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Gurtoo S, Karthikkeyan G, Behera SK, Kotimoole CN, Najar MA, Modi PK, Ks S, Pinto SM, Ab A. A comparative proteomic analysis for non-invasive early prediction of hypoxic-ischemic injury in asphyxiated neonates. Proteomics Clin Appl 2024; 18:e2200054. [PMID: 37787895 DOI: 10.1002/prca.202200054] [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: 07/08/2022] [Revised: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
AIM Hypoxic Ischemic Encephalopathy (HIE) is one of the principal causes of neonatal mortality and long-term morbidity worldwide. The neonatal signs of mild cerebral injury are subtle, making an early precise diagnosis difficult. Delayed detection, poor prognosis, and lack of specific biomarkers for the disease are increasing mortality rates. In this study, we intended to identify specific biomarkers using comparative proteomic analysis to predict the severity of perinatal asphyxia so that its outcome can also be prevented. EXPERIMENTAL DESIGN A case-control study was conducted on 38 neonates, and urine samples were collected within 24 and 72 h of life. A tandem mass spectrometry-based quantitative proteomics approach, followed by validation via sandwich ELISA, was performed. RESULTS The LC-MS/MS-based proteomics analysis resulted in the identification of 1201 proteins in urine, with 229, 244, and 426 being differentially expressed in HIE-1, HIE-2, and HIE-3, respectively. Axon guidance, Diseases of programmed cell death, and Detoxification of reactive oxygen species pathways were significantly enriched in mild HIE versus severe HIE. Among the differentially expressed proteins in various stages of HIE, we chose to validate four proteins - APP, AGT, FABP1, and FN1 - via sandwich ELISA. Individual and cumulative ROC curves were plotted. AGT and FABP1 together showed high sensitivity, specificity, and accuracy as potential biomarkers for early diagnosis of HIE. CONCLUSION Establishing putative urinary biomarkers will facilitate clinicians to more accurately screen neonates for brain injury and monitor the disease progression. Prompt treatment of neonates may reduce mortality and neurodevelopmental impairment.
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Affiliation(s)
- Sumrati Gurtoo
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Gayathree Karthikkeyan
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, 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
| | - Sahana Ks
- Yenepoya Medical College and Hospital, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Arun Ab
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
- Yenepoya Institute of Arts Science Commerce and Management, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
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Tsusaka T, Najar MA, Schwarz B, Bohrnsen E, Oses-Prieto JA, Lee C, Burlingame AL, Bosio CM, Burslem GM, Goldberg EL. Reversible histone deacetylase activity catalyzes lysine acylation. bioRxiv 2023:2023.11.17.567549. [PMID: 38014285 PMCID: PMC10680841 DOI: 10.1101/2023.11.17.567549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Starvation and low carbohydrate diets lead to the accumulation of the ketone body, β-hydroxybutyrate (BHB), whose blood concentrations increase more than 10-fold into the millimolar range. In addition to providing a carbon source, BHB accumulation triggers lysine β-hydroxybutyrylation (Kbhb) of proteins via unknown mechanisms. As with other lysine acylation events, Kbhb marks can be removed by histone deacetylases (HDACs). Here, we report that class I HDACs unexpectedly catalyze protein lysine modification with β-hydroxybutyrate (BHB). Mutational analyses of the HDAC2 active site reveal a shared reliance on key amino acids for classical deacetylation and non-canonical HDAC-catalyzed β-hydroxybutyrylation. Also consistent with reverse HDAC activity, Kbhb formation is driven by mass action and substrate availability. This reverse HDAC activity is not limited to BHB but also extends to multiple short-chain fatty acids. The reversible activity of class I HDACs described here represents a novel mechanism of PTM deposition relevant to metabolically-sensitive proteome modifications.
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Affiliation(s)
- Takeshi Tsusaka
- Department of Physiology, University of California, San Francisco; San Francisco, CA, 94158, USA
| | - Mohd. Altaf Najar
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
| | - Benjamin Schwarz
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases; Hamilton, MT, 59840, USA
| | - Eric Bohrnsen
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases; Hamilton, MT, 59840, USA
| | - Juan A. Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco; San Francisco, CA, 94158, USA
| | - Christina Lee
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, 94720, USA
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco; San Francisco, CA, 94158, USA
| | - Catharine M. Bosio
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases; Hamilton, MT, 59840, USA
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
| | - Emily L. Goldberg
- Department of Physiology, University of California, San Francisco; San Francisco, CA, 94158, USA
- Chan-Zuckerberg Biohub; San Francisco, CA, 94158, USA
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Dcunha R, Kumari S, Najar MA, Aravind A, Suvarna KS, Hanumappa A, Mutalik SP, Mutalik S, Kalthur SG, Rajanikant GK, Siddiqui S, Alrumman S, Alamri SAM, Raghu SV, Adiga SK, Kannan N, Thottethodi Subrahmanya KP, Kalthur G. High doses of GrassOut Max poses reproductive hazard by affecting male reproductive function and early embryogenesis in Swiss albino mice. Chemosphere 2023:139215. [PMID: 37336444 DOI: 10.1016/j.chemosphere.2023.139215] [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] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
Clethodim is a widely used and approved class II herbicide, with little information about its impact on the reproductive system. Herein, we investigated the male reproductive toxicity of clethodim using a mouse model. GrassOut Max (26% clethodim-equivalent) or 50 mg kg-1 body weight analytical grade clethodim (≥90%) were given orally to male mice for 10 d in varying doses. All parameters were assessed at 35 d from the first day of treatment. Significant decrease in testicular weight, decreased germ cell population, elevated DNA damage in testicular cells and lower serum testosterone level was observed post clethodim-equivalent exposure. Epididymal spermatozoa were characterized with significant decrease in motility, elevated DNA damage, abnormal morphology, chromatin immaturity and, decreased acetylated-lysine of sperm proteins. In the testicular cells of clethodim-equivalent treated mice, the expression of Erβ and Gper was significantly higher. Proteomic analysis revealed lower metabolic activity, poor sperm-oocyte binding potential and defective mitochondrial electron transport in spermatozoa of clethodim-equivalent treated mice. Further, fertilizing ability of spermatozoa was compromised and resulted in defective preimplantation embryo development. Together, our data suggest that clethodim exposure risks male reproductive function and early embryogenesis in Swiss albino mice via endocrine disrupting function.
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Affiliation(s)
- Reyon Dcunha
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sandhya Kumari
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Keerthana Sandesh Suvarna
- Division of Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Ananda Hanumappa
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sadhana P Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Srinivas Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Sneha Guruprasad Kalthur
- Department of Anatomy, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - G K Rajanikant
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India
| | - Sazada Siddiqui
- Department of Biology, College of Sciences, King Khalid University, Abha, 11362, Saudi Arabia
| | - Sulaiman Alrumman
- Department of Biology, College of Sciences, King Khalid University, Abha, 11362, Saudi Arabia
| | | | - Shamprasad Varija Raghu
- Neurogenetics Lab, Department of Applied Zoology, Mangalore University, Mangalagangotri, 574199, Karnataka, India
| | - Satish Kumar Adiga
- Division of Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Nagarajan Kannan
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA; Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Guruprasad Kalthur
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India.
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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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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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Nagendra AH, Najar MA, Bose B, Shenoy PS. High concentration of sodium fluoride in drinking water induce hypertrophy versus atrophy in mouse skeletal muscle via modulation of sarcomeric proteins. J Hazard Mater 2022; 432:128654. [PMID: 35286933 DOI: 10.1016/j.jhazmat.2022.128654] [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] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Fluoride at high doses is a well-known toxic agent for the musculoskeletal system, primarily in bone and cartilage cells. Research on fluoride toxicity concerning particularly on the skeletal muscle is scanty. We hypothesized that during skeletal fluorosis, along with bone, muscle is also affected, so we have evaluated the effects of Sodium fluoride (NaF) on mouse skeletal muscles. Sodium fluoride (80 ppm) was administered to 5-week-old C57BL6 mice drinking water for 15 and 60 days, respectively. We carried out histology, primary culture, molecular and proteomic analysis of fluoride administered mouse skeletal muscles. Results indicated an increase in the muscle mass (hypertrophy) in vivo and myotubes ex vivo by activating the IGF1/PI3/Akt/mTOR signalling pathway due to short term NaF exposure. The long-term exposure of mice to NaF caused loss of muscle proteins leading to muscle atrophy due to activation of the ubiquitin-proteasome pathway. Differentially expressed proteins were characterized and mapped using a proteomic approach. Moreover, the factors responsible for protein synthesis and PI3/Akt/mTOR pathway were upregulated, leading to muscle hypertrophy during the short term NaF exposure. Long term exposure to NaF resulted in down-regulation of metabolic pathways. Elevated myostatin resulted in the up-regulation of the muscle-specific E3 ligases-MuRF1, promoting the ubiquitination and proteasome-mediated degradation of critical sarcomeric proteins.
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Affiliation(s)
- Apoorva H Nagendra
- Stem cells and Regenerative medicine centre, Yenepoya research centre, Yenepoya Deemed to be University, University Road, Derlakatte, Mangalore 575018, Karnataka, India
| | - Mohd Altaf Najar
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Bipasha Bose
- Stem cells and Regenerative medicine centre, Yenepoya research centre, Yenepoya Deemed to be University, University Road, Derlakatte, Mangalore 575018, Karnataka, India.
| | - P Sudheer Shenoy
- Stem cells and Regenerative medicine centre, Yenepoya research centre, Yenepoya Deemed to be University, University Road, Derlakatte, Mangalore 575018, Karnataka, India.
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Thimmappa PY, Nair AS, Najar MA, Mohanty V, Shastry S, Prasad TSK, Joshi MB. Quantitative phosphoproteomics reveals diverse stimuli activate distinct signaling pathways during neutrophil activation. Cell Tissue Res 2022; 389:241-257. [PMID: 35622142 PMCID: PMC9287233 DOI: 10.1007/s00441-022-03636-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/11/2022] [Indexed: 12/19/2022]
Abstract
Neutrophils display functional heterogeneity upon responding diversely to physiological and pathological stimulations. During type 2 diabetes (T2D), hyperglycemia constitutively activates neutrophils, leading to reduced response to infections and on the other hand, elevated metabolic intermediates such as homocysteine induce bidirectional activation of platelets and neutrophils leading to thrombosis. Hence, in the context of T2D-associated complications, we examined the influence of high glucose, homocysteine, and LPS representing effector molecules of hyperglycemia, thrombosis, and infection, respectively, on human neutrophil activation to identify distinct signaling pathways by quantitative phosphoproteomics approach. High glucose activated C-Jun-N-Terminal Kinase, NTRK1, SYK, and PRKACA kinases associated with Rho GTPase signaling and phagocytosis, whereas LPS induced AKT1, SRPK2, CSNK2A1, and TTN kinases involved in cytokine signaling and inflammatory response. Homocysteine treatment led to activatation of LRRK2, FGR, MAPK3, and PRKCD kinases which are associated with neutrophil degranulation and cytoskeletal remodeling. Diverse inducers differentially modulated phosphorylation of proteins associated with neutrophil functions such as oxidative burst, degranulation, extracellular traps, and phagocytosis. Further validation of phosphoproteomics data on selected kinases revealed neutrophils pre-cultured under high glucose showed impeded response to LPS to phosphorylate p-ERK1/2Thr202/Tyr204, p-AKTSer473, and C-Jun-N-Terminal KinaseSer63 kinases. Our study provides novel phosphoproteome signatures that may be explored to understand neutrophil biology in T2D-associated complications.
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Affiliation(s)
- Pooja Yedehalli Thimmappa
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Aswathy S Nair
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575020, India
| | - Varshasnatha Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575020, India
| | - Shamee Shastry
- Department of Immunohematology and Blood Transfusion, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | | | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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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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Arefian M, Antil N, Najar MA, Behera SK, Subba P, Prasad TSK. Identifying Novel Genes and Proteins Involved in Salt Stress Perception and Signaling of Rice Seedlings. OMICS 2022; 26:151-164. [PMID: 35073185 DOI: 10.1089/omi.2021.0210] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rice is one of the most important crops worldwide. Crop production is constrained markedly, however, by abiotic stresses such as salinity. To elucidate early stress response signaling networks involved in rice, we report in this study an original quantitative proteomic analysis of the rice seedlings subjected to short-term salt stress. We detected 570 differentially regulated proteins (DRPs) in the root sample. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis demonstrated that DRPs of the root were mainly involved in membrane trafficking, kinase activity, and ion toxicity responses. Interactome analysis revealed the central role of root proteins involved in membrane trafficking in the early response to salinity, such as cell surface receptor-like kinases (RLKs), phosphatidylinositols (PIs), calcium-dependent protein kinases 1 and 5, calcineurin B-like protein-interacting proteins, protein phosphatase 2C (PP2C) inhibitors, and abscisic acid receptors (PYL5/10), indicating activation of S-type anion channel. Furthermore, the proteogenomic analysis revealed 128 unique genome search-specific peptides with high-quality mass spectromety (MS/MS) spectra. We identified 38 novel protein-coding genes, refined the annotation of 17 existing gene models, and suggested several novel stress-responsive proteins, such as RLK5, peroxidase 27, and growth-regulating factor 2. Novel peptides had an ortholog match in the curated protein sequence set of other plant species. In conclusion, this study identifies novel stress-responsive proteins and genes of rice, thus warrant future consideration as candidates for molecular breeding of stress-tolerant crop varieties.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya, (Deemed to be University), Mangalore, India
| | - Neelam Antil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya, (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya, (Deemed to be University), Mangalore, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya, (Deemed to be University), Mangalore, India
| | - Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya, (Deemed to be University), Mangalore, India
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10
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Kalal BS, Modi PK, Najar MA, Behera SK, Upadhya D, Prasad TSK, Pai VR. Hyperphosphorylation of HDAC2 promotes drug resistance in a novel dual drug resistant mouse melanoma cell line model: an in vitro study. Am J Cancer Res 2021; 11:5881-5901. [PMID: 35018231 PMCID: PMC8727796] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023] Open
Abstract
Drug-resistant melanoma is very difficult to treat, and a novel approach is needed to overcome resistance. The present study aims at identifying the alternate pathways utilized in the dual drug-resistant mouse melanoma cells (B16F10R) for their survival and proliferation. The dual drug-resistant mouse melanoma, B16F10R, was established by treating the cells with a combination of U0126 (MEK1/2 inhibitor) and LY294002 (PI3K-AKT kinase inhibitor) in a dose-escalating manner till they attained a resistance fold factor of ≥2. The altered phosphoproteome in the B16F10R, as compared to the parental B16F10C, was analyzed using a high-resolution Orbitrap Fusion Tribrid mass spectrometer. Histone deacetylases 2 (HDAC2) was validated for its role in drug resistance by using its inhibitor, valproic acid (VPA). In the B16F10R cells, 363 altered phosphoproteins were identified, among which 126 were hyperphosphorylated, and 137 were hypophosphorylated (1.5-fold change). Pathway analysis shows the altered phosphoproteins are from RNA metabolism and cell cycle proteins. Inhibition of HDAC2 by VPA induces apoptosis in B16F10C and B16F10R. The present study highlights the role of HDAC2, a cell cycle regulator, in the development of resistance to dual drugs in murine melanoma. Therefore, designing leads for targeting HDAC2 along with key signaling pathways may be explored in treatment strategies.
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Affiliation(s)
- Bhuvanesh Sukhlal Kalal
- Department of Biochemistry, Yenepoya Medical College, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Dinesh Upadhya
- Centre for Molecular Neurosciences, Department of Anatomy, Kasturba Medical College, Manipal Academy of Higher Education ManipalUdupi 576104, Karnataka, India
| | | | - Vinitha Ramanath Pai
- Department of Biochemistry, Yenepoya Medical College, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
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11
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Shaikh SB, Najar MA, Prabhu A, Rex DAB, Chanderasekaran J, Behera SK, Modi PK, Prasad TSK, Bhandary YP. The unique molecular targets associated antioxidant and antifibrotic activity of curcumin in in vitro model of acute lung injury: A proteomic approach. Biofactors 2021; 47:627-644. [PMID: 33864298 DOI: 10.1002/biof.1732] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
Bleomycin (BLM) injury is associated with the severity of acute lung injury (ALI) leading to fibrosis, a high-morbidity, and high-mortality respiratory disease of unknown etiology. BLM-induced ALI is marked by the activation of a potent fibrogenic cytokine transcription growth factor beta-1 (TGFβ-1), which is considered a critical cytokine in the progression of alveolar injury. Previously, our work demonstrated that a diet-derived compound curcumin (diferuloylmethane), represents its antioxidative and antifibrotic application in TGF-β1-mediated BLM-induced alveolar basal epithelial cells. However, curcumin-specific protein targets, as well as its mechanism using mass spectrometry-based proteomic approach, remain elusive. To elucidate the underlying mechanism, a quantitative proteomics approach and bioinformatics analysis were employed to identify the protein targets of curcumin in BLM or TGF-β1-treated cells. With subsequent in vitro experiments, curcumin-related pathways and cellular processes were predicted and validated. The current study discusses two separate proteomics experiments using BLM and TGF-β1-treated cells with the proteomics approach, various unique target proteins were identified, and proteomic analysis revealed that curcumin reversed the expressions of unique proteins like DNA topoisomerase 2-alpha (TOP2A), kinesin-like protein (KIF11), centromere protein F (CENPF), and so on BLM or TGF-β1 injury. For the first time, the current study reveals that curcumin restores TGF-β1 induced peroxisomes like PEX-13, PEX-14, PEX-19, and ACOX1. This was verified by subsequent in vitro assays. This study generated molecular evidence to deepen our understanding of the therapeutic role of curcumin at the proteomic level and may be useful to identify molecular targets for future drug discovery.
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Affiliation(s)
- Sadiya Bi Shaikh
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Ashwini Prabhu
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, India
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | | | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, 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
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12
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Shaikh SB, Najar MA, Prasad TSK, Bhandary YP. Comparative protein profiling reveals the inhibitory role of curcumin on IL-17A mediated minichromosome maintenance (MCM) proteins as novel putative markers for acute lung injury in vivo. Biomed Pharmacother 2021; 141:111715. [PMID: 34198046 DOI: 10.1016/j.biopha.2021.111715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
The Pro-inflammatory cytokine, Interleukin 17A (IL-17A) plays a vital role in the pathogenesis of inflammatory-induced acute lung injury (ALI). But, the mechanisms of this pro-inflammatory cytokine in response to activation after replication stress are not yet known. Control on DNA replication (DR) is vital for maintaining genome stability. Minichromosome maintenance (MCM) proteins play essential roles in various cancers, but their involvement during ALI is not yet been discussed. The present study was carried out to assess the participation of IL-17A during replication stress and to evaluate the contribution of curcumin on this. Mass spectrometry-based proteomic approach has been used on mice lung tissues treated with IL-17A, as a prime mediator to cause injury and curcumin a natural polyphenol as an intervention. Several trends were identified from the proteomic subset which revealed that IL-17A induces expressions of proteins like MCM2, MCM3, and MCM6 along with other proteins involved in DR. Interestingly, curcumin was found in suppressing the expression levels of these proteins. This was also confirmed via validating LC-MS/MS data using appropriate molecular techniques. Pathway and gene ontology analysis were performed with DAVID GO databases. Apart from this, the present study also reports the unique contribution of curcumin in suppressing the mRNA levels of other MCMs like MCM4, MCM5, and MCM7 as well as of ORC1 and ORC2. Hence, the present study revolves around linking the replication stress by pro-inflammatory effects, highlighting the implications for ALI and therapies. This study, therefore, enhances our capacity to therapeutically target DR-specific proteins.
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Affiliation(s)
- Sadiya Bi Shaikh
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore 575018, Karnataka, India; Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA.
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | - Yashodhar P Bhandary
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore 575018, Karnataka, India.
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13
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Patavardhan SS, Awasthi K, Suresh S, Subba P, Najar MA, D'Souza L, Nivas SK, Prasad TSK. Proteome dataset of chili pepper plant ( Capsicum frutescens) infested by broad mite (Polyphagotarsonemus latus). Data Brief 2021; 36:107095. [PMID: 34041315 PMCID: PMC8142047 DOI: 10.1016/j.dib.2021.107095] [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: 02/16/2021] [Revised: 04/08/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022] Open
Abstract
The dataset presented in this article is associated with the TMT (Tandem mass tag) labeled proteomics of chili pepper plant (Capsicum frutescens) infested by a broad mite (Polyphagotarsonemus latus). Data was captured using a nano liquid chromatography system coupled with high-resolution Orbitrap FusionTribridmass spectrometer. Proteomics data was analyzed using the Proteome Discoverer version 2.4 tool using MASCOT and SequestHT algorithms. We have identified a total of 5,807 proteins supported by 48,555 unique peptides and 1,279,655 peptide-spectrum matches. Individually, 5,186 proteins were detected in healthy leaf samples, 5,193 in infested leaf sample, 5,194 proteins in healthy meristem sample, and 5,196 proteins in infested meristem samples. Datasets obtained from reciprocal blast against the Arabidopsis thaliana proteome database enabled the prediction of protein-protein interactions, and subcellular localization of differentially expressed proteins, which are also included in this article. Data presented in this article has been deposited in the ProteomeXchange Consortium via the PRIDE repository, which can be accessed through the accession ID: PXD018653.
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Affiliation(s)
- Sachin S Patavardhan
- Laboratory of Applied Biology, St Aloysius College (Autonomous), Mangalore, India.,Department of Biosciences, Mangalore University, Mangalore, India
| | - Kriti Awasthi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Suhasini Suresh
- Laboratory of Applied Biology, St Aloysius College (Autonomous), Mangalore, India
| | - Pratigya Subba
- 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
| | - Leo D'Souza
- Laboratory of Applied Biology, St Aloysius College (Autonomous), Mangalore, India
| | - Shashi Kiran Nivas
- Laboratory of Applied Biology, St Aloysius College (Autonomous), Mangalore, India
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14
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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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15
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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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16
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Karthikkeyan G, Najar MA, Pervaje R, Pervaje SK, Modi PK, Prasad TSK. Identification of Molecular Network Associated with Neuroprotective Effects of Yashtimadhu ( Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson's Disease Model. ACS Omega 2020; 5:26611-26625. [PMID: 33110989 PMCID: PMC7581237 DOI: 10.1021/acsomega.0c03420] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/24/2020] [Indexed: 05/04/2023]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder, whose treatment with modern therapeutics leads to a plethora of side effects with prolonged usage. Therefore, the management of PD with complementary and alternative medicine is often pursued. In the Ayurveda system of alternative medicine, Yashtimadhu choorna, a Medhya Rasayana (nootropic), prepared from the dried roots of Glycyrrhiza glabra L. (licorice), is prescribed for the management of PD with a favorable outcome. We pursued to understand the neuroprotective effects of Yashtimadhu choorna against a rotenone-induced cellular model of PD using differentiated IMR-32 cells. Cotreatment with Yashtimadhu choorna extract rescued rotenone-induced apoptosis and hyperphosphorylation of ERK-1/2. Quantitative proteomic analysis of six peptide fractions from independent biological replicates acquired 1,561,169 mass spectra, which when searched resulted in 565,008 peptide-spectrum matches mapping to 30,554 unique peptides that belonged to 4864 human proteins. Proteins commonly identified in biological replicates and >4 PSMs were considered for further analysis, leading to a refined set of 3720 proteins. Rotenone treatment differentially altered 144 proteins (fold ≥1.25 or ≤0.8), involved in mitochondrial, endoplasmic reticulum, and autophagy functions. Cotreatment with Yashtimadhu choorna extract rescued 84 proteins from the effect of rotenone and an additional regulation of 4 proteins. Network analysis highlighted the interaction of proteins and pathways regulated by them, which can be targeted for neuroprotection. Validation of proteomics data highlighted that Yashtimadhu confers neuroprotection by preventing mitochondrial oxidative stress and apoptosis. This discovery will pave the way for understanding the molecular action of Ayurveda drugs and developing novel therapeutics for PD.
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Affiliation(s)
- Gayathree Karthikkeyan
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - 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
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17
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Mohanty V, Pinto SM, Subbannayya Y, Najar MA, Murthy KB, Prasad TSK, Murthy KR. Digging Deeper for the Eye Proteome in Vitreous Substructures: A High-Resolution Proteome Map of the Normal Human Vitreous Base. ACTA ACUST UNITED AC 2020; 24:379-389. [DOI: 10.1089/omi.2020.0020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- 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
| | - Kalpana Babu Murthy
- Department of vitreo retina, Vittala International Institute of Ophthalmology, Bangalore, India
- Department of vitreo retina, Prabha Eye Clinic and Research Centre, Bangalore, India
| | | | - Krishna R. Murthy
- Department of vitreo retina, Vittala International Institute of Ophthalmology, Bangalore, India
- Department of vitreo retina, Prabha Eye Clinic and Research Centre, Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
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18
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Advani J, Verma R, Chatterjee O, Devasahayam Arokia Balaya R, Najar MA, Ravishankara N, Suresh S, Pachori PK, Gupta UD, Pinto SM, Chauhan DS, Tripathy SP, Gowda H, Prasad TK. Rise of Clinical Microbial Proteogenomics: A Multiomics Approach to Nontuberculous Mycobacterium—The Case ofMycobacterium abscessusUC22. ACTA ACUST UNITED AC 2019; 23:1-16. [DOI: 10.1089/omi.2018.0116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Oishi Chatterjee
- 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
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rex Devasahayam Arokia Balaya
- 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
| | - Namitha Ravishankara
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bangalore, India
| | - Sneha Suresh
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bangalore, India
| | - Praveen Kumar Pachori
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Umesh D. Gupta
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Devendra S. Chauhan
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Srikanth Prasad Tripathy
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, 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
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Karthikkeyan G, Subbannayya Y, Najar MA, Mohanty V, Pinto SM, Arunachalam C, Prasad TSK, Murthy KR. Human Optic Nerve: An Enhanced Proteomic Expression Profile. OMICS 2018; 22:642-652. [PMID: 30346883 DOI: 10.1089/omi.2018.0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ophthalmology and visual health are new frontiers for postgenomic research and technologies such as proteomics. In this context, the optic nerve and retina extend as the outgrowth of the brain, wherein the latter receives the optical input and the former relays the information for processing. While efforts to understand the optic nerve proteome have been made earlier, there exists a lacuna in its biochemical composition and molecular functions. We report, in this study, a high-resolution mass spectrometry-based approach using an Orbitrap Fusion Tribrid mass spectrometer to elucidate the human optic nerve proteomic profile. Raw spectra were searched against NCBI Human RefSeq 75 database using SEQUEST HT and MASCOT algorithms. We identified nearly 35,000 peptides in human optic nerve samples, corresponding to 5682 proteins, of which 3222 proteins are being reported for the first time. Label-free quantification using spectral abundance pointed out to neuronal structural proteins such as myelin basic protein, glial fibrillary acidic protein, and proteolipid protein 1 as the most abundant proteins. We also identified several neurotransmitter receptors and postsynaptic density synaptosomal scaffold proteins. Pathway analysis revealed that a majority of the proteins are structural proteins and have catalytic and binding activity. This study is one of the largest proteomic profiles of the human optic nerve and offers the research community an initial baseline optic nerve proteome for further studies. This will also help understand the protein dynamics of the human optic nerve under normal conditions.
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Affiliation(s)
- Gayathree Karthikkeyan
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Yashwanth Subbannayya
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Mohd Altaf Najar
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Varshasnata Mohanty
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Sneha M Pinto
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Cynthia Arunachalam
- 2 Department of Ophthalmology, Yenepoya Medical College, Yenepoya (Deemed to be University) , Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India .,3 Institute of Bioinformatics , International Tech Park, Bangalore, Karnataka, India
| | - Krishna R Murthy
- 3 Institute of Bioinformatics , International Tech Park, Bangalore, Karnataka, India .,4 Vittala International Institute of Ophthalmology , Bangalore, Karnataka, India .,5 Manipal Academy of Higher Education , Manipal, Karnataka, India
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