and 6 protein translocation events. The IL-17A signaling pathway map data is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway : WP5242).
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Affiliation(s)
- D. A. B. Rex
- grid.413027.30000 0004 1767 7704Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Shobha Dagamajalu
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Mahesh Manjunath Gouda
- grid.13648.380000 0001 2180 3484Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg (UKE), Martinistrasse 52, 20251 Hamburg, Germany
| | - G. P. Suchitha
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Jaikanth Chanderasekaran
- Department of Pharmacology, School of Pharmacy and Technology Management, SVKM’S NMIMS University, Hyderabad, Telangana India
| | - Rajesh Raju
- grid.413027.30000 0004 1767 7704Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - T. S. Keshava Prasad
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
| | - Yashodhar Prabhakar Bhandary
- grid.413027.30000 0004 1767 7704Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018 India
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13
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Chatterjee O, Gopalakrishnan L, Pullimamidi D, Raj C, Yelamanchi S, Gangadharappa BS, Nair B, Mahadevan A, Raju R, Keshava Prasad TS. A molecular network map of orexin-orexin receptor signaling system. J Cell Commun Signal 2023; 17:217-227. [PMID: 36480100 PMCID: PMC10030760 DOI: 10.1007/s12079-022-00700-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 12/13/2022] Open
Abstract
Orexins are excitatory neuropeptides, which are predominantly associated with feeding behavior, sleep-wake cycle and energy homeostasis. The orexinergic system comprises of HCRTR1 and HCRTR2, G-protein-coupled receptors of rhodopsin family and the endogenous ligands processed from HCRT pro-hormone, Orexin A and Orexin B. These neuropeptides are biosynthesized by the orexin neurons present in the lateral hypothalamus area, with dense projections to other brain regions. The orexin-receptor signaling is implicated in various metabolic as well as neurological disorders, making it a promising target for pharmacological interventions. However, there is limited information available on the collective representation of the signal transduction pathways pertaining to the orexin-orexin receptor signaling system. Here, we depict a compendium of the Orexin A/B stimulated reactions in the form of a basic signaling pathway map. This map catalogs the reactions into five categories: molecular association, activation/inhibition, catalysis, transport, and gene regulation. A total of 318 downstream molecules were annotated adhering to the guidelines of NetPath curation. This pathway map can be utilized for further assessment of signaling events associated with orexin-mediated physiological functions and is freely available on WikiPathways, an open-source pathway database ( https://www.wikipathways.org/index.php/Pathway:WP5094 ).
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Affiliation(s)
- Oishi Chatterjee
- Institute of Bioinformatics, International Tech Park, 560 066, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, 690 525, Kollam, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), 575 018, Mangalore, India
| | - Lathika Gopalakrishnan
- Institute of Bioinformatics, International Tech Park, 560 066, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), 575 018, Mangalore, India
- Manipal Academy of Higher Education (MAHE), 576 104, Manipal, India
| | | | - Chinmayi Raj
- Institute of Bioinformatics, International Tech Park, 560 066, Bangalore, India
| | - Soujanya Yelamanchi
- Institute of Bioinformatics, International Tech Park, 560 066, Bangalore, India
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, 690 525, Kollam, India
| | - Anita Mahadevan
- Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, 560 029, Bangalore, India
- Department of Neuropathology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, 560 029, Bangalore, India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), 575 018, Mangalore, India.
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), 575 018, Mangalore, India.
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14
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Husain AA, Pinto SM, Subbannayya Y, Kapoor S, Khulkhule P, Bhartiya N, Prasad TSK, Daginawala HF, Singh LR, Kashyap RS. Development of multiple reaction monitoring (MRM) assays to identify Brucella abortus proteins in the serum of humans and livestock. Proteomics Clin Appl 2023; 17:e2200009. [PMID: 35925648 DOI: 10.1002/prca.202200009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 01/25/2023]
Abstract
In the present study, a targeted multiple reaction monitoring-mass spectrometry (MRM-MS) approach was developed to screen and identify protein biomarkers for brucellosis in humans and livestock. The selection of proteotypic peptides was carried out by generating in silico tryptic peptides of the Brucella proteome. Using bioinformatics analysis, 30 synthetic peptides corresponding to 10 immunodominant Brucella abortus proteins were generated. MRM-MS assays for the accurate detection of these peptides were optimized using 117 serum samples of human and livestock stratified as clinically confirmed (45), suspected (62), and control (10). Using high throughput MRM assays, transitions for four peptides were identified in several clinically confirmed and suspected human and livestock serum samples. Of these, peptide NAIYDVVTR corresponding to B. abortus proteins: BruAb2_0537 was consistently detected in the clinically confirmed serum samples of both humans and livestock with 100% specificity. To conclude, a high throughput MRM-MS-based protocol for detecting endogenous B. abortus peptides in serum samples of humans and livestock was developed. The developed protocol will help design sensitive assays to accurately diagnose brucellosis in humans and livestock. The data associated with this study are deposited in Panorama Public (https://panoramaweb.org/rNOZCy.url with ProteomeXchange ID: PXD034407).
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Affiliation(s)
- Aliabbas A Husain
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Saketh Kapoor
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Payal Khulkhule
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Nidhi Bhartiya
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Hatim F Daginawala
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Lokendra R Singh
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Rajpal Singh Kashyap
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
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15
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Husain AA, Pinto SM, Agarwal N, Behera SK, Khulkhule PR, Bhartiya NM, Subbannayya Y, Prasad TSK, Singh LR, Daginawala HF, Kashyap RS. Comprehensive Proteomic Analysis of Brucella melitensis ATCC23457 Strain Reveals Metabolic Adaptations in Response to Nutrient Stress. Curr Microbiol 2022; 80:20. [PMID: 36460801 DOI: 10.1007/s00284-022-03105-y] [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] [Received: 07/08/2022] [Accepted: 10/29/2022] [Indexed: 12/04/2022]
Abstract
In the present study, a comprehensive proteomic analysis of Brucella melitensis (B. melitensis) strain ATCC23457 was carried out to investigate proteome alterations in response to in vitro-induced nutrient stress. Our analysis resulted in the identification of 2440 proteins, including 365 hypothetical proteins and 850 potentially secretory proteins representing ~77.8% of the B. melitensis proteome. Utilizing a proteogenomics approach, we provide translational evidence for eight novel putative protein-coding genes and confirmed the coding potential of 31 putatively annotated pseudogenes, thus refining the existing genome annotation. Further, using a label-free quantitative proteomic approach, new insights into the cellular processes governed by nutrient stress, including enrichment of amino acid metabolism (E), transcription (K), energy production and conversion (C), and biogenesis (J) processes were obtained. Pathway analysis revealed the enrichment of survival and homeostasis maintenance pathways, including type IV secretion system, nitrogen metabolism, and urease pathways in response to nutrient limitation. To conclude, our analysis demonstrates the utility of in-depth proteomic analysis in enabling improved annotation of the B. melitensis genome. Further, our results indicate that B. melitensis undergoes metabolic adaptations during nutrient stress similar to other Brucella. sp, and adapts itself for long-term persistence and survival.
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Affiliation(s)
- Aliabbas A Husain
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Nupur Agarwal
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Santosh K Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Payal R Khulkhule
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Nidhi M Bhartiya
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India.
| | - Lokendra R Singh
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Hatim F Daginawala
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Rajpal S Kashyap
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India.
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Rex DAB, Suchitha GP, Palollathil A, Kanichery A, Prasad TSK, Dagamajalu S. The network map of urotensin-II mediated signaling pathway in physiological and pathological conditions. J Cell Commun Signal 2022; 16:601-608. [PMID: 35174439 PMCID: PMC9733756 DOI: 10.1007/s12079-022-00672-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Urotensin-II is a polypeptide ligand with neurohormone-like activity. It mediates downstream signaling pathways through G-protein-coupled receptor 14 (GPR14) also known as urotensin receptor (UTR). Urotensin-II is the most potent endogenous vasoconstrictor in mammals, promoting cardiovascular remodelling, cardiac fibrosis, and cardiomyocyte hypertrophy. It is also involved in other physiological and pathological activities, including neurosecretory effects, insulin resistance, atherosclerosis, kidney disease, and carcinogenic effects. Moreover, it is a notable player in the process of inflammatory injury, which leads to the development of inflammatory diseases. Urotensin-II/UTR expression stimulates the accumulation of monocytes and macrophages, which promote the adhesion molecules expression, chemokines activation and release of inflammatory cytokines at inflammatory injury sites. Therefore, urotensin-II turns out to be an important therapeutic target for the treatment options and management of associated diseases. The main downstream signaling pathways mediated through this urotensin-II /UTR system are RhoA/ROCK, MAPKs and PI3K/AKT. Due to the importance of urotensin-II systems in biomedicine, we consolidated a network map of urotensin-II /UTR signaling. The described signaling map comprises 33 activation/inhibition events, 31 catalysis events, 15 molecular associations, 40 gene regulation events, 60 types of protein expression, and 11 protein translocation events. The urotensin-II signaling pathway map is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5158 ). The availability of comprehensive urotensin-II signaling in the public resource will help understand the regulation and function of this pathway in normal and pathological conditions. We believe this resource will provide a platform to the scientific community in facilitating the identification of novel therapeutic drug targets for diseases associated with urotensin-II signaling.
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Affiliation(s)
- D. A. B. Rex
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - G. P. Suchitha
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - Akhina Palollathil
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - Anagha Kanichery
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - T. S. Keshava Prasad
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - Shobha Dagamajalu
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
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17
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Ramesh P, Bajire SK, Kanichery A, Najar MA, Shastry RP, Prasad TSK. 6-Methylcoumarin rescues bacterial quorum sensing induced ribosome-inactivating stress in Caenorhabditis elegans. Microb Pathog 2022; 173:105833. [PMID: 36265737 DOI: 10.1016/j.micpath.2022.105833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Bacterial pathogenicity has for long posed severe effects on patient care. Pseudomonas aeruginosa is a common cause of hospital-acquired infections and nosocomial illnesses. It is known to infect the host by colonizing through quorum sensing and the production of exotoxins. METHODS The current effort is an analysis of proteomic alterations caused by P. aeruginosa PAO1 to study the effects of quorum sensing inhibitor 6-Methylcoumarin on PAO1 infectivity in the Caenorhabditis elegans model. RESULTS Through tandem mass tag-based quantitative proteomics approaches, 229 proteins were found to be differentially regulated in infection and upon inhibition. Among these, 34 proteins were found to be dysregulated in both infection and quorum-sensing inhibition conditions. Along with the dysregulation of proteins involved in host-pathogen interaction, PAO1 was found to induce ribosome-inactivating stress accompanied by the downregulating mitochondrial proteins. This in turn caused dysregulation of apoptosis. The expression of multiple proteins involved in ribosome biogenesis and structure, oxidative phosphorylation, and mitochondrial enzymes were altered due to infection. This mechanism, adapted by PAO1 to survive in the host, was inhibited by 6-Methylcoumarin by rescuing the downregulation of ribosomal and mitochondrial proteins. CONCLUSIONS Taken together, the data reflect the molecular alterations due to quorum sensing and the usefulness of inhibitors in controlling pathogenesis.
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Affiliation(s)
- Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - Sukesh Kumar Bajire
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - Anagha Kanichery
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - Rajesh P Shastry
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
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18
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Anusha-Kiran Y, Mol P, Dey G, Bhat FA, Chatterjee O, Deolankar SC, Philip M, Prasad TSK, Srinivas Bharath MM, Mahadevan A. Regional heterogeneity in mitochondrial function underlies region specific vulnerability in human brain ageing: Implications for neurodegeneration. Free Radic Biol Med 2022; 193:34-57. [PMID: 36195160 DOI: 10.1016/j.freeradbiomed.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 12/01/2022]
Abstract
Selective neuronal vulnerability (SNV) of specific neuroanatomical regions such as frontal cortex (FC) and hippocampus (HC) is characteristic of age-associated neurodegenerative diseases (NDDs), although its pathogenetic basis remains unresolved. We hypothesized that physiological differences in mitochondrial function in neuroanatomical regions could contribute to SNV. To investigate this, we evaluated mitochondrial function in human brains (age range:1-90 y) in FC, striatum (ST), HC, cerebellum (CB) and medulla oblongata (MD), using enzyme assays and quantitative proteomics. Striking differences were noted in resistant regions- MD and CB compared to the vulnerable regions- FC, HC and ST. At younger age (25 ± 5 y), higher activity of electron transport chain enzymes and upregulation of metabolic and antioxidant proteins were noted in MD compared to FC and HC, that was sustained with increasing age (≥65 y). In contrast, the expression of synaptic proteins was higher in FC, HC and ST (vs. MD). In line with this, quantitative phospho-proteomics revealed activation of upstream regulators (ERS, PPARα) of mitochondrial metabolism and inhibition of synaptic pathways in MD. Microtubule Associated Protein Tau (MAPT) showed overexpression in FC, HC and ST both in young and older age (vs. MD). MAPT hyperphosphorylation and the activation of its kinases were noted in FC and HC with age. Our study demonstrates that regional heterogeneity in mitochondrial and other cellular functions contribute to SNV and protect regions such as MD, while rendering FC and HC vulnerable to NDDs. The findings also support the "last in, first out" hypothesis of ageing, wherein regions such as FC, that are the most recent to develop phylogenetically and ontogenetically, are the first to be affected in ageing and NDDs.
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Affiliation(s)
- Yarlagadda Anusha-Kiran
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), No. 2900, Hosur Road, Bangalore, 560029, India; Department of Clinical Psychopharmacology and Neurotoxicology, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, India
| | - Praseeda Mol
- Institute of Bioinformatics, International Technology Park, White Field, Bangalore, 560066, India; Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690525, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, White Field, Bangalore, 560066, India
| | - Firdous Ahmad Bhat
- Institute of Bioinformatics, International Technology Park, White Field, Bangalore, 560066, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, White Field, Bangalore, 560066, India; Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690525, India
| | - Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Mariamma Philip
- Department of Biostatistics, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - M M Srinivas Bharath
- Department of Clinical Psychopharmacology and Neurotoxicology, NIMHANS, No. 2900, Hosur Road, Bangalore, 560029, India.
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), No. 2900, Hosur Road, Bangalore, 560029, India.
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19
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Deolankar SC, Najar MA, Ramesh P, Kanichery A, Kudva AK, Raghu SV, Prasad TSK. Discovery of Molecular Networks of Neuroprotection Conferred by Brahmi Extract in Aβ 42-Induced Toxicity Model of Drosophila melanogaster Using a Quantitative Proteomic Approach. Mol Neurobiol 2022; 60:303-316. [PMID: 36261695 DOI: 10.1007/s12035-022-03066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022]
Abstract
Accumulation of Aβ42 peptides forming plaque in various regions of the brain is a hallmark of Alzheimer's disease (AD) progression. However, to date, there is no effective management strategy reported for attenuation of Aβ42-induced toxicity in the early stages of the disease. Alternate medicinal systems such as Ayurveda in the past few decades show promising results in the management of neuronal complications. Medhya Rasayana such as Brahmi is known for its neuroprotective properties via resolving memory-related issues, while the underlying molecular mechanism of the same remains unclear. In the present study, we aimed to understand the neuroprotective effects of the aqueous extract of Bacopa monnieri and Centella asiatica (both commonly known as Brahmi) against the Aβ42 expressing model of the Drosophila melanogaster. By applying a quantitative proteomics approach, the study identified > 90% of differentially expressed proteins from Aβ42 expressing D. melanogaster were either restored to their original expression pattern or showed no change in expression pattern upon receiving either Brahmi extract treatment. The Brahmi restored proteins were part of neuronal pathways associated with cell cycle re-entry, apoptosis, and mitochondrial dynamics. The neuroprotective effect of Brahmi was also validated by negative geotaxis behavioral analysis suggesting its protective role against behavioral deficits exerted by Aβ42 toxicity. We believe that these discoveries will provide a platform for developing novel therapeutics for AD management by deciphering molecular targets of neuroprotection conferred by an aqueous extract of Bacopa monnieri or Centella asiatica.
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Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Anagha Kanichery
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Avinash K Kudva
- Department of Biochemistry, Mangalore University, Mangalore, India
| | | | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India.
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20
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Anam Z, Kumari G, Mukherjee S, Rex DAB, Biswas S, Maurya P, Ravikumar S, Gupta N, Kushawaha AK, Sah RK, Chaurasiya A, Singhal J, Singh N, Kaushik S, Prasad TSK, Pati S, Ranganathan A, Singh S. Complementary crosstalk between palmitoylation and phosphorylation events in MTIP regulates its role during Plasmodium falciparum invasion. Front Cell Infect Microbiol 2022; 12:924424. [PMID: 36250062 PMCID: PMC9556994 DOI: 10.3389/fcimb.2022.924424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/10/2022] [Indexed: 11/19/2022] Open
Abstract
Post-translational modifications (PTMs) including phosphorylation and palmitoylation have emerged as crucial biomolecular events that govern many cellular processes including functioning of motility- and invasion-associated proteins during Plasmodium falciparum invasion. However, no study has ever focused on understanding the possibility of a crosstalk between these two molecular events and its direct impact on preinvasion- and invasion-associated protein–protein interaction (PPI) network-based molecular machinery. Here, we used an integrated in silico analysis to enrich two different catalogues of proteins: (i) the first group defines the cumulative pool of phosphorylated and palmitoylated proteins, and (ii) the second group represents a common set of proteins predicted to have both phosphorylation and palmitoylation. Subsequent PPI analysis identified an important protein cluster comprising myosin A tail interacting protein (MTIP) as one of the hub proteins of the glideosome motor complex in P. falciparum, predicted to have dual modification with the possibility of a crosstalk between the same. Our findings suggested that blocking palmitoylation led to reduced phosphorylation and blocking phosphorylation led to abrogated palmitoylation of MTIP. As a result of the crosstalk between these biomolecular events, MTIP’s interaction with myosin A was found to be abrogated. Next, the crosstalk between phosphorylation and palmitoylation was confirmed at a global proteome level by click chemistry and the phenotypic effect of this crosstalk was observed via synergistic inhibition in P. falciparum invasion using checkerboard assay and isobologram method. Overall, our findings revealed, for the first time, an interdependence between two PTM types, their possible crosstalk, and its direct impact on MTIP-mediated invasion via glideosome assembly protein myosin A in P. falciparum. These insights can be exploited for futuristic drug discovery platforms targeting parasite molecular machinery for developing novel antimalarial therapeutics.
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Affiliation(s)
- Zille Anam
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Geeta Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Soumyadeep Mukherjee
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | | | - Shreeja Biswas
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Preeti Maurya
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Susendaran Ravikumar
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Nutan Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | | | - Raj Kumar Sah
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Ayushi Chaurasiya
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Jhalak Singhal
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Niharika Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shikha Kaushik
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Soumya Pati
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
- *Correspondence: Shailja Singh, ; Anand Ranganathan, ; Soumya Pati,
| | - Anand Ranganathan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Shailja Singh, ; Anand Ranganathan, ; Soumya Pati,
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Shailja Singh, ; Anand Ranganathan, ; Soumya Pati,
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21
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Rex DAB, Vaid N, Deepak K, Dagamajalu S, Prasad TSK. A comprehensive review on current understanding of bradykinin in COVID-19 and inflammatory diseases. Mol Biol Rep 2022; 49:9915-9927. [PMID: 35596055 PMCID: PMC9122735 DOI: 10.1007/s11033-022-07539-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/28/2022] [Indexed: 12/28/2022]
Abstract
Bradykinin, a member of the kallikrein–kinin system (KKS), is a potent, short-lived vasoactive peptide that acts as a vasodilator and an inflammatory mediator in a number of signaling mechanisms. Bradykinin induced signaling is mediated through kinin B1 (BDKRB1) and B2 (BDKRB2) transmembrane receptors coupled with different subunits of G proteins (Gαi/Gα0, Gαq and Gβ1γ2). The bradykinin-mediated signaling mechanism activates excessive pro-inflammatory cytokines, including IL-6, IL-1β, IL-8 and IL-2. Upregulation of these cytokines has implications in a wide range of clinical conditions such as inflammation leading to fibrosis, cardiovascular diseases, and most recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In SARS-CoV-2 infection, bradykinin is found to be at raised levels and is reported to trigger a diverse array of symptoms. All of this brings bradykinin to the core point as a molecule of immense therapeutic value. Our understanding of its involvement in various pathways has expanded with time. Therefore, there is a need to look at the overall picture that emerges from the developments made by deciphering the bradykinin mediated signaling mechanisms involved in the pathological conditions. It will help devise strategies for developing better treatment modalities in the implicated diseases. This review summarizes the current state of knowledge on bradykinin mediated signaling in the diverse conditions described above, with a marked emphasis on the therapeutic potential of targeting the bradykinin receptor.
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Affiliation(s)
- Devasahayam Arokiar Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Neelanchal Vaid
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - K Deepak
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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22
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Najar MA, Arefian M, Sidransky D, Gowda H, Prasad TSK, Modi PK, Chatterjee A. Tyrosine Phosphorylation Profiling Revealed the Signaling Network Characteristics of CAMKK2 in Gastric Adenocarcinoma. Front Genet 2022; 13:854764. [PMID: 35646067 PMCID: PMC9136244 DOI: 10.3389/fgene.2022.854764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) is a serine/threonine protein kinase which functions via the calcium-triggered signaling cascade with CAMK1, CAMK4, and AMPKα as the immediate downstream substrates. CAMKK2 is reported to be overexpressed in gastric cancer; however, its signaling mechanism is poorly understood. We carried out label-free quantitative tyrosine phosphoproteomics to investigate tyrosine-mediated molecular signaling associated with CAMKK2 in gastric cancer cells. Using a high-resolution Orbitrap Fusion Tribrid Fourier-transform mass spectrometer, we identified 350 phosphotyrosine sites mapping to 157 proteins. We observed significant alterations in 81 phosphopeptides corresponding to 63 proteins upon inhibition of CAMKK2, among which 16 peptides were hyperphosphorylated corresponding to 13 proteins and 65 peptides were hypophosphorylated corresponding to 51 proteins. We report here that the inhibition of CAMKK2 leads to changes in the phosphorylation of several tyrosine kinases such as PKP2, PTK2, EPHA1, EPHA2, PRKCD, MAPK12, among others. Pathway analyses revealed that proteins are differentially phosphorylated in response to CAMKK2 inhibition involved in focal adhesions, actin cytoskeleton, axon guidance, and signaling by VEGF. The western blot analysis upon inhibition and/or silencing of CAMKK2 revealed a decrease in phosphorylation of PTK2 at Y925, c-JUN at S73, and STAT3 at Y705, which was in concordance with the mass spectrometry data. The study indicates that inhibition of CAMKK2 has an anti-oncogenic effect in gastric cells regulating phosphorylation of STAT3 through PTK2/c-JUN in gastric cancer.
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Affiliation(s)
- Mohd. Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - David Sidransky
- Department of Oncology and Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
- *Correspondence: Prashant Kumar Modi, ; Aditi Chatterjee,
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- *Correspondence: Prashant Kumar Modi, ; Aditi Chatterjee,
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23
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Maurya R, Tripathi A, Kumar M, Antil N, Yamaryo‐Botté Y, Kumar P, Bansal P, Doerig C, Botté CY, Prasad TSK, Sharma P. PI4-kinase and PfCDPK7 signaling regulate phospholipid biosynthesis in Plasmodium falciparum. EMBO Rep 2022; 23:e54022. [PMID: 34866326 PMCID: PMC8811644 DOI: 10.15252/embr.202154022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/11/2021] [Indexed: 02/05/2023] Open
Abstract
PfCDPK7 is an atypical member of the calcium-dependent protein kinase (CDPK) family and is crucial for the development of Plasmodium falciparum. However, the mechanisms whereby PfCDPK7 regulates parasite development remain unknown. Here, we perform quantitative phosphoproteomics and phospholipid analysis and find that PfCDPK7 promotes phosphatidylcholine (PC) synthesis by regulating two key enzymes involved in PC synthesis, phosphoethanolamine-N-methyltransferase (PMT) and ethanolamine kinase (EK). In the absence of PfCDPK7, both enzymes are hypophosphorylated and PMT is degraded. We further find that PfCDPK7 interacts with 4'-phosphorylated phosphoinositides (PIPs) generated by PI4-kinase. Inhibition of PI4K activity disrupts the vesicular localization PfCDPK7. P. falciparum PI4-kinase, PfPI4K is a prominent drug target and one of its inhibitors, MMV39048, has reached Phase I clinical trials. Using this inhibitor, we demonstrate that PfPI4K controls phospholipid biosynthesis and may act in part by regulating PfCDPK7 localization and activity. These studies not only unravel a signaling pathway involving PfPI4K/4'-PIPs and PfCDPK7 but also provide novel insights into the mechanism of action of a promising series of candidate anti-malarial drugs.
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Affiliation(s)
- Ranjana Maurya
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Anuj Tripathi
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Manish Kumar
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
- Institute of BioinformaticsInternational Tech ParkBangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Neelam Antil
- Institute of BioinformaticsInternational Tech ParkBangaloreIndia
- ApicoLipid TeamInstitute of Advanced BiosciencesCNRS UMR5309Université Grenoble AlpesINSERM U1209GrenobleFrance
- Amrita School of BiotechnologyAmrita Vishwa VidyapeethamKollamIndia
| | - Yoshiki Yamaryo‐Botté
- Center for Systems Biology and Molecular MedicineYenepoya Research CentreYenepoya (Deemed to be University)MangaloreIndia
| | - Praveen Kumar
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Priyanka Bansal
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Christian Doerig
- NIMHANS IOB Proteomics and Bioinformatics LaboratoryNeurobiology Research CentreNational Institute of Mental Health and Neuro SciencesBangaloreIndia
| | - Cyrille Y Botté
- Center for Systems Biology and Molecular MedicineYenepoya Research CentreYenepoya (Deemed to be University)MangaloreIndia
| | - T S Keshava Prasad
- Institute of BioinformaticsInternational Tech ParkBangaloreIndia
- Amrita School of BiotechnologyAmrita Vishwa VidyapeethamKollamIndia
- School of Health and Biomedical SciencesRMIT UniversityBundooraVic.Australia
| | - Pushkar Sharma
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
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24
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Dasgupta M, Kumaresan A, Saraf KK, Nag P, Sinha MK, Aslam M. K. M, Karthikkeyan G, Prasad TSK, Modi PK, Datta TK, Ramesha K, Manimaran A, Jeyakumar S. Deep Metabolomic Profiling Reveals Alterations in Fatty Acid Synthesis and Ketone Body Degradations in Spermatozoa and Seminal Plasma of Astheno-Oligozoospermic Bulls. Front Vet Sci 2022; 8:755560. [PMID: 35087889 PMCID: PMC8787163 DOI: 10.3389/fvets.2021.755560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022] Open
Abstract
Male fertility is extremely important in dairy animals because semen from a single bull is used to inseminate several thousand females. Asthenozoospermia (reduced sperm motility) and oligozoospermia (reduced sperm concentration) are the two important reasons cited for idiopathic infertility in crossbred bulls; however, the etiology remains elusive. In this study, using a non-targeted liquid chromatography with tandem mass spectrometry-based approach, we carried out a deep metabolomic analysis of spermatozoa and seminal plasma derived from normozoospermic and astheno-oligozoospermic bulls. Using bioinformatics tools, alterations in metabolites and metabolic pathways between normozoospermia and astheno-oligozoospermia were elucidated. A total of 299 and 167 metabolites in spermatozoa and 183 and 147 metabolites in seminal plasma were detected in astheno-oligozoospermic and normozoospermic bulls, respectively. Among the mapped metabolites, 75 sperm metabolites were common to both the groups, whereas 166 and 50 sperm metabolites were unique to astheno-oligozoospermic and normozoospermic bulls, respectively. Similarly, 86 metabolites were common to both the groups, whereas 45 and 37 seminal plasma metabolites were unique to astheno-oligozoospermic and normozoospermic bulls, respectively. Among the differentially expressed metabolites, 62 sperm metabolites and 56 seminal plasma metabolites were significantly dysregulated in astheno-oligozoospermic bulls. In spermatozoa, selenocysteine, deoxyuridine triphosphate, and nitroprusside showed significant enrichment in astheno-oligozoospermic bulls. In seminal plasma, malonic acid, 5-diphosphoinositol pentakisphosphate, D-cysteine, and nicotinamide adenine dinucleotide phosphate were significantly upregulated, whereas tetradecanoyl-CoA was significantly downregulated in the astheno-oligozoospermia. Spermatozoa from astheno-oligozoospermic bulls showed alterations in the metabolism of fatty acid and fatty acid elongation in mitochondria pathways, whereas seminal plasma from astheno-oligozoospermic bulls showed alterations in synthesis and degradation of ketone bodies, pyruvate metabolism, and inositol phosphate metabolism pathways. The present study revealed vital information related to semen metabolomic differences between astheno-oligozoospermic and normospermic crossbred breeding bulls. It is inferred that fatty acid synthesis and ketone body degradations are altered in the spermatozoa and seminal plasma of astheno-oligozoospermic crossbred bulls. These results open up new avenues for further research, and current findings can be applied for the modulation of identified pathways to restore sperm motility and concentration in astheno-oligozoospermic bulls.
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Affiliation(s)
- Mohua Dasgupta
- Theriogenology Laboratory, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Arumugam Kumaresan
- Theriogenology Laboratory, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Kaustubh Kishor Saraf
- Theriogenology Laboratory, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Pradeep Nag
- Theriogenology Laboratory, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Manish Kumar Sinha
- Theriogenology Laboratory, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Muhammad Aslam M. K.
- Base Farm, Kerala Veterinary and Animal Sciences University, Kolahalamedu, India
| | - Gayathree Karthikkeyan
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - T. S. Keshava Prasad
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Tirtha Kumar Datta
- Animal Genomics Laboratory, Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Karnal, India
| | - Kerekoppa Ramesha
- Dairy Production Section, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Ayyasamy Manimaran
- Dairy Production Section, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
| | - Sakthivel Jeyakumar
- Dairy Production Section, Southern Regional Station of Indian Council of Agricultural Research (ICAR)—National Dairy Research Institute, Bengaluru, India
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25
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Rex DAB, Dagamajalu S, Kandasamy RK, Raju R, Prasad TSK. SARS-CoV-2 signaling pathway map: A functional landscape of molecular mechanisms in COVID-19. J Cell Commun Signal 2021; 15:601-608. [PMID: 34181169 PMCID: PMC8237035 DOI: 10.1007/s12079-021-00632-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 12/27/2022] Open
Abstract
Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has been declared a pandemic by WHO. The clinical manifestation and disease progression in COVID-19 patients varies from minimal symptoms to severe respiratory issues with multiple organ failure. Understanding the mechanism of SARS-CoV-2 interaction with host cells will provide key insights into the effective molecular targets for the development of novel therapeutics. Recent studies have identified virus-mediated phosphorylation or activation of some major signaling pathways, such as ERK1/2, JNK, p38, PI3K/AKT and NF-κB signaling, that potentially elicit the cytokine storm that serves as a major cause of tissue injuries. Several studies highlight the aggressive inflammatory response particularly 'cytokine storm' in SARS-CoV-2 patients. A depiction of host molecular dynamics triggered by SARS-CoV-2 in the form of a network of signaling molecules will be helpful for COVID-19 research. Therefore, we developed the signaling pathway map of SARS-CoV-2 infection using data mined from the recently published literature. This integrated signaling pathway map of SARS-CoV-2 consists of 326 proteins and 73 reactions. These include information pertaining to 1,629 molecular association events, 30 enzyme catalysis events, 43 activation/inhibition events, and 8,531 gene regulation events. The pathway map is publicly available through WikiPathways: https://www.wikipathways.org/index.php/Pathway:WP5115 .
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Affiliation(s)
- D. A. B. Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018 India
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26
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Gopalakrishnan L, Chatterjee O, Ravishankar N, Suresh S, Raju R, Mahadevan A, Prasad TSK. Opioid receptors signaling network. J Cell Commun Signal 2021; 16:475-483. [PMID: 34724150 DOI: 10.1007/s12079-021-00653-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022] Open
Abstract
Opioid receptors belong to the class A G-protein-coupled receptors and are activated by alkaloid opiates such as morphine, and endogenous ligands such as endorphins and enkephalins. Opioid receptors are widely distributed in the human body and are involved in numerous physiological processes through three major classical opioid receptor subtypes; the mu, delta and kappa along with a lesser characterized subtype, opioid receptor-like (ORL1). Opioids are the most potent analgesics and have been extensively used as a therapeutic drug for the treatment of pain and related disorders. Chronic administration of clinically used opioids is associated with adverse effects such as drug tolerance, addiction and constipation. Several investigations attempted to identify the molecular signaling networks associated with endogenous as well as synthetic opiates, however, there is a paucity of a cumulative depiction of these signaling events. Here, we report a systemic collection of downstream molecules pertaining to four subtypes of opioid receptors (MOR, KOR, DOR and ORL1) in the form of a signaling pathway map. We manually curated reactions induced by the activation of opioid receptors from the literature into five categories- molecular association, activation/inhibition, catalysis, transport, and gene regulation. This led to a dataset of 180 molecules, which is collectively represented in the opioid receptor signaling network following NetPath criteria. We believe that the public availability of an opioid receptor signaling pathway map can accelerate biomedical research in this area because of its high therapeutic significance. The opioid receptors signaling pathway map is uploaded to a freely available web resource, WikiPathways enabling ease of access ( https://www.wikipathways.org/index.php/Pathway:WP5093 ).
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Affiliation(s)
- Lathika Gopalakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore, 560 066, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576 104, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575 018, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, 560 066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575 018, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, India
| | - Namitha Ravishankar
- Institute of Bioinformatics, International Tech Park, Bangalore, 560 066, India
| | - Sneha Suresh
- Institute of Bioinformatics, International Tech Park, Bangalore, 560 066, India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575 018, India.
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, 560 029, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Neurobiology Research Centre, Bangalore, 560 029, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575 018, India.
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27
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Rex DAB, Deepak K, Vaid N, Dagamajalu S, Kandasamy RK, Flo TH, Keshava Prasad TS. A modular map of Bradykinin-mediated inflammatory signaling network. J Cell Commun Signal 2021; 16:301-310. [PMID: 34714516 PMCID: PMC8554507 DOI: 10.1007/s12079-021-00652-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/03/2021] [Indexed: 12/15/2022] Open
Abstract
Bradykinin, a member of the kallikrein-kinin system (KKS), is associated with an inflammatory response pathway with diverse vascular permeability functions, including thrombosis and blood coagulation. In majority, bradykinin signals through Bradykinin Receptor B2 (B2R). B2R is a G protein-coupled receptor (GPCR) coupled to G protein family such as Gαqs, Gαq/Gα11, Gαi1, and Gβ1γ2. B2R stimulation leads to the activation of a signaling cascade of downstream molecules such as phospholipases, protein kinase C, Ras/Raf-1/MAPK, and PI3K/AKT and secondary messengers such as inositol-1,4,5-trisphosphate, diacylglycerol and Ca2+ ions. These secondary messengers modulate the production of nitric oxide or prostaglandins. Bradykinin-mediated signaling is implicated in inflammation, chronic pain, vasculopathy, neuropathy, obesity, diabetes, and cancer. Despite the biomedical importance of bradykinin, a resource of bradykinin-mediated signaling pathway is currently not available. Here, we developed a pathway resource of signaling events mediated by bradykinin. By employing data mining strategies in the published literature, we describe an integrated pathway reaction map of bradykinin consisting of 233 reactions. Bradykinin signaling pathway events included 25 enzyme catalysis reactions, 12 translocations, 83 activation/inhibition reactions, 11 molecular associations, 45 protein expression and 57 gene regulation events. The pathway map is made publicly available on the WikiPathways Database with the ID URL: https://www.wikipathways.org/index.php/Pathway:WP5132. The bradykinin-mediated signaling pathway map will facilitate the identification of novel candidates as therapeutic targets for diseases associated with dysregulated bradykinin signaling.
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Affiliation(s)
- D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - K Deepak
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Neelanchal Vaid
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - Richard Kumaran Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491, Trondheim, Norway.,College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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28
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Solanki HS, Raja R, Zhavoronkov A, Ozerov IV, Artemov AV, Advani J, Radhakrishnan A, Babu N, Puttamallesh VN, Syed N, Nanjappa V, Subbannayya T, Sahasrabuddhe NA, Patil AH, Prasad TSK, Gaykalova D, Chang X, Sathyendran R, Mathur PP, Rangarajan A, Sidransky D, Pandey A, Izumchenko E, Gowda H, Chatterjee A. Correction: Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor. Oncoscience 2021; 8:108-109. [PMID: 34589558 PMCID: PMC8460121 DOI: 10.18632/oncoscience.546] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Hitendra S Solanki
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha 751024, India.,These authors contributed equally to the manuscript
| | - Remya Raja
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,These authors contributed equally to the manuscript
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD 21218, USA
| | - Ivan V Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD 21218, USA
| | - Artem V Artemov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD 21218, USA
| | - Jayshree Advani
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | | | - Niraj Babu
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,School of Biotechnology, Amrita University, Kollam 690525, India
| | - Nazia Syed
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | | | | | | | - Arun H Patil
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha 751024, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Daria Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Xiaofei Chang
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rachana Sathyendran
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Premendu Prakash Mathur
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha 751024, India
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - 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 Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
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29
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DasGupta M, Kumaresan A, Saraf KK, Paul N, Sajeevkumar T, Karthikkeyan G, Prasad TSK, Modi PK, Ramesha K, Manimaran A, Jeyakumar S. Deciphering metabolomic alterations in seminal plasma of crossbred (Bos taurus X Bos indicus) bulls through comparative deep metabolomic analysis. Andrologia 2021; 54:e14253. [PMID: 34549825 DOI: 10.1111/and.14253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/14/2021] [Accepted: 09/13/2021] [Indexed: 12/31/2022] Open
Abstract
The incidence of sub-fertility is higher in crossbred bulls compared to zebu bulls. In the present study, we analysed the metabolomic profile of seminal plasma from crossbred and zebu bulls and uncovered differentially expressed metabolites between these two breeds. Using a high-throughput LC-MS/MS-based approach, we identified 990 and 1,002 metabolites in crossbred and zebu bull seminal plasma respectively. After excluding the exogenous metabolites, we found that 50 and 68 putative metabolites were unique to crossbred and zebu bull seminal plasma, respectively, whilst 87 metabolites were common to both. After data normalisation, 63 metabolites were found to be dysregulated between crossbred and zebu bull seminal plasma. Observed pathways included Linoleic acid metabolism (observed metabolite was phosphatidylcholine) in crossbred bull seminal plasma whereas inositol phosphate metabolism (observed metabolites were phosphatidylinositol-3,4,5-trisphosphate/inositol 1,3,4,5,6-pentakisphosphate/myo-inositol hexakisphosphate) was observed in zebu bull seminal plasma. Abundance of Tetradecanoyl-CoA was significantly higher, whilst abundance of Taurine was significantly lower in crossbred bull seminal plasma. In conclusion, the present study established the seminal plasma metabolomic profile in crossbred and zebu bulls and suggest that increased lipid peroxidation coupled with low concentrations of antioxidants in seminal plasma might be associated with high incidence of sub-fertility in crossbred bulls.
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Affiliation(s)
- Mohua DasGupta
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Arumugam Kumaresan
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Kaustubh Kishor Saraf
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Nilendu Paul
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | | | - Gayathree Karthikkeyan
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - T S Keshava Prasad
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Kerekoppa Ramesha
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Ayyasamy Manimaran
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Sakthivel Jeyakumar
- Dairy Production Section, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
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30
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Najar MA, Aravind A, Dagamajalu S, Sidransky D, Ashktorab H, Smoot DT, Gowda H, Prasad TSK, Modi PK, Chatterjee A. Hyperactivation of MEK/ERK pathway by Ca 2+ /calmodulin-dependent protein kinase kinase 2 promotes cellular proliferation by activating cyclin-dependent kinases and minichromosome maintenance protein in gastric cancer cells. Mol Carcinog 2021; 60:769-783. [PMID: 34437731 DOI: 10.1002/mc.23343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023]
Abstract
Although CAMKK2 is overexpressed in several cancers, its role and relevant downstream signaling pathways in gastric cancer (GC) are poorly understood. Treatment of AGS GC cells with a CAMKK2 inhibitor, STO-609, resulted in decreased cell proliferation, cell migration, invasion, colony-forming ability, and G1/S-phase arrest. Quantitative phosphoproteomics in AGS cells with the CAMKK2 inhibitor led to the identification of 9603 unique phosphosites mapping to 3120 proteins. We observed decreased phosphorylation of 1101 phosphopeptides (1.5-fold) corresponding to 752 proteins upon CAMKK2 inhibition. Bioinformatics analysis of hypo-phosphorylated proteins revealed enrichment of MAPK1/MAPK3 signaling. Kinase enrichment analysis of hypo-phosphorylated proteins using the X2K Web tool identified ERK1, cyclin-dependant kinase 1 (CDK1), and CDK2 as downstream substrates of CAMKK2. Moreover, inhibition of CAMKK2 and MEK1 resulted in decreased phosphorylation of ERK1, CDK1, MCM2, and MCM3. Immunofluorescence results were in concordance with our mass spectroscopy data and Western blot analysis results. Taken together, our data reveal the essential role of CAMKK2 in the pathobiology of GC through the activation of the MEK/ERK1 signaling cascade.
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Affiliation(s)
- Mohd A Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, District of Columbia, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical Center, Nashville, Tennessee, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant K Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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31
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Dagamajalu S, Rex DAB, Suchitha GP, Rai AB, Rainey JK, Prasad TSK. The network map of Elabela signaling pathway in physiological and pathological conditions. J Cell Commun Signal 2021; 16:145-154. [PMID: 34339006 DOI: 10.1007/s12079-021-00640-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Elabela (ELA; also called Apela and Toddler) is one of the recently discovered ligand among the two endogenous peptide ligands (Apelin and Elabela) of the apelin receptor (APLNR, also known as APJ). Elabela-induced signaling plays a crucial role in diverse biological processes, including formation of the embryonic cardiovascular system and early placental development by reducing the chances of occurrence of preeclampsia during pregnancy. It also plays the major role in the renoprotection by reducing kidney injury and the inflammatory response and regulation of gene expression associated with heart failure and fibrosis. Elabela may be processed into different active peptides, each of which binds to APLNR and predominantly activates the signals through PI3K/AKT pathway. Owing to its biomedical importance, we developed a consolidated signaling map of Elabela, in accordance with the NetPath criteria. The presented Elabela signaling map comprises 12 activation/inhibition events, 15 catalysis events, 1 molecular association, 34 gene regulation events and 32 protein expression events. The Elabela signaling pathway map is freely made available through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5100 ).
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Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - G P Suchitha
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Akhila B Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Jan K Rainey
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and School of Biomedical Engineering, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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32
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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33
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Sivagurunathan S, Selvan LDN, Khan AA, Parameswaran S, Bhattacharjee H, Gogoi K, Gowda H, Keshava Prasad TS, Pandey A, Kumar SA, Rishi P, Rishi E, Ratra D, Bhende M, Janakiraman N, Biswas J, Krishnakumar S. Proteomics-based approach for differentiation of age-related macular degeneration sub-types. Indian J Ophthalmol 2021; 69:647-654. [PMID: 33595494 PMCID: PMC7942106 DOI: 10.4103/ijo.ijo_470_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purpose: Age-related macular degeneration (AMD) is one of the leading causes of irreversible central vision loss in the elderly population. The current study aims to find non-invasive prognostic biomarkers in the urine specimens of the AMD patients. Methods: Peripheral blood and urine samples were collected from 23 controls and 61 AMD patients. Genomic DNA was extracted from the buffy coat of peripheral blood. Allele specific PCR was used to assay SNPs in complement factor H (CFH), complement component 3 (C3). Comparative proteomic analysis of urine samples from early AMD, choroidal neovascular membrane (CNVM), geographic atrophy (GA), and healthy controls was performed using isobaric labelling followed by mass spectrometry. Validation was performed using enzyme-linked immunosorbent assay (ELISA). Results: Comparative proteomic analysis of urine samples identified 751 proteins, of which 383 proteins were found to be differentially expressed in various groups of AMD patients. Gene ontology classification of differentially expressed proteins revealed the majority of them were involved in catalytic functions and binding activities. Pathway analysis showed cell adhesion molecule pathways (CAMs), Complement and coagulation cascades, to be significantly deregulated in AMD. Upon validation by ELISA, SERPINA-1 (Alpha1 antitrypsin), TIMP-1 (Tissue inhibitor of matrix metaloprotease-1), APOA-1 (Apolipoprotein A-1) were significantly over-expressed in AMD (n = 61) patients compared to controls (n = 23). A logistic model of APOA-1 in combination with CFH and C3 polymorphisms predicted the risk of developing AMD with 82% accuracy. Conclusion: This study gives us a preliminary data on non-invasive predictive biomarkers for AMD, which can be further validated in a large cohort and translated for diagnostic use.
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Affiliation(s)
- Sivapriya Sivagurunathan
- L&T Opthalmic Pathology, Vision Research Foundation, Sankara Nethralaya; Centre for Biotechnology, Anna University, Chennai, India
| | | | - Aafaque Ahmad Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sowmya Parameswaran
- Radheshyam Kanoi Stem Cell Laboratory, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | | | - Krishna Gogoi
- Sri Sankaradeva Nethralaya, Beltola, Guwahati, Assam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - S Ashok Kumar
- Centre for Biotechnology, Anna University, Chennai, India
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, India
| | - Ekta Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, India
| | - Dhanashree Ratra
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, India
| | - Muna Bhende
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, India
| | - Narayanan Janakiraman
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Jyotirmay Biswas
- L&T Opthalmic Pathology, Vision Research Foundation; Department of Uvea, Sankara Nethralaya, Chennai, India
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Najar MA, Modi PK, Ramesh P, Sidransky D, Gowda H, Prasad TSK, Chatterjee A. Molecular Profiling Associated with Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2)-Mediated Carcinogenesis in Gastric Cancer. J Proteome Res 2021; 20:2687-2703. [PMID: 33844560 DOI: 10.1021/acs.jproteome.1c00008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gastric cancer is the fifth most common cancer and the third leading cause of cancer-related death worldwide. We showed previously that calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2), a serine-threonine kinase, is highly expressed in gastric cancer and leads to progression. In the present study, we identified the molecular networks involved in CAMKK2-mediated progression of gastric adenocarcinoma. Treatment of gastric cancer cell lines with a CAMKK2 inhibitor, STO-609, resulted in decreased cell migration, invasion, and colony-forming ability and a G1/S-phase arrest. In addition, tandem mass tag (TMT)-based quantitative proteomic analysis resulted in the identification of 7609 proteins, of which 219 proteins were found to be overexpressed and 718 downregulated (1.5-fold). Our data identified several key downregulated proteins involved in cell division and cell proliferation, which included DNA replication licensing factors, replication factor C, origin recognition complex, replication protein A and GINS, and mesenchymal markers, upon CAMKK2 inhibition. Immunoblotting and immunofluorescence results showed concordance with our mass spectroscopy data. Taken together, our study supports CAMKK2 as a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
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Mohanty V, Subbannayya Y, Patil S, Puttamallesh VN, Najar MA, Datta KK, Pinto SM, Begum S, Mohanty N, Routray S, Abdulla R, Ray JG, Sidransky D, Gowda H, Prasad TSK, Chatterjee A. Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue. J Cell Commun Signal 2021; 15:447-459. [PMID: 33683571 DOI: 10.1007/s12079-021-00609-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
Loss of cell differentiation is a hallmark for the progression of oral squamous cell carcinoma (OSCC). Archival Formalin-Fixed Paraffin-Embedded (FFPE) tissues constitute a valuable resource for studying the differentiation of OSCC and can offer valuable insights into the process of tumor progression. In the current study, we performed LC-MS/MS-based quantitative proteomics of FFPE specimens from pathologically-confirmed well-differentiated, moderately-differentiated, and poorly-differentiated OSCC cases. The data were analyzed in four technical replicates, resulting in the identification of 2376 proteins. Of these, 141 and 109 were differentially expressed in moderately-differentiated and poorly differentiated OSCC cases, respectively, compared to well-differentiated OSCC. The data revealed significant metabolic reprogramming with respect to lipid metabolism and glycolysis with proteins belonging to both these processes downregulated in moderately-differentiated OSCC when compared to well-differentiated OSCC. Signaling pathway analysis indicated the alteration of extracellular matrix organization, muscle contraction, and glucose metabolism pathways across tumor grades. The extracellular matrix organization pathway was upregulated in moderately-differentiated OSCC and downregulated in poorly differentiated OSCC, compared to well-differentiated OSCC. PADI4, an epigenetic enzyme transcriptional regulator, and its transcriptional target HIST1H1B were both found to be upregulated in moderately differentiated and poorly differentiated OSCC, indicating epigenetic events underlying tumor differentiation. In conclusion, the findings support the advantage of using high-resolution mass spectrometry-based FFPE archival blocks for clinical and translational research. The candidate signaling pathways identified in the study could be used to develop potential therapeutic targets for OSCC.
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Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Shankargouda Patil
- Division of Oral Pathology, College of Dentistry, Department of Maxillofacial Surgery and Diagnostic Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Keshava K Datta
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Sameera Begum
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Neeta Mohanty
- Department of Oral Pathology & Microbiology, Institute of Dental Sciences, Siksha'O'Anusandhan University, Bhubaneswar, Odisha, 751003, India
| | - Samapika Routray
- Department of Oral Pathology & Microbiology, Institute of Dental Sciences, Siksha'O'Anusandhan University, Bhubaneswar, Odisha, 751003, India.,Department of Dental Surgery, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India
| | - Riaz Abdulla
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R. Ahmed Dental College & Hospital, Kolkata, West Bengal, 700 014, India.,Department of Pathology, Burdwan Dental College and Hospital, Burdwan, West Bengal, 713101, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, 21231, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India. .,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India. .,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Bansal P, Antil N, Kumar M, Yamaryo-Botté Y, Rawat RS, Pinto S, Datta KK, Katris NJ, Botté CY, Prasad TSK, Sharma P. Protein kinase TgCDPK7 regulates vesicular trafficking and phospholipid synthesis in Toxoplasma gondii. PLoS Pathog 2021; 17:e1009325. [PMID: 33635921 PMCID: PMC7909640 DOI: 10.1371/journal.ppat.1009325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/20/2021] [Indexed: 02/06/2023] Open
Abstract
Apicomplexan parasites are causative agents of major human diseases. Calcium Dependent Protein Kinases (CDPKs) are crucial components for the intracellular development of apicomplexan parasites and are thus considered attractive drug targets. CDPK7 is an atypical member of this family, which initial characterization suggested to be critical for intracellular development of both Apicomplexa Plasmodium falciparum and Toxoplasma gondii. However, the mechanisms via which it regulates parasite replication have remained unknown. We performed quantitative phosphoproteomics of T. gondii lacking TgCDPK7 to identify its parasitic targets. Our analysis lead to the identification of several putative TgCDPK7 substrates implicated in critical processes like phospholipid (PL) synthesis and vesicular trafficking. Strikingly, phosphorylation of TgRab11a via TgCDPK7 was critical for parasite intracellular development and protein trafficking. Lipidomic analysis combined with biochemical and cellular studies confirmed that TgCDPK7 regulates phosphatidylethanolamine (PE) levels in T. gondii. These studies provide novel insights into the regulation of these processes that are critical for parasite development by TgCDPK7. In this study, we demonstrate that protein kinase TgCDPK7 regulates cellular processes like vesicular trafficking and the synthesis of phospholipids, which are critical for the development of the parasite Toxoplasma gondii. It regulates the localization of a small GTPase TgRab11a by phosphorylating it at a specific site, which is critical for trafficking of important parasite proteins and is important for parasite division. TgCDPK7 may regulate key enzymes involved biogenesis of phosphatidylethanolamine, which may contribute to the synthesis of this important phospholipid. These and other studies shed light on a novel signaling pathway in apicomplexan parasite Toxoplasma gondii.
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Affiliation(s)
- Priyanka Bansal
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
| | - Neelam Antil
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Manish Kumar
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team, Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Rahul Singh Rawat
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
| | - Sneha Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Keshava K. Datta
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Nicholas J. Katris
- ApicoLipid Team, Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Cyrille Y. Botté
- ApicoLipid Team, Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- NIMHANS IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka, India
| | - Pushkar Sharma
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
- * E-mail:
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Ashokan M, Ramesha KP, Hallur S, Karthikkeyan G, Rana E, Azharuddin N, Raj SR, Jeyakumar S, Kumaresan A, Kataktalware MA, Das DN, Keshava Prasad TS. Differences in milk metabolites in Malnad Gidda (Bos indicus) cows reared under pasture-based feeding system. Sci Rep 2021; 11:2831. [PMID: 33531582 PMCID: PMC7854684 DOI: 10.1038/s41598-021-82412-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
The milk and milk products from cows reared under grazing system are believed to be healthier and hence have high demand compared to milk from cows reared in the non-grazing system. However, the effect of grazing on milk metabolites, specifically lipids has not been fully understood. In this study, we used acetonitrile precipitation and methanol:chloroform methods for extracting the milk metabolites followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) run to identify the different metabolites between the milk of grazing and non-grazing early lactating Malnad Gidda cows. Various carbohydrates, amino acids, nucleosides and vitamin derivatives were found to be differentially abundant in grazing cows. A total of 35 metabolites were differentially regulated (fold change above 1.5) between the two groups. Tyrosyl-threonine, histidinyl-cysteine, 1-methyladenine, L-cysteine and selenocysteine showed fold change above 3 in grazing cows. The lipid profile of milk showed a lesser difference between grazing and non-grazing cows as compared to polar metabolites. To the best of our knowledge, this is the largest inventory of milk metabolomics data of an Indian cattle (Bos indicus) breed. We believe that our study would help to emerge a field of Nutri-metabolomics and veterinary omics research.
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Affiliation(s)
- M. Ashokan
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - Kerekoppa P. Ramesha
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - Sweta Hallur
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018 India
| | - Gayathree Karthikkeyan
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018 India
| | - Ekta Rana
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - N. Azharuddin
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - S. Reshma Raj
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - S. Jeyakumar
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - A. Kumaresan
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - Mukund A. Kataktalware
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - D. N. Das
- grid.419332.e0000 0001 2114 9718Southern Regional Station, ICAR-National Dairy Research Institute, Adugodi, Bangalore, 560030 India
| | - T. S. Keshava Prasad
- grid.413027.30000 0004 1767 7704Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018 India
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DasGupta M, Kumaresan A, Saraf KK, Karthikkeyan G, Prasad TSK, Modi PK, Ramesha K, Jeyakumar S, Manimaran A. Preliminary comparative deep metabolomic analysis of spermatozoa from zebu and crossbred cattle suggests associations between metabolites, sperm quality and fertility. Reprod Fertil Dev 2021; 33:427-436. [DOI: 10.1071/rd20304] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
Poor semen quality and infertility/subfertility are more frequent in crossbred than zebu bulls. Using a high-throughput liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based approach, we established the preliminary metabolomic profile of crossbred and zebu bull spermatozoa (n=3 bulls each) and identified changes in sperm metabolomics between the two groups. In all, 1732 and 1240 metabolites were detected in zebu and crossbred bull spermatozoa respectively. After excluding exogenous metabolites, 115 and 87 metabolites were found to be unique to zebu and crossbred bull spermatozoa respectively whereas 71 metabolites were common to both. In the normalised data, 49 metabolites were found to be differentially expressed between zebu and crossbred bull spermatozoa. The significantly enriched (P<0.05) pathways in spermatozoa were taurine and hypotaurine metabolism (observed metabolites taurine and hypotaurine) in zebu and glycerophospholipid metabolism (observed metabolites phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine) in crossbred bulls. The abundance of nitroprusside (variable importance in projection (VIP) score >1.5) was downregulated, whereas that of l-cysteine, acetyl coenzyme A and 2′-deoxyribonucleoside 5′-diphosphate (VIP scores >1.0) was upregulated in crossbred bull spermatozoa. In conclusion, this study established the metabolomic profile of zebu and crossbred bull spermatozoa and suggests that aberrations in taurine, hypotaurine and glycerophospholipid metabolism may be associated with the higher incidence of infertility/subfertility in crossbred bulls.
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Mohanty V, Subbannayya Y, Patil S, Abdulla R, Ganesh MS, Pal A, Ray JG, Sidransky D, Gowda H, Prasad TSK, Chatterjee A. Molecular alterations in oral cancer between tobacco chewers and smokers using serum proteomics. Cancer Biomark 2021; 31:361-373. [PMID: 34024816 DOI: 10.3233/cbm-203077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Tobacco exposure (through smoking or chewing) is one of the predominant risk factors associated with the development of oral squamous cell carcinoma (OSCC). Despite the growing number of patients diagnosed with OSCC, there are few circulating biomarkers for identifying individuals at a higher risk of developing the disease. Successful identification of candidate molecular markers for risk assessment could aid in the early detection of oral lesions and potentially be used for community screening of high-risk populations. OBJECTIVE Identification of differentially expressed proteins in the serum of oral cancer patients which can serve as biomarkers for the diagnosis of the onset of oral cancer among tobacco users. METHODS We employed a tandem mass tag (TMT)-based quantitative proteomics approach to study alterations in the serum proteomes of OSCC patients based on their tobacco exposure habits (chewing and smoking) compared to healthy individuals with no history of using any form of tobacco or any symptoms of the disease. RESULTS Mass spectrometry-based analysis resulted in the identification of distinct signatures in the serum of OSCC patients who either chewed or smoked tobacco. Pathway analysis revealed opposing effects of dysregulated proteins enriched in the complement-coagulation signaling cascades with a high expression of the Serpin family of proteins observed in OSCC patients who chewed tobacco compared to healthy individuals whereas these proteins showed decreased levels in OSCC patients who smoked. ELISA-based validation further confirmed our findings revealing higher expression of SERPINA6 and SERPINF1 across serum of OSCC patients who chewed tobacco compared to healthy individuals. CONCLUSIONS This study serves as a benchmark for the identification of serum-based protein markers that may aid in the identification of high-risk patients who either chew tobacco or smoke tobacco.
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Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Shankargouda Patil
- Division of Oral Pathology, College of Dentistry, Department of Maxillofacial Surgery and Diagnostic Sciences, Jazan University, Jazan, Saudi Arabia
| | - Riaz Abdulla
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Mandakulutur S Ganesh
- Department of Surgical Oncology, Vydehi Institute of Oncology, Bangalore, Karnataka, India
| | - Arnab Pal
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R Ahmed Dental College and Hospital, Kolkata, West Bengal, India
- Department of Pathology, Burdwan Dental College and Hospital, Burdwan, West Bengal, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Institute of Bioinformatics, International Tech Park, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Institute of Bioinformatics, International Tech Park, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
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Dagamajalu S, Vijayakumar M, Shetty R, Rex DAB, Narayana Kotimoole C, Prasad TSK. Proteogenomic examination of esophageal squamous cell carcinoma (ESCC): new lines of inquiry. Expert Rev Proteomics 2020; 17:649-662. [PMID: 33151123 DOI: 10.1080/14789450.2020.1845146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Esophageal squamous cell carcinoma (ESCC), a histopathologic subtype of esophageal cancer is a major cause of cancer-related morbidity and mortality worldwide. This is primarily because patients are diagnosed at an advanced stage by the time symptoms appear. The genomics and mass spectrometry-based proteomics continue to provide important leads toward biomarker discovery for ESCC. However, such leads are yet to be translated into clinical utilities. Areas covered: We gathered information pertaining to proteomics and proteogenomics efforts in ESCC from the literature search until 2020. An overview of omics approaches to discover the candidate biomarkers for ESCC were highlighted. We present a summary of recent investigations of alterations in the level of gene and protein expression observed in biological samples including body fluids, tissue/biopsy and in vitro-based models. Expert opinion: A large number of protein-based biomarkers and therapeutic targets are being used in cancer therapy. Several candidates are being developed as diagnostics and prognostics for the management of cancers. High-resolution proteomic and proteogenomic approaches offer an efficient way to identify additional candidate biomarkers for diagnosis, monitoring of disease progression, prediction of response to chemo and radiotherapy. Some of these biomarkers can also be developed as therapeutic targets.
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Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
| | - Manavalan Vijayakumar
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University) , Mangalore, India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University) , Mangalore, India
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
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41
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Rajesh MK, Gangaraj KP, Prabhudas SK, Prasad TSK. The complete chloroplast genome data of Areca catechu (Arecaceae). Data Brief 2020; 33:106444. [PMID: 33195770 PMCID: PMC7644867 DOI: 10.1016/j.dib.2020.106444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
Areca is a genus comprising about 50 species endemic to the humid tropics. Arecanut (Areca catechu L.) is a commercially and economically important crop in South and Southeast Asia. In addition to its contribution to the agricultural economies of countries where the crop is grown, arecanut holds an important place in the religious, cultural, and social milieu of the rural folks. The nuts have been used since time immemorial in traditional Indian (Unani and Ayurveda) and Chinese herbal systems of medicine for the treatment of various disorders like rheumatism, parasitic infection, diseases of gastrointestinal tracts, and depression. Here, we report the complete chloroplast (cp) genome sequence of arecanut. The cp genome of A. catechu was a typical circular DNA molecule with a size of 158,689 bp in length. The genome possessed a typical quadripartite structure composed of a pair of inverted repeats (IRa and IRb) of 27,137 bp separated by a large single-copy (LSC) region of 86,814 bp and a small single-copy (SSC) region of 17,601 bp and a GC content of 37.3%. The cp genome of arecanut encodes a set of 133 genes, comprising 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes; among these, 21 contained introns. A total of 70 SSR loci were detected, the majority being in inter-genic regions. Phylogenetic analysis revealed that A. catechu was closely related to A. vestiaria.
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Affiliation(s)
- M K Rajesh
- ICAR-Central Plantation Crops Research Institute, Kasaragod 671124, Kerala, India
| | - K P Gangaraj
- ICAR-Central Plantation Crops Research Institute, Kasaragod 671124, Kerala, India
| | - Sudheesh K Prabhudas
- SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, Karnataka, India
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42
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Dey G, Mohanty AK, Sreenivasamurthy SK, Kumar M, Kumar A, Prasad TSK. Proteomics dataset of adult Anopheles Stephensi female brain. Data Brief 2020; 32:106243. [PMID: 32984457 PMCID: PMC7495016 DOI: 10.1016/j.dib.2020.106243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/11/2020] [Accepted: 08/25/2020] [Indexed: 11/27/2022] Open
Abstract
Mosquitoes with their ability to transmit several pathogens of human disease pose a serious threat to healthcare worldwide. Although much has been done to prevent the disease transmission by mosqitos. The rising rate of resistance in mosquitos towards conventionally used control strategies necessitates developing of novel strategies to counter disease transmission. The mosquito brain plays a key role in host-seeking, finding mates and selection of oviposition sites. However, not much is know about the underlying physiological processes in mosquito brain. The data presented in this study describes the proteins that have been identified in the brain tissue of adult female Anopheles stephensi and their associated processes. Interpretation of the data can be related to the previously published article “Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes” [1].
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Affiliation(s)
- Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Ajeet Kumar Mohanty
- ICMR-National Institute of Malaria Research, Field Station, Campal, Panaji, Goa 403001, India
| | | | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre, Indira Nagar, Puducherry-605 006, UT, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Deralakatte, Mangalore-575018, India
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43
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Dagamajalu S, Rex DAB, Palollathil A, Shetty R, Bhat G, Cheung LWT, Prasad TSK. Correction to: A pathway map of AXL receptor-mediated signaling network. J Cell Commun Signal 2020; 15:149. [PMID: 32990931 DOI: 10.1007/s12079-020-00583-2] [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: 11/28/2022] Open
Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Akhina Palollathil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Guruprasad Bhat
- Department of Medical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Lydia W T Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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44
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Thoduvayil S, Dhandapani G, Brahma R, Devasahayam Arokia Balaya R, Mangalaparthi KK, Patel K, Kumar M, Tennyson J, Satheeshkumar PK, Kulkarni MJ, Pinto SM, Prasad TSK, Madanan MG. Triton X-114 Fractionated Subcellular Proteome of Leptospira interrogans Shows Selective Enrichment of Pathogenic and Outer Membrane Proteins in the Detergent Fraction. Proteomics 2020; 20:e2000170. [PMID: 32846045 DOI: 10.1002/pmic.202000170] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/30/2020] [Indexed: 12/28/2022]
Abstract
The Triton X-114-based solubilization and temperature-dependent phase separation of proteins is used for subcellular fractionation where, aqueous, detergent, and pellet fractions represents cytoplasmic, outer membrane (OM), and inner membrane proteins, respectively. Mass spectrometry-based proteomic analysis of Triton X-114 fractions of proteomic analysis of Leptospira interrogans identified 2957 unique proteins distributed across the fractions. The results are compared with bioinformatics predictions on their subcellular localization and pathogenic nature. Analysis of the distribution of proteins across the Triton X-114 fractions with the predicted characteristics is performed based on "number" of unique type of proteins, and "quantity" which represents the amount of unique protein. The highest number of predicted outer membrane proteins (OMPs) and pathogenic proteins are found in aqueous and pellet fractions, whereas detergent fraction representing the OM has the highest quantity of OMPs and pathogenic proteins though lower in number than the aqueous and pellet fractions. This leaves the possibility of an upsurge in pathogenic proteins and OMPs on the OM under pathogenic conditions suggesting their potential use to combat leptospirosis. Further, the Triton X-114 subcellular fractions are more correlated to enrichment of pathogenic proteins predicted by MP3 software than predicted localization.
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Affiliation(s)
- Sikha Thoduvayil
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India.,Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Gunasekaran Dhandapani
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India.,Department of Chemical Sciences, Ariel University, Ariel, 70400, Israel
| | - Rahul Brahma
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India
| | - Rex Devasahayam Arokia Balaya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, 575018, India
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bengaluru, 560029, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690525, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jebasingh Tennyson
- School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - P K Satheeshkumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Mahesh J Kulkarni
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, 575018, India.,Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, 575018, India.,Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bengaluru, 560029, India
| | - Madathiparambil G Madanan
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India
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Dagamajalu S, Rex DAB, Gopalakrishnan L, Karthikkeyan G, Gurtoo S, Modi PK, Mohanty V, Mujeeburahiman M, Soman S, Raju R, Tiwari V, Prasad TSK. A network map of endothelin mediated signaling pathway. J Cell Commun Signal 2020; 15:277-282. [PMID: 32915369 DOI: 10.1007/s12079-020-00581-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023] Open
Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Lathika Gopalakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Gayathree Karthikkeyan
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Sumrati Gurtoo
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - M Mujeeburahiman
- Department of Urology, Yenepoya Medical College Hospital, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Sowmya Soman
- Department of Biochemistry, University of Kerala, Thiruvananthapuram, 695581, India
| | - Rajesh Raju
- Computational Biology Group, Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Vinod Tiwari
- Neuroscience and Pain Research Lab, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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46
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Dagamajalu S, Rex DAB, Palollathil A, Shetty R, Bhat G, Cheung LWT, Prasad TSK. A pathway map of AXL receptor-mediated signaling network. J Cell Commun Signal 2020; 15:143-148. [PMID: 32829427 DOI: 10.1007/s12079-020-00580-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/17/2020] [Indexed: 01/06/2023] Open
Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Akhina Palollathil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Guruprasad Bhat
- Department of Medical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Lydia W T Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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Mangalaparthi KK, Patel K, Khan AA, Manoharan M, Karunakaran C, Murugan S, Gupta R, Gupta R, Khanna-Gupta A, Chaudhuri A, Kumar P, Nair B, Kumar RV, Prasad TSK, Chatterjee A, Pandey A, Gowda H. Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort. Front Oncol 2020; 10:1457. [PMID: 32974170 PMCID: PMC7469928 DOI: 10.3389/fonc.2020.01457] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/09/2020] [Indexed: 12/18/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most common histological subtype of esophageal cancer in India. Cigarette smoking and chewing tobacco are known risk factors associated with ESCC. However, genomic alterations associated with ESCC in India are not well-characterized. In this study, we carried out exome sequencing to characterize the mutational landscape of ESCC tumors from subjects with a varied history of tobacco usage. Whole exome sequence analysis of ESCC from an Indian cohort revealed several genes that were mutated or had copy number changes. ESCC from tobacco chewers had a higher frequency of C:G > A:T transversions and 2-fold enrichment for mutation signature 4 compared to smokers and non-users of tobacco. Genes, such as TP53, CSMD3, SYNE1, PIK3CA, and NOTCH1 were found to be frequently mutated in Indian cohort. Mutually exclusive mutation patterns were observed in PIK3CA–NOTCH1, DNAH5–ZFHX4, MUC16–FAT1, and ZFHX4–NOTCH1 gene pairs. Recurrent amplifications were observed in 3q22-3q29, 11q13.3-q13.4, 7q22.1-q31.1, and 8q24 regions. Approximately 53% of tumors had genomic alterations in PIK3CA making this pathway a promising candidate for targeted therapy. In conclusion, we observe enrichment of mutation signature 4 in ESCC tumors from patients with a history of tobacco chewing. This is likely due to direct exposure of esophagus to tobacco carcinogens when it is chewed and swallowed. Genomic alterations were frequently observed in PIK3CA-AKT pathway members independent of the history of tobacco usage. PIK3CA pathway can be potentially targeted in ESCC which currently has no effective targeted therapeutic options.
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Affiliation(s)
- Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Aafaque A Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | | | | | - Ravi Gupta
- Medgenome Labs Pvt. Ltd., Bangalore, India
| | | | | | | | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India.,Manipal Academy of Higher Education, Manipal, India.,Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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48
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Kasaragod S, Mohanty V, Tyagi A, Behera SK, Patil AH, Pinto SM, Prasad TSK, Modi PK, Gowda H. CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets. F1000Res 2020; 9:344. [PMID: 33274046 PMCID: PMC7684676 DOI: 10.12688/f1000research.23214.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
Cancer genome sequencing studies have revealed a number of variants in coding regions of several genes. Some of these coding variants play an important role in activating specific pathways that drive proliferation. Coding variants present on cancer cell surfaces by the major histocompatibility complex serve as neo-antigens and result in immune activation. The success of immune therapy in patients is attributed to neo-antigen load on cancer cell surfaces. However, which coding variants are expressed at the protein level can't be predicted based on genomic data. Complementing genomic data with proteomic data can potentially reveal coding variants that are expressed at the protein level. However, identification of variant peptides using mass spectrometry data is still a challenging task due to the lack of an appropriate tool that integrates genomic and proteomic data analysis pipelines. To overcome this problem, and for the ease of the biologists, we have developed a graphical user interface (GUI)-based tool called CusVarDB. We integrated variant calling pipeline to generate sample-specific variant protein database from next-generation sequencing datasets. We validated the tool with triple negative breast cancer cell line datasets and identified 423, 408, 386 and 361 variant peptides from BT474, MDMAB157, MFM223 and HCC38 datasets, respectively.
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Affiliation(s)
- Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ankur Tyagi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Arun H. Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
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49
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Kasaragod S, Mohanty V, Tyagi A, Behera SK, Patil AH, Pinto SM, Prasad TSK, Modi PK, Gowda H. CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets. F1000Res 2020; 9:344. [PMID: 33274046 PMCID: PMC7684676 DOI: 10.12688/f1000research.23214.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2020] [Indexed: 03/31/2024] Open
Abstract
Cancer genome sequencing studies have revealed a number of variants in coding regions of several genes. Some of these coding variants play an important role in activating specific pathways that drive proliferation. Coding variants present on cancer cell surfaces by the major histocompatibility complex serve as neo-antigens and result in immune activation. The success of immune therapy in patients is attributed to neo-antigen load on cancer cell surfaces. However, which coding variants are expressed at the protein level can't be predicted based on genomic data. Complementing genomic data with proteomic data can potentially reveal coding variants that are expressed at the protein level. However, identification of variant peptides using mass spectrometry data is still a challenging task due to the lack of an appropriate tool that integrates genomic and proteomic data analysis pipelines. To overcome this problem, and for the ease of the biologists, we have developed a graphical user interface (GUI)-based tool called CusVarDB. We integrated variant calling pipeline to generate sample-specific variant protein database from next-generation sequencing datasets. We validated the tool with triple negative breast cancer cell line datasets and identified 423, 408, 386 and 361 variant peptides from BT474, MDMAB157, MFM223 and HCC38 datasets, respectively.
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Affiliation(s)
- Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ankur Tyagi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Arun H. Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
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Rex DAB, Agarwal N, Prasad TSK, Kandasamy RK, Subbannayya Y, Pinto SM. A comprehensive pathway map of IL-18-mediated signalling. J Cell Commun Signal 2019; 14:257-266. [PMID: 31863285 DOI: 10.1007/s12079-019-00544-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Interleukin-18 (IL-18) is a member of the IL-1 family of cytokines and was initially described as an IFN-γ-inducing factor derived from anti-CD3-stimulated T-helper (Th)1 cells. IL-18 plays a significant role in the activation of hematopoietic cell types mediating both Th1 and Th2 responses and is the primary inducer of interferon-γ in these cells. The biological activity of IL-18 is mediated through its binding to the IL-18 receptor complex and activation of nuclear factor-κB (NF-κB), culminating in the production and release of several cytokines, chemokines, and cellular adhesion molecules. In certain cell types, IL-18 also activates mitogen-activated protein kinases (MAPKs) and phosphoinositide 3-kinase/ AKT serine/threonine kinase (PI3K/AKT) signaling modules leading to the production and release of proinflammatory cytokines. IL-18-mediated signaling acts as one of the vital components of the immunomodulatory cytokine networks involved in host defense, inflammation, and tissue regeneration. Albeit its biomedical importance, a comprehensive resource of IL-18 mediated signaling pathway is currently lacking. In this study, we report on the development of an integrated pathway map of IL-18/IL-18R signaling. The pathway map was developed through literature mining from published literature based on manual curation guidelines adapted from NetPath and includes information on 16 protein-protein interaction events, 38 enzyme-catalysis events, 12 protein translocation events, 26 activations/inhibition events, transcriptional regulators, 230 gene regulation events and 84 induced protein expression events. The IL-18 signaling pathway can be freely accessed through the WikiPathways database (https://www.wikipathways.org/index.php/Pathway:WP4754).
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Affiliation(s)
- D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Nupur Agarwal
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Richard K Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India. .,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India. .,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
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