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Syed Masoodhu S, Natarajan N, Vasudevan M. Modification of bentonite with black cotton soil and carboxyl methyl cellulose for the enhancement of hydraulic performance of geosynthetic clay liners. Water Sci Technol 2024; 89:1846-1859. [PMID: 38619907 DOI: 10.2166/wst.2024.093] [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] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/13/2024] [Indexed: 04/17/2024]
Abstract
Geosynthetic clay liners (GCLs) are mostly used as flow barriers in landfills and waste containments due to their low hydraulic conductivity to prevent the leachate from reaching the environment. The self-healing and swell-shrink properties of soft clays (expansive soils) such as bentonite enable them as promising materials for the GCL core layers. However, it is important to modify their physico-chemical properties in order to overcome the functional limitations of GCL under different hydraulic conditions. In the present study, locally available black cotton soil (BCS) is introduced in the presence of an anionic polymer named carboxymethyl cellulose (CMC) as an alternative to bentonite to enhance the hydraulic properties of GCL under different compositions. The modified GCL is prepared by stitching the liner with an optimum percentage of CMC along with various percentages of BCS mixed with bentonite. Hydraulic conductivity tests were performed on the modified GCL using the flexi-wall permeameter. The results suggest that the lowest hydraulic conductivity of 4.58 × 10-10 m/s is obtained when 25% of BCS is blended with bentonite and an optimum 8% CMC and further addition of BCS results in the reduction of the hydraulic conductivity.
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Affiliation(s)
- S Syed Masoodhu
- Department of Civil Engineering, Dr Mahalingam College of Engineering and Technology, Pollachi, Tamil Nadu 642003, India
| | - N Natarajan
- Department of Civil Engineering, Dr Mahalingam College of Engineering and Technology, Pollachi, Tamil Nadu 642003, India E-mail:
| | - M Vasudevan
- Department of Agricultural Engineering, Bannari Amman Institute of Technology, Sathyamangalam, Tamil Nadu 638 401, India
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2
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Balbhim SS, Sarkar S, Vasudevan M, Ghosh SK. Three-amino acid loop extension homeodomain proteins regulate stress responses and encystation in Entamoeba. Mol Microbiol 2023. [PMID: 37424153 DOI: 10.1111/mmi.15121] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
It is interesting to identify factors involved in the regulation of the encystation of Entamoeba histolytica that differentiate trophozoites into cysts. Evolutionarily conserved three amino acid loop extension (TALE) homeodomain proteins act as transcription factors and execute a variety of functions that are essential for life. A TALE homeodomain (EhHbox) protein-encoding gene has been identified in E. histolytica (Eh) that is highly upregulated during heat shock, glucose, and serum starvation. Its ortholog, EiHbox1, a putative homeobox protein in E. invadens (Ei), is also highly upregulated during the early hours of encystation, glucose starvation, and heat shock. They belong to the PBX family of TALE homeobox proteins and have conserved residues in the homeodomain that are essential for DNA binding. Both are localized in the nucleus during encystation and under different stress conditions. The electrophoretic mobility shift assay confirmed that the recombinant GST-EhHbox binds to the reported TGACAG and TGATTGAT motifs. Down-regulation of EiHbox1 by gene silencing reduced Chitin synthase, Jacob, and increased Jessie gene expression, resulting in defective cysts and decreased encystation efficiency and viability. Overall, our results suggest that the TALE homeobox family has been conserved during evolution and acts as a transcription factor to control the differentiation of Entamoeba by regulating the key encystation-induced genes.
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Affiliation(s)
- Sonar Shubham Balbhim
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shilpa Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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3
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Sarangi P, Senthilkumar MB, Kumar N, Senguttuvan S, Vasudevan M, Jayandharan GR. Potential role of long non-coding RNA H19 and Neat1 in haemophilic arthropathy. J Cell Mol Med 2023; 27:1745-1749. [PMID: 37183540 PMCID: PMC10273061 DOI: 10.1111/jcmm.17770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023] Open
Affiliation(s)
- Pratiksha Sarangi
- Department of Biological Sciences and BioengineeringIndian Institute of TechnologyKanpurIndia
| | | | - Narendra Kumar
- Department of Biological Sciences and BioengineeringIndian Institute of TechnologyKanpurIndia
| | | | - Madavan Vasudevan
- Genomics and Data ScienceTheomics International Pvt Ltd.BangaloreIndia
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4
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Krishna MB, Johnson BS, Vasudevan M, Pillai SM, Laloraya M. miRNA-mRNA Network in PBMCs of PCOS Women Identifies Overactivated Stress-Activated Kinases. Cell Physiol Biochem 2023; 57:137-156. [PMID: 37125425 DOI: 10.33594/000000622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND/AIMS Earlier studies have revealed the miRNAs and mRNAs involved in Polycystic Ovarian Syndrome (PCOS), but little is known about their regulatory networks. METHODS To address this issue, we applied a comprehensive miRNA, mRNA profiling approach in peripheral blood of PCOS patients. We identified 30 differential miRNAs and 3310 differential transcripts. A robust computational framework was created to integrate matched miRNA and mRNA expression profiles in PCOS using feed-forward loops. RESULTS The network consisted of differential miRNAs, transcription factors (TFs), and their common predicted target genes. The key network consisted of 14 non-orphan network clusters with 50 TF-gene pairs, 8 TF-TF pairs, 6 miRNA-TF pairs and 36 miRNA- gene pairs which were later dissected into 16 subclusters. Gene ontology annotations revealed that a host of signals (hormone, growth factors -EGF/ PDGF, thrombopoietin, oxidative stress and vitamin/nutrition) regulate MAPK signaling altering angiogenesis, JAK-STAT signaling, apoptosis, inflammatory and immune response and steroidogenesis in PCOS women. CONCLUSION MAPK signaling is identified as the syndrome´s major dysregulated pathway. Our data imparts a robust foundation to expand the work and pave the way to focus efforts on p38MAPK targeted therapeutic strategies in PCOS.
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Affiliation(s)
- Meera B Krishna
- Female Reproduction and Metabolic Syndromes Laboratory, Division of Molecular Reproduction Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Betcy Susan Johnson
- Female Reproduction and Metabolic Syndromes Laboratory, Division of Molecular Reproduction Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Madavan Vasudevan
- Bionivid Technology [P] Ltd, Kasturi Nagar, East of NGEF, Bengaluru, India
| | - Sathy M Pillai
- SAMAD -IVF Hospitals, V.V.Road, Pattoor, Thiruvananthapuram, Kerala, India
| | - Malini Laloraya
- Female Reproduction and Metabolic Syndromes Laboratory, Division of Molecular Reproduction Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India,
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Qamar N, Pandey M, Vasudevan M, Kumar A, Shasany AK. Glandular trichome specificity of menthol biosynthesis pathway gene promoters from Mentha × piperita. Planta 2022; 256:110. [PMID: 36350410 DOI: 10.1007/s00425-022-04029-4] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Several cis-elements including Myb-binding motifs together confer glandular trichome specificity as revealed from heterologous expression and analysis of menthol biosynthesis pathway gene promoters. Glandular Trichomes (GTs) are result of division of epidermal cells that produce diverse metabolites. Species of mint family are important for their essential oil containing many high-value terpenoids, biosynthesized and stored in these GTs. Hence, GTs constitute attractive targets for metabolic engineering and GT-specific promoters are important. In this investigation, the upstream regions of the Mentha × piperita menthol biosynthetic pathway genes (-)-limonene synthase, (-)-P450 limonene-3- hydroxylase, (-)-trans-isopiperitenol dehydrogenase, (-)-Isopiperitenone reductase, ( +)-Pulegone reductase, (-)-Menthone reductase/ (-)-Menthol dehydrogenase and a branched pathway gene ( +)-menthofuran synthase were isolated and characterized. These fragments, fused to β-glucuronidase (GUS) reporter gene of pBI101 binary vector, are able to drive high level gene expression in transgenic tobacco trichomes with strong signals in GTs, except for (-)-Isopiperitenone reductase. The GT-enriched tissue from transformed plants were analysed for GUS enzyme activity and RNA expression which correlates the GUS staining. To characterize the cis-elements responsible for GT-specific expression, a series of 5' deletion constructs for MpPLS and MpPMFS were cloned and analysed in stable transgenic tobacco lines. The specificity of trichome expression was located to - 797 to- 598 bp sequence for (-)-limonene synthase and- 629 to - 530 bp for ( +)-menthofuran synthase promoters containing specific Myb-binding motifs in addition to other unique motifs described for developmental regulation without any defined pattern. All other pathway promoters also recruits specific but different Myb factors as indicated by this analysis.
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Affiliation(s)
- Nida Qamar
- Biotechnology Division, CSIR -Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Mytrai Pandey
- Biotechnology Division, CSIR -Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | | | - Ashish Kumar
- Biotechnology Division, CSIR -Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Ajit Kumar Shasany
- Biotechnology Division, CSIR -Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa, New Delhi, 110012, India.
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Bhattacharya A, Chatterjee S, Bhaduri U, Singh AK, Vasudevan M, Sashidhara KV, Guha R, Nazir A, Rath SK, Natesh N, Kundu TK. Butyrylation Meets Adipogenesis-Probed by a p300-Catalyzed Acylation-Specific Small Molecule Inhibitor: Implication in Anti-obesity Therapy. J Med Chem 2022; 65:12273-12291. [PMID: 36074919 DOI: 10.1021/acs.jmedchem.2c00943] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The enzyme p300, besides having acetyltransferase activity, can also catalyze other acylation modifications, whose physiological implications are still being investigated. Here, we report that the level of histone butyrylation increases globally as well as locally in the promoters of pro-adipogenic genes during adipogenesis. To delineate the role of p300-catalyzed butyrylation from acetylation in adipogenesis, we identified a semisynthetic derivative (LTK-14A) of garcinol, which specifically inhibited histone butyrylation without affecting acetylation. Treatment of 3T3L1 cells with LTK-14A abolished adipogenesis with downregulation of pro-adipogenic genes along with inhibition of H4K5 butyrylation. Administering LTK-14A to high-fat diet-fed and genetically obese db/db mice led to attenuation/decrease in their weight gain. The reduced obesity could be partially attributed to the inhibition of H4K5 butyrylation in adipocytes and liver. This report therefore not only, for the first time, causally links histone butyrylation with adipogenesis but also presents a probable candidate for anti-obesity therapeutics.
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Affiliation(s)
- Aditya Bhattacharya
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Sourav Chatterjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Utsa Bhaduri
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Akash Kumar Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | | | - Koneni V Sashidhara
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Rajdeep Guha
- Division of Laboratory Animal Facility, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Aamir Nazir
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Srikanta Kumar Rath
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Nagashayana Natesh
- Central Government Health Scheme Wellness Centre Number 8, Domlur, Bangalore 560071, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Division of Neuroscience and Aging Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
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7
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Singh AK, Neo SH, Liwang C, Pang KKL, Leng JCK, Sinha SH, Shetty MS, Vasudevan M, Rao VJ, Joshi I, Eswaramoorthy M, Pavon MV, Sheila AR, Navakkode S, Kundu TK, Sajikumar S. Glucose derived carbon nanosphere (CSP) conjugated TTK21, an activator of the histone acetyltransferases CBP/p300, ameliorates amyloid-beta 1-42 induced deficits in plasticity and associativity in hippocampal CA1 pyramidal neurons. Aging Cell 2022; 21:e13675. [PMID: 35962576 PMCID: PMC9470894 DOI: 10.1111/acel.13675] [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: 12/03/2019] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 01/25/2023] Open
Abstract
The master epigenetic regulator lysine acetyltransferase (KAT) p300/CBP plays a pivotal role in neuroplasticity and cognitive functions. Recent evidence has shown that in several neurodegenerative diseases, including Alzheimer's disease (AD), the expression level and function of p300/CBP are severely compromised, leading to altered gene expression causing pathological conditions. Here, we show that p300/CBP activation by a small-molecule TTK21, conjugated to carbon nanosphere (CSP) ameliorates Aβ-impaired long-term potentiation (LTP) induced by high-frequency stimulation, theta burst stimulation, and synaptic tagging/capture (STC). This functional rescue was correlated with CSP-TTK21-induced changes in transcription and translation. Mechanistically, we observed that the expression of a large number of synaptic plasticity- and memory-related genes was rescued, presumably by the restoration of p300/CBP mediated acetylation. Collectively, these results suggest that small-molecule activators of p300/CBP could be a potential therapeutic molecule for neurodegenerative diseases like AD.
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Affiliation(s)
- Akash K. Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics UnitJawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Sin H. Neo
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Christine Liwang
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Karen K. L. Pang
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Jason C. K. Leng
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Sarmistha H. Sinha
- Transcription and Disease Laboratory, Molecular Biology and Genetics UnitJawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Mahesh S. Shetty
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore,Lee Kong Chian School of Medicine, Nanyang Technological UniversitySingaporeSingapore
| | - Madavan Vasudevan
- Department of Neuroscience and PharmacologyIowa Neuroscience Institute, Carver College of Medicine, University of IowaIowa CityIowaUSA
| | - Vinay J. Rao
- Transcription and Disease Laboratory, Molecular Biology and Genetics UnitJawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Ila Joshi
- Transcription and Disease Laboratory, Molecular Biology and Genetics UnitJawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | | | - Maria V. Pavon
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Ang R. Sheila
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Sheeja Navakkode
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore,Chemistry and Physics of Materials UnitJawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Tapas K. Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics UnitJawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia,Division of Neuroscience and Aging BiologyCSIR‐Central Drug Research Institute Sector 10LucknowUttar PradeshIndia
| | - Sreedharan Sajikumar
- Department of PhysiologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore,Life Science Institute Neurobiology Programme (LSI)National University of SingaporeSingaporeSingapore,Healthy Longevity Translational Research ProgrammeYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
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Mishra P, Beura S, Sikder S, Dhal AK, Vasudevan M, Roy M, Rakshit J, Budhwar R, Kundu TK, Modak R. vp1524, a Vibrio parahaemolyticus NAD+ dependent deacetylase, regulates host response during infection by induction of host histone deacetylation. J Biochem 2022; 171:673-693. [PMID: 35325168 DOI: 10.1093/jb/mvac027] [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: 01/15/2022] [Accepted: 03/14/2022] [Indexed: 11/12/2022] Open
Abstract
Gram negative intracellular pathogen V. parahaemolyticus manifests its infection through a series of effector proteins released into the host via the type III secretion system. Most of these effector proteins alter signalling pathways of the host to facilitate survival and proliferation of bacteria inside host cells. Here, we report V. parahaemolyticus (serotype O3:K6) infection induced histone deacetylation in host intestinal epithelial cells, particularly deacetylation of H3K9, H3K56, H3K18 and H4K16 residues. We found a putative NAD+ dependent deacetylase, vp1524 (vpCobB) of Vibrio parahaemolyticus, was overexpressed during infection. Biochemical assays revealed that Vp1524 is a functional NAD+ dependent Sir2 family deacetylase in vitro, which was capable of deacetylating acetylated histones. Furthermore, we observed that vp1524 is expressed and localized to the nuclear periphery of the host cells during infection. Consequently, Vp1524 translocated to nuclear compartments of transfected cells, deacetylated histones, specifically causing deacetylation of those residues (K56, K16, K18) associated with V. parahaemolyticus infection. This infection induced deacetylation resulted in transcriptional repression of several host genes involved in epigenetic regulation, immune response, autophagy etc. Thus, our study shows that a V. parahaemolyticus lysine deacetylase Vp1524 is secreted inside the host cells during infection, modulating host gene expression through histone deacetylation.
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Affiliation(s)
- Pragyan Mishra
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar: 751024, Odisha, INDIA
| | - Shibangini Beura
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar: 751024, Odisha, INDIA
| | - Sweta Sikder
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru: 560064, INDIA
| | - Ajit Ku Dhal
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar: 751024, Odisha, INDIA
| | - Madavan Vasudevan
- Theomics International Pvt Ltd, 28, Income Tax Layout, Sadananda Nagar, NGEF Layout, Bengaluru - 560038, INDIA
| | - Manjima Roy
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar: 751024, Odisha, INDIA
| | - Joydeep Rakshit
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar: 751024, Odisha, INDIA
| | - Roli Budhwar
- Bionivid Technology Pvt. Ltd., 4C-209 1st Floor 4th Cross Kasturi Nagar Near New Horizon College Bangalore-560043 INDIA
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru: 560064, INDIA.,Division of Neuroscience and Ageing, Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, INDIA
| | - Rahul Modak
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar: 751024, Odisha, INDIA
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Singh AK, Rooge SB, Varshney A, Vasudevan M, Kumar M, Geffers R, Kumar V, Sarin SK. Identification of miRNAs associated with dendritic cell dysfunction during acute and chronic hepatitis B virus infection. J Med Virol 2021; 93:3697-3706. [PMID: 33107616 DOI: 10.1002/jmv.26629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 07/13/2020] [Revised: 10/08/2020] [Accepted: 10/25/2020] [Indexed: 12/14/2022]
Abstract
The uptake or expression of hepatitis B virus (HBV) proteins by dendritic cells (DCs) is considered important for disease outcome. Differential expression of microRNA (miRNA) may have a role in viral persistence and hepatocellular injury. The miRNA expression was investigated by microarray in DCs from different stages of HBV infection and liver disease namely, immune active (IA; n = 20); low replicative (LR; n = 20); HBeAg negative (n = 20); acute viral hepatitis (AVH, n = 20) and healthy controls (n = 20). miRNA levels were analyzed by unsupervised hierarchical clustering and principal component analyses and validated by quantitative polymerase Chain Reaction (qPCR). The miRNA-messenger RNA (mRNA)regulatory networks identified 19 miRNAs and 12 target gene interactions in major histocompatibility complex and other immune pathways. miR-2278, miR-615-3p, and miR-3681-3p were downregulated in the IA group compared to healthy control, miR-152-3p and miR-3613-3p in the LR group compared to IA group and miR-152-3p and miR-503-3p in HBe negative compared to LR group. However, miR-7-1-1-3p, miR-192-5p, miR-195-5p, and miR-32-5p in LR, miR-342-3p, and miR-940 in HBe negative, and miR-34a-5p, miR-130b-3p, miR-221-3p, miR-320a, miR-324-5p, and miR-484 in AVH were upregulated. Further, qPCR confirmed changes in miRNA levels and their target genes associated with antigen processing and presentation. Thus, a deregulated network of miRNAs-mRNAs in DCs seems responsible for an impaired immune response during HBV pathogenesis.
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Affiliation(s)
- Avishek Kumar Singh
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
- Vascular and Interventional Translational Laboratory, Departments of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Aditi Varshney
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | | | - Manoj Kumar
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vijay Kumar
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv Kumar Sarin
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
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10
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Vasudevan M, Hopkins P, Hickling D, Divithotawela C, Naidoo R, Collins P, Chambers D, Lee J. Gastroparesis after Lung Transplantation is Common but Not Associated with Inferior Outcomes. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Vasudevan M, Alagarsamy S, Mehrolia S, Jeevananda S. Can bot be my mental health therapist? - A pandemic panorama. J Psychiatr Res 2021; 134:30-31. [PMID: 33360221 DOI: 10.1016/j.jpsychires.2020.12.052] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 11/26/2022]
Affiliation(s)
- M Vasudevan
- School of Business and Management, Christ University, Bangalore, India.
| | | | - Sangeeta Mehrolia
- School of Business and Management, Christ University, Bangalore, India.
| | - S Jeevananda
- School of Business and Management, Christ University, Bangalore, India.
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12
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Berlin M, Natarajan N, Vasudevan M, Kumar GS. Impact of Skin on the Movement of Nitrates in a Fractured Porous Media: Numerical Investigations. Arab J Sci Eng 2021. [DOI: 10.1007/s13369-020-05174-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Balaganesh P, Vasudevan M, Suneethkumar SM, Shahir S, Natarajan N. Evaluation of Sugarcane and Soil Quality Amended by Sewage Sludge Derived Compost and Chemical Fertilizer. NEPT 2020. [DOI: 10.46488/nept.2020.v19i04.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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14
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Menon M, Budhwar R, Shukla RN, Bankar K, Vasudevan M, Ranga U. The Signature Amino Acid Residue Serine 31 of HIV-1C Tat Potentiates an Activated Phenotype in Endothelial Cells. Front Immunol 2020; 11:529614. [PMID: 33101270 PMCID: PMC7546421 DOI: 10.3389/fimmu.2020.529614] [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: 01/27/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
The natural cysteine to serine variation at position 31 of Tat in HIV-1C disrupts the dicysteine motif attenuating the chemokine function of Tat. We ask if there exists a trade-off in terms of a gain of function for HIV-1C Tat due to this natural variation. We constructed two Tat-expression vectors encoding Tat proteins discordant for the serine 31 residue (CS-Tat vs. CC-Tat), expressed the proteins in Jurkat cells under doxycycline control, and performed the whole transcriptome analysis to compare the early events of Tat-induced host gene expression. Our analysis delineated a significant enrichment of pathways and gene ontologies associated with the angiogenic signaling events in CS-Tat stable cells. Subsequently, we validated and compared angiogenic signaling events induced by CS- vs. CC-Tat using human umbilical vein endothelial cells (HUVEC) and the human cerebral microvascular endothelial cell line (hCMEC/D3). CS-Tat significantly enhanced the production of CCL2 from HUVEC and induced an activated phenotype in endothelial cells conferring on them enhanced migration, invasion, and in vitro morphogenesis potential. The ability of CS-Tat to induce the activated phenotype in endothelial cells could be of significance, especially in the context of HIV-associated cardiovascular and neuronal disorders. The findings from the present study are likely to help appreciate the functional significance of the SAR (signature amino acid residues) influencing the unique biological properties.
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Affiliation(s)
- Malini Menon
- Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | | | | | | | | | - Udaykumar Ranga
- Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
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Mallu ACT, Vasudevan M, Allanki S, Nathan AA, Ravi MM, Ramanathan GS, Pradeepa R, Mohan V, Dixit M. Prediabetes uncovers differential gene expression at fasting and in response to oral glucose load in immune cells. Clin Nutr 2020; 40:1247-1259. [PMID: 32863060 DOI: 10.1016/j.clnu.2020.08.007] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Metabolic disorders including diabetes are associated with immune cell dysfunction. However, the effect of normal glucose metabolism or impairment thereof on immune cell gene expression is not well known. Hence, in this cross-sectional pilot study, we sought to determine the differences in gene expression in the peripheral blood mono-nuclear cells (PBMCs) of normal glucose tolerant (NGT) and prediabetic (PD) Asian Indian men, at fasting and in response to 75 g oral glucose load. METHODS Illumina HT12 bead chip-based microarray was performed on PBMCs at fasting and 2-h post load conditions for NGT (N = 6) and PD (N = 9) subjects. Following normalization and due quality control of the raw data, differentially expressed genes (DEGs) under different conditions within and across the two groups were identified using GeneSpring GX V12.0 software. Paired and unpaired Student's t-tests were applied along with fold change cut-offs for appropriate comparisons. Validation of the microarray data was carried out through real-time qPCR analysis. Significantly regulated biological pathways were analyzed by employing DEGs and DAVID resource. Deconvolution of the DEGs between NGT and PD subjects at fasting was performed using CIBERSORT and genes involved in regulatory T-cell (Treg) function were further analyzed for biological significance. RESULTS Glucose load specifically altered the expression of 112 genes in NGT and 356 genes in PD subjects. Biological significance analysis revealed transient up-regulation of innate and adaptive immune response related genes following oral glucose load in NGT individuals, which was not observed in PD subjects. Instead, in the PD group, glucose load led to an increase in the expression of pro-atherogenic and anti-angiogenic genes. Comparison of gene expression at fasting state in PD versus NGT revealed 21,707 differentially expressed genes. Biological significance analysis of the immune function related genes between these two groups (at fasting) revealed higher gene expression of members of the TLR signaling, MHC class II molecules, and T-cell receptor, chemotaxis and adhesion pathways in PD subjects. Expression of interferon-γ (IFN-γ) and TNFα was higher and that of type-1 interferons and TGF-β was lower at fasting state in PD subjects compared to NGT. Additionally, expression of multiple proteasome subunits and protein arginine methyl transferase genes (PRMTs) were higher and that of Treg specific genes was significantly distinct at fasting in PD subjects compared to NGT. CONCLUSION Prediabetes uncovers constitutive TLR activation, enhanced IFN-γ signaling, and Treg dysfunction at fasting along with altered gene expression response to oral glucose load.
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Affiliation(s)
- Abhiram Charan Tej Mallu
- Laboratory of Vascular Biology, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | | | - Srinivas Allanki
- Laboratory of Vascular Biology, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Abel Arul Nathan
- Laboratory of Vascular Biology, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Mahalakshmi M Ravi
- Institute Hospital, Indian Institute of Technology Madras, Chennai, India
| | | | - Rajendra Pradeepa
- Department of Diabetology, Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, India
| | - Viswanathan Mohan
- Department of Diabetology, Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, India
| | - Madhulika Dixit
- Laboratory of Vascular Biology, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
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16
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Raguraman R, Parameswaran S, Kanwar JR, Vasudevan M, Chitipothu S, Kanwar RK, Krishnakumar S. Gene expression profiling of tumor stroma interactions in retinoblastoma. Exp Eye Res 2020; 197:108067. [PMID: 32585195 DOI: 10.1016/j.exer.2020.108067] [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: 06/27/2019] [Revised: 04/23/2020] [Accepted: 05/08/2020] [Indexed: 01/18/2023]
Abstract
We aimed to identify the critical molecular pathways altered upon tumor stroma interactions in retinoblastoma (RB). In vitro 2 D cocultures of RB tumor cells (Weri-Rb-1 and NCC-RbC-51) with primary bone marrow stromal cells (BMSC) was established. Global gene expression patterns in coculture samples were assessed using Affymetrix Prime view human gene chip microarray and followed with bioinformatics analyses. Key upregulated genes from Weri-Rb-1 + BMSC and NCC-RbC-51 + BMSC coculture were validated using qRT-PCR to ascertain their role in RB progression. Whole genome microarray experiments identified significant (P ≤ 0.05, 1.1 log 2 FC) transcriptome level changes induced upon coculture of RB cells with BMSC. A total of 1155 genes were downregulated and 1083 upregulated in Weri-Rb-1 + BMSC coculture. Similarly, 1865 genes showed downregulation and 1644 genes were upregulation in NCC-RbC-51 + BMSC coculture. The upregulated genes were significantly associated with pathways of focal adhesion, PI3K-Akt signalling, ECM-receptor interaction, JAK-STAT, TGF-β signalling thus contributing to RB progression. Validation of key genes by qRT-PCR revealed significant overexpression of IL8, IL6, MYC and SMAD3 in the case of Weri-Rb-1 + BMSC coculture and IL6 in the case of NCC-RbC-51 + BMSC coculture. The microarray expression study on in vitro RB coculture models revealed the pathways that could be involved in the progression of RB. The gene signature obtained in a stimulated model when a growing tumor interacts with its microenvironment may provide new horizons for potential targeted therapy in RB.
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Affiliation(s)
- Rajeswari Raguraman
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, 600006, Tamil Nadu, India; School of Medicine, Institute for Innovation in Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, 3216, VIC, Australia
| | - Sowmya Parameswaran
- Radheshyam Kanoi Stem Cell Laboratory, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, 600006, Tamil Nadu, India
| | - Jagat Rakesh Kanwar
- School of Medicine, Institute for Innovation in Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, 3216, VIC, Australia
| | | | - Srujana Chitipothu
- Central Research Instrumentation Facility, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, 600006, Tamil Nadu, India
| | - Rupinder Kaur Kanwar
- School of Medicine, Institute for Innovation in Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, 3216, VIC, Australia
| | - Subramanian Krishnakumar
- Larsen & Toubro Department of Ocular Pathology, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, 600006, Tamil Nadu, India; School of Medicine, Institute for Innovation in Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, 3216, VIC, Australia.
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Subuddhi A, Kumar M, Majumder D, Sarkar A, Ghosh Z, Vasudevan M, Kundu M, Basu J. Unraveling the role of H3K4 trimethylation and lncRNA HOTAIR in SATB1 and DUSP4-dependent survival of virulent Mycobacterium tuberculosis in macrophages. Tuberculosis (Edinb) 2019; 120:101897. [PMID: 32090865 DOI: 10.1016/j.tube.2019.101897] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 07/11/2019] [Revised: 12/15/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022]
Abstract
The modification of chromatin influences host transcriptional programs during bacterial infection, at times skewing the balance in favor of pathogen survival. To test the role of chromatin modifications during Mycobacterium tuberculosis infection, we analysed genome-wide deposition of H3K4me3 marks in macrophages infected with either avirulent M. tuberculosis H37Ra or virulent H37Rv, by chromatin immunoprecipitation, followed by sequencing. We validated differences in association of H3K4me3 at the loci of special AT-rich sequence binding protein 1 (SATB1) and dual specificity MAP kinase phosphatase 4 (DUSP4) between H37Rv and H37Ra-infected macrophages, and demonstrated their role in regulating bacterial survival in macrophages as well as the expression of chemokines. SATB1 repressed gp91phox (an NADPH oxidase subunit) thereby regulating reactive oxygen species (ROS) generation during infection. Long non-coding RNA HOX transcript antisense RNA (HOTAIR) was upregulated in H37Ra-, but downregulated in H37Rv-infected macrophages. HOTAIR overexpression correlated with deposition of repressive H3K27me3 marks around the TSSs of DUSP4 and SATB1, suggesting that its downregulation favors the transcription of SATB1 and DUSP4. In summary, we have delineated histone modification- and lncRNA-dependent mechanisms regulating gene expression patterns facilitating survival of virulent M. tuberculosis. Our observations raise the possibility of harnessing histone-modifying enzymes to develop host-directed therapies for tuberculosis.
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Affiliation(s)
| | - Manish Kumar
- Department of Chemistry, Bose Institute, Kolkata, 700009, India
| | | | - Arijita Sarkar
- Division of Bioinformatics, Bose Institute, Kolkata, 700054, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, 700054, India
| | | | | | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, 700009, India.
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18
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Gupta M, Sharma G, Saxena D, Budhwar R, Vasudevan M, Gupta V, Gupta A, Gupta R, Chandran D. Dual RNA-Seq analysis of Medicago truncatula and the pea powdery mildew Erysiphe pisi uncovers distinct host transcriptional signatures during incompatible and compatible interactions and pathogen effector candidates. Genomics 2019; 112:2130-2145. [PMID: 31837401 DOI: 10.1016/j.ygeno.2019.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/14/2019] [Accepted: 12/09/2019] [Indexed: 12/29/2022]
Abstract
Powdery mildew (PM) is a serious fungal disease of legumes. To gain novel insights into PM pathogenesis and host resistance/susceptibility, we used dual RNA-Seq to simultaneously capture host and pathogen transcriptomes at 1 d post-inoculation of resistant and susceptible Medicago truncatula genotypes with the PM Erysiphe pisi (Ep). Differential expression analysis indicates that R-gene mediated resistance against Ep involves extensive transcriptional reprogramming. Functional enrichment of differentially expressed host genes and in silico analysis of co-regulated promoters suggests that amplification of PTI, activation of the JA/ET signaling network, and regulation of growth-defense balance correlate with resistance. In contrast, processes that favor biotrophy, including suppression of defense signaling and programmed cell death, and weaker cell wall defenses are important susceptibility factors. Lastly, Ep effector candidates and genes with known/putative virulence functions were identified, representing a valuable resource that can be leveraged to improve our understanding of legume-PM interactions.
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Affiliation(s)
- Megha Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India; Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Gunjan Sharma
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Divya Saxena
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Roli Budhwar
- Bionivid Technology Pvt. Ltd., Kasturi Nagar, Bangalore, India
| | | | - Varsha Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Arunima Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Rashi Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Divya Chandran
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India.
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19
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Mitra SD, Ganaie F, Bankar K, Velu D, Mani B, Vasudevan M, Shome R, Rahman H, Kumar Ghosh S, Shome BR. Genome-wide analysis of mammary gland shows modulation of transcriptome landscape with alternative splice variants in Staphylococcus aureus mastitis in mice. Gene 2019; 735:144278. [PMID: 31821873 DOI: 10.1016/j.gene.2019.144278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 02/23/2019] [Revised: 11/22/2019] [Accepted: 11/24/2019] [Indexed: 01/25/2023]
Abstract
Epidemiological mapping shows Staphylococcus aureus to be the leading mastitis causing pathogen in India with diverse genetic lineages circulating in the dairy cattle population. We previously reported that endemic clonal strains of S. aureus isolated from subclinical mastitis lead to specific alteration of epigenetic modulators resulting in deviating immune response in intramammary infection mouse model. However, the extent of transcriptome modulation and associated alternative splicing in S. aureus mastitis is poorly understood. Hence, to gain a deeper insight of the extent of modulation of transcriptome landscape, we expanded the study here using high throughput, paired-end RNA sequencing analysis of the mouse mammary gland inoculated with three strains of S. aureus (SA1, SA2, and SA3) possessing specific genotype, virulence and enterotoxin traits. Overall, we detected 35,878 transcripts in S. aureus inoculated mammary gland, 23% more than those annotated in the reference genome. Expression of 20,756 transcripts was > 1 fragment per kilobase of transcript per million mapped fragments and 25.95% of multi-exonic genes were alternatively spliced. We noted Alternative Splicing (AS) events for > 100 immune-related genes. S. aureus infection quantitatively altered AS events in mice mammary gland. Collectively, the majority of differentially expressed significant genes clustered into immune-associated, cell adhesion and metabolic process categories. We observed AS events for 379 transcripts of genes putatively encoding several splicing associated proteins and transcription factors besides inflammatory mediators. The present analysis provides new insights into global transcriptome landscape and AS events in host-defense related genes in response to S. aureus intramammary infection, suggesting the need for studies focusing on multi-target and/or network therapeutics approach to combat mastitis.
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Affiliation(s)
- Susweta Das Mitra
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India; Department of Biotechnology, Assam University, Silchar, AS, India; School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, KA, India
| | - Feroze Ganaie
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India; Department of Medicine, Division of Pulmonary/Allergy/Critical care, University of Alabama at Birmingham, AL, USA
| | - Kiran Bankar
- Bionivid Technology Pvt. Ltd., Bangalore, KA, India
| | - Dhanikachalam Velu
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India
| | - Bhuvana Mani
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India
| | | | - Rajeswari Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India
| | - Habibur Rahman
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India; International Livestock Research Institute, Pusa, DL, India
| | | | - Bibek Ranjan Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, KA, India.
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20
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Vasantharaja P, Vasudevan M, Parameswaran P. Effect of welding techniques on the microstructure and mechanical properties of reduced activation ferritic-martensitic (RAFM) steel weld joints. Fusion Engineering and Design 2019. [DOI: 10.1016/j.fusengdes.2019.111289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Behera AK, Kumar M, Shanmugam MK, Bhattacharya A, Rao VJ, Bhat A, Vasudevan M, Gopinath KS, Mohiyuddin A, Chatterjee A, Sethi G, Kundu TK. Functional interplay between YY1 and CARM1 promotes oral carcinogenesis. Oncotarget 2019; 10:3709-3724. [PMID: 31217904 PMCID: PMC6557205 DOI: 10.18632/oncotarget.26984] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 05/13/2019] [Indexed: 12/29/2022] Open
Abstract
Coactivator associated arginine methyltransferase 1 (CARM1) has been functionally implicated in maintenance of pluripotency, cellular differentiation and tumorigenesis; where it plays regulatory roles by virtue of its ability to coactivate transcription as well as to modulate protein function as an arginine methyltransferase. Previous studies establish an oncogenic function of CARM1 in the context of colorectal and breast cancer, which correlate to its overexpressed condition. However, the mechanism behind its deregulated expression in the context of cancer has not been addressed before. In the present study we uncover an oncogenic function of CARM1 in the context of oral cancer, where it was found to be overexpressed. We also identify YY1 to be a positive regulator of CARM1 gene promoter, where silencing of YY1 in oral cancer cell line could lead to reduction in expression of CARM1. In this context, YY1 showed concomitant overexpression in oral cancer patient samples compared to adjacent normal tissue. Cell line based experiments as well as xenograft study revealed pro-neoplastic functions of YY1 in oral cancer. Transcriptomics analysis as well as qRT-PCR validation clearly indicated pro-proliferative, pro-angiogenic and pro-metastatic role of YY1 in oral cancer. We also show that YY1 is a substrate of CARM1 mediated arginine methylation, where the latter could coactivate YY1 mediated reporter gene activation in vivo. Taken together, CARM1 and YY1 were found to regulate each other in a positive feedback loop to facilitate oral cancer progression.
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Affiliation(s)
- Amit K Behera
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Aditya Bhattacharya
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Vinay J Rao
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Akshay Bhat
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Madavan Vasudevan
- Bionivid Technology Private Limited, Kasturi Nagar, Bangalore 560043, India
| | - Kodaganur S Gopinath
- Department of Surgical Oncology, HCG Bangalore Institute of Oncology, Bangalore 560027, India
| | - Azeem Mohiyuddin
- Department of Pathology, Sri Devaraj Urs Academy of Higher Education and Research Center, Kolar, Bangalore 563101, India.,Department of Ear, Nose and Throat, Sri Devaraj Urs Academy of Higher Education and Research Center, Kolar, Bangalore 563101, India.,Department of Head and Neck Surgery, Sri Devaraj Urs Academy of Higher Education and Research Center, Kolar, Bangalore 563101, India
| | - Anupam Chatterjee
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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Pandit H, Kale K, Yamamoto H, Thakur G, Rokade S, Chakraborty P, Vasudevan M, Kishore U, Madan T, Fichorova RN. Surfactant Protein D Reverses the Gene Signature of Transepithelial HIV-1 Passage and Restricts the Viral Transfer Across the Vaginal Barrier. Front Immunol 2019; 10:264. [PMID: 30984160 PMCID: PMC6447669 DOI: 10.3389/fimmu.2019.00264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/31/2019] [Indexed: 01/02/2023] Open
Abstract
Effective prophylactic strategy against the current epidemic of sexually transmitted HIV-1 infection requires understanding of the innate gatekeeping mechanisms at the genital mucosa. Surfactant protein D (SP-D), a member of the collectin family of proteins naturally present in the vaginal tract, is a potential HIV-1 entry inhibitor at the cellular level. Human EpiVaginal tissues compartmentalized in culture inserts were apically exposed to HIV-1 and/or a recombinant fragment of human SP-D (rfhSP-D) and viral passage was assessed in the basal chamber containing mononuclear leukocytes. To map the gene signature facilitating or resisting the transepithelial viral transfer, microarray analysis of the HIV-1 challenged EpiVaginal tissues was performed in the absence or presence of rfhSP-D. Mucosal biocompatibility of rfhSP-D was assessed ex vivo and in the standard rabbit vaginal irritation model. The passage of virus through the EpiVaginal tissues toward the underlying target cells was associated with a global epithelial gene signature including differential regulation of genes primarily involved in inflammation, tight junctions and cytoskeletal framework. RfhSP-D significantly inhibited HIV-1 transfer across the vaginal tissues and was associated with a significant reversal of virus induced epithelial gene signature. Pro-inflammatory NF-κB and mTOR transcripts were significantly downregulated, while expression of the tight junctions and cytoskeletal genes was upheld. In the absence of virus, rfhSP-D directly interacted with the EpiVaginal tissues and upregulated expression of genes related to structural stability of the cell and epithelial integrity. There was no increment in the viral acquisition by the PBMCs present in basal chambers wherein, the EpiVaginal tissues in apical chambers were treated with rfhSP-D. The effective concentrations of rfhSP-D had no effect on lactobacilli, epithelial barrier integrity and were safe on repeated applications onto the rabbit vaginal mucosa. This pre-clinical safety data, coupled with its efficacy of restricting viral passage via reversal of virus-induced gene expression of the vaginal barrier, make a strong argument for clinical trials of rfhSP-D as a topical anti-HIV microbicide.
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Affiliation(s)
- Hrishikesh Pandit
- Department of Innate Immunity, ICMR National Institute for Research in Reproductive Health, Mumbai, India.,Laboratory of Genital Tract Biology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States
| | - Kavita Kale
- Department of Innate Immunity, ICMR National Institute for Research in Reproductive Health, Mumbai, India
| | - Hidemi Yamamoto
- Laboratory of Genital Tract Biology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States
| | - Gargi Thakur
- Department of Innate Immunity, ICMR National Institute for Research in Reproductive Health, Mumbai, India
| | - Sushama Rokade
- Department of Innate Immunity, ICMR National Institute for Research in Reproductive Health, Mumbai, India
| | - Payal Chakraborty
- Genome Informatics Research Group, Bionivid Technology Pvt. Ltd., Bengaluru, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt. Ltd., Bengaluru, India
| | - Uday Kishore
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Taruna Madan
- Department of Innate Immunity, ICMR National Institute for Research in Reproductive Health, Mumbai, India
| | - Raina Nakova Fichorova
- Laboratory of Genital Tract Biology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States
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23
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Dhanasekaran K, Bose A, Rao VJ, Boopathi R, Shankar SR, Rao VK, Swaminathan A, Vasudevan M, Taneja R, Kundu TK. Unraveling the role of aurora A beyond centrosomes and spindle assembly: implications in muscle differentiation. FASEB J 2018; 33:219-230. [PMID: 29995440 DOI: 10.1096/fj.201800997] [Citation(s) in RCA: 8] [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] [Indexed: 12/19/2022]
Abstract
Aurora kinases are critical mitotic serine/threonine kinases and are often implicated in tumorigenesis. Recent studies of the interphase functions for aurora kinase (Aurk)A have considerably expanded our understanding of its role beyond mitosis. To identify the unknown targets of AurkA, we used peptide array-based screening and found E2F4 to be a novel substrate. Phosphorylation of E2F4 by AurkA at Ser75 regulates its DNA binding and subcellular localization. Because E2F4 plays an important role in skeletal muscle differentiation, we attempted to gain insight into E2F4 phosphorylation in this context. We observed that a block in E2F4 phosphorylation retained it better within the nucleus and inhibited muscle differentiation. RNA sequencing analysis revealed a perturbation of the gene network involved in the process of muscle differentiation and mitochondrial biogenesis. Collectively, our findings establish a novel role of AurkA in the process of skeletal muscle differentiation.-Dhanasekaran, K., Bose, A., Rao, V. J., Boopathi, R., Shankar, S. R., Rao, V. K., Swaminathan, A., Vasudevan, M., Taneja, R., Kundu, T. K. Unravelling the role of aurora A beyond centrosomes and spindle assembly: implications in muscle differentiation.
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Affiliation(s)
- Karthigeyan Dhanasekaran
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Arnab Bose
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Vinay J Rao
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Ramachandran Boopathi
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Shilpa Rani Shankar
- Department of Physiology, Cellular Differentiation, and Apoptosis, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; and
| | - Vinay Kumar Rao
- Department of Physiology, Cellular Differentiation, and Apoptosis, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; and
| | - Amrutha Swaminathan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Reshma Taneja
- Department of Physiology, Cellular Differentiation, and Apoptosis, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; and
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Bulagonda EP, Manivannan B, Mahalingam N, Lama M, Chanakya PP, Khamari B, Jadhao S, Vasudevan M, Nagaraja V. Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection. Sci Rep 2018; 8:8447. [PMID: 29855598 PMCID: PMC5981450 DOI: 10.1038/s41598-018-26874-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/17/2018] [Indexed: 01/18/2023] Open
Abstract
Elizabethkingia anophelis has now emerged as an opportunistic human pathogen. However, its mechanisms of transmission remain unexplained. Comparative genomic (CG) analysis of E. anopheles endophthalmitis strain surprisingly found from an eye infection patient with twenty-five other E. anophelis genomes revealed its potential to participate in horizontal gene transfer. CG analysis revealed that the study isolate has an open pan genome and has undergone extensive gene rearrangements. We demonstrate that the strain is naturally competent, hitherto not reported in any members of Elizabethkingia. Presence of competence related genes, mobile genetic elements, Type IV, VI secretory systems and a unique virulence factor arylsulfatase suggests a different lineage of the strain. Deciphering the genome of E. anophelis having a reservoir of antibiotic resistance genes and virulence factors associated with diverse human infections may open up avenues to deal with the myriad of its human infections and devise strategies to combat the pathogen.
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Affiliation(s)
- Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India.
| | - Bhavani Manivannan
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | - Niranjana Mahalingam
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India.,Department of Microbiology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, Andhra Pradesh, India
| | - Manmath Lama
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | - Pachi Pulusu Chanakya
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | - Sudhir Jadhao
- Bionivid technology Pvt Ltd, 4C-209, 4th cross, Kasturi Nagar, Bengaluru, India
| | - Madavan Vasudevan
- Bionivid technology Pvt Ltd, 4C-209, 4th cross, Kasturi Nagar, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India. .,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
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25
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Gupta A, Venkataraman B, Vasudevan M, Bankar KG. Publisher Correction: Co-expression network analysis of toxin-antitoxin loci in Mycobacterium tuberculosis reveals key modulators of cellular stress. Sci Rep 2018; 8:7554. [PMID: 29748643 PMCID: PMC5945647 DOI: 10.1038/s41598-018-25178-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,Department of Biochemistry and Centre for Innovation in Infectious Diseases Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, 110021, India.
| | - Balaji Venkataraman
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
| | - Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
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26
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Sanan-Mishra N, Tripathi A, Goswami K, Shukla RN, Vasudevan M, Goswami H. ARMOUR - A Rice miRNA: mRNA Interaction Resource. Front Plant Sci 2018; 9:602. [PMID: 29868062 PMCID: PMC5952065 DOI: 10.3389/fpls.2018.00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/16/2018] [Indexed: 05/09/2023]
Abstract
ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.
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Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kavita Goswami
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rohit N. Shukla
- Genome Informatics Research Group, Bionivid Technology Private Limited, Bengaluru, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Private Limited, Bengaluru, India
| | - Hitesh Goswami
- Genome Informatics Research Group, Bionivid Technology Private Limited, Bengaluru, India
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27
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Singh AK, Rooge SB, Varshney A, Vasudevan M, Bhardwaj A, Venugopal SK, Trehanpati N, Kumar M, Geffers R, Kumar V, Sarin SK. Global microRNA expression profiling in the liver biopsies of hepatitis B virus-infected patients suggests specific microRNA signatures for viral persistence and hepatocellular injury. Hepatology 2018; 67:1695-1709. [PMID: 29194684 DOI: 10.1002/hep.29690] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/13/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023]
Abstract
UNLABELLED Hepatitis B virus (HBV) can manipulate the microRNA (miRNA) regulatory networks in infected cells to create a permissive environment for viral replication, cellular injury, disease onset, and its progression. The aim of the present study was to understand the miRNA networks and their target genes in the liver of hepatitis B patients involved in HBV replication, liver injury, and liver fibrosis. We investigated differentially expressed miRNAs by microarray in liver biopsy samples from different stages of HBV infection and liver disease (immune-tolerant [n = 8], acute viral hepatitis [n = 8], no fibrosis [n = 16], early [F1+F2, n = 19] or late [F3+F4, n = 14] fibrosis, and healthy controls [n = 7]). miRNA expression levels were analyzed by unsupervised principal component analysis and hierarchical clustering. Analysis of miRNA-mRNA regulatory networks identified 17 miRNAs and 18 target gene interactions with four distinct nodes, each representing a stage-specific gene regulation during disease progression. The immune-tolerant group showed elevated miR-199a-5p, miR-221-3p, and Let-7a-3p levels, which could target genes involved in innate immune response and viral replication. In the acute viral hepatitis group, miR-125b-5p and miR-3613-3p were up, whereas miR-940 was down, which might affect cell proliferation through the signal transducer and activator of transcription 3 pathway. In early fibrosis, miR-34b-3p, miR-1224-3p, and miR-1227-3p were up, while miR-499a-5p was down, which together possibly mediate chronic inflammation. In advanced fibrosis, miR-1, miR-10b-5p, miR-96-5p, miR-133b, and miR-671-5p were up, while miR-20b-5p and miR-455-3p were down, possibly allowing chronic disease progression. Interestingly, only 8 of 17 liver-specific miRNAs exhibited a similar expression pattern in patient sera. CONCLUSION miRNA signatures identified in this study corroborate previous findings and provide fresh insight into the understanding of HBV-associated liver diseases which may be helpful in developing early-stage disease diagnostics and targeted therapeutics. (Hepatology 2018;67:1695-1709).
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Affiliation(s)
- Avishek Kumar Singh
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | | | - Aditi Varshney
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | | | - Ankit Bhardwaj
- Department of Clinical Research, Institute of Liver and Biliary Sciences
| | - Senthil Kumar Venugopal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India.,Faculty of Life Sciences & Biotechnology, South Asian University, New Delhi, India
| | - Nirupama Trehanpati
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Manoj Kumar
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vijay Kumar
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv Kumar Sarin
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India.,Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
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28
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Behera AK, Bhattacharya A, Vasudevan M, Kundu TK. p53 mediated regulation of coactivator associated arginine methyltransferase 1 (CARM1) expression is critical for suppression of adipogenesis. FEBS J 2018; 285:1730-1744. [PMID: 29575726 DOI: 10.1111/febs.14440] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 08/11/2017] [Revised: 01/31/2018] [Accepted: 03/19/2018] [Indexed: 11/27/2022]
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1/PRMT4) is a type I arginine methyltransferase that mediates transcriptional activation via methylation of histone H3 on R17, R26, and R42. CARM1 is also a coactivator of transcription of various transcription factors such as NF-kB, MEF2C, β-catenin, p53, PPAR-gamma etc. CARM1 has been functionally implicated in maintenance of pluripotency, cellular differentiation, and tumorigenesis; where its expression status plays an important role. Although its expression has been shown to be regulated by a few miRNAs in different contexts at post-transcriptional level, transcriptional regulation of CARM1 gene is still unexplored. In this report we demonstrate that CARM1 is a p53 responsive gene, where p53 could suppress CARM1 promoter-driven luciferase expression. CARM1 gene expression was found to be repressed by p53 in 3T3L1 preadipocytes when activated with Nutlin-3a treatment. Ectopic overexpression of CARM1 could rescue inhibitory effect of p53 on adipogenesis, suggesting a role of p53-CARM1 axis of regulation operational in the context of adipocyte differentiation. p53 and CARM1 showed antagonistic regulatory influence on PPAR-gamma expression; which suggests that p53-mediated suppression of adipogenesis could be partly via repression of CARM1 expression. Taken together these observations provide convincing mechanistic explanation for p53 function in the context of adipocyte differentiation process.
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Affiliation(s)
- Amit K Behera
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Aditya Bhattacharya
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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29
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Behera AK, Bhattacharya A, Vasudevan M, Kundu TK. p53 mediated regulation of Coactivator associated arginine methyltransferase 1 (CARM1) expression is critical for suppression of adipogenesis. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.lb13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Kalmodia S, Parameswaran S, Ganapathy K, Yang W, Barrow CJ, Kanwar JR, Roy K, Vasudevan M, Kulkarni K, Elchuri SV, Krishnakumar S. Characterization and Molecular Mechanism of Peptide-Conjugated Gold Nanoparticle Inhibiting p53-HDM2 Interaction in Retinoblastoma. Mol Ther Nucleic Acids 2017; 9:349-364. [PMID: 29246314 PMCID: PMC5684491 DOI: 10.1016/j.omtn.2017.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 01/12/2023]
Abstract
Inhibition of the interaction between p53 and HDM2 is an effective therapeutic strategy in cancers that harbor a wild-type p53 protein such as retinoblastoma (RB). Nanoparticle-based delivery of therapeutic molecules has been shown to be advantageous in localized delivery, including to the eye, by overcoming ocular barriers. In this study, we utilized biocompatible gold nanoparticles (GNPs) to deliver anti-HDM2 peptide to RB cells. Characterization studies suggested that GNP-HDM2 was stable in biologically relevant solvents and had optimal cellular internalization capability, the primary requirement of any therapeutic molecule. GNP-HDM2 treatment in RB cells in vitro suggested that they function by arresting RB cells at the G2M phase of the cell cycle and initiating apoptosis. Analysis of molecular changes in GNP-HDM2-treated cells by qRT-PCR and western blotting revealed that the p53 protein was upregulated; however, transactivation of its downstream targets was minimal, except for the PUMA-BCl2 and Bax axis. Global gene expression and in silico bioinformatic analysis of GNP-HDM2-treated cells suggested that upregulation of p53 might presumptively mediate apoptosis through the induction of p53-inducible miRNAs.
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Affiliation(s)
- Sushma Kalmodia
- Department of Nano Biotechnology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, Nungambakkam, Chennai 600 006, India; Centre for Chemistry and Biotechnology, Deakin University, Geelong Campus, Waurn Ponds, VIC 3216, Australia
| | - Sowmya Parameswaran
- Radheshyam Kanoi Stem Cell Laboratory, Vision Research Foundation, Sankara Nethralaya, 18, College Road, Nungambakkam, Chennai 600 006, India
| | - Kalaivani Ganapathy
- Department of Nano Biotechnology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, Nungambakkam, Chennai 600 006, India
| | - Wenrong Yang
- Centre for Chemistry and Biotechnology, Deakin University, Geelong Campus, Waurn Ponds, VIC 3216, Australia
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Geelong Campus, Waurn Ponds, VIC 3216, Australia
| | - Jagat R Kanwar
- Nanomedicine -Laboratory of Immunology and Molecular Biomedical Research (NLIMBR), School of Medicine (SoM), Centre for Molecular and Medicine Research (C-MMR), Deakin University, Geelong Campus, Waurn Ponds, VIC 3217, Australia
| | - Kislay Roy
- Nanomedicine -Laboratory of Immunology and Molecular Biomedical Research (NLIMBR), School of Medicine (SoM), Centre for Molecular and Medicine Research (C-MMR), Deakin University, Geelong Campus, Waurn Ponds, VIC 3217, Australia
| | | | | | - Sailaja V Elchuri
- Department of Nano Biotechnology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, Nungambakkam, Chennai 600 006, India
| | - Subramanian Krishnakumar
- Department of Nano Biotechnology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, Nungambakkam, Chennai 600 006, India.
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31
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Gupta A, Venkataraman B, Vasudevan M, Gopinath Bankar K. Co-expression network analysis of toxin-antitoxin loci in Mycobacterium tuberculosis reveals key modulators of cellular stress. Sci Rep 2017; 7:5868. [PMID: 28724903 PMCID: PMC5517426 DOI: 10.1038/s41598-017-06003-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 06/07/2017] [Indexed: 11/09/2022] Open
Abstract
Research on toxin-antitoxin loci (TA loci) is gaining impetus due to their ubiquitous presence in bacterial genomes and their observed roles in stress survival, persistence and drug tolerance. The present study investigates the expression profile of all the seventy-nine TA loci found in Mycobacterium tuberculosis. The bacterium was subjected to multiple stress conditions to identify key players of cellular stress response and elucidate a TA-coexpression network. This study provides direct experimental evidence for transcriptional activation of each of the seventy-nine TA loci following mycobacterial exposure to growth-limiting environments clearly establishing TA loci as stress-responsive modules in M. tuberculosis. TA locus activation was found to be stress-specific with multiple loci activated in a duration-based response to a particular stress. Conditions resulting in arrest of cellular translation led to greater up-regulation of TA genes suggesting that TA loci have a primary role in arresting translation in the cell. Our study identifed higBA2 and vapBC46 as key loci that were activated in all the conditions tested. Besides, relBE1, higBA3, vapBC35, vapBC22 and higBA1 were also upregulated in multpile stresses. Certain TA modules exhibited co-activation across multiple conditions suggestive of a common regulatory mechanism.
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Affiliation(s)
- Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,Department of Biochemistry and Centre for Innovation in Infectious Diseases Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, 110021, India.
| | - Balaji Venkataraman
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
| | - Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
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32
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Trehanpati N, Sehgal R, Patra S, Vyas A, Vasudevan M, Khosla R, Khanam A, Kumar G, Maiwall R, Ramakrishna G, Kottilil S, Sarin SK. miRNA signatures can predict acute liver failure in hepatitis E infected pregnant females. Heliyon 2017; 3:e00287. [PMID: 28413835 PMCID: PMC5384411 DOI: 10.1016/j.heliyon.2017.e00287] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/07/2017] [Accepted: 03/28/2017] [Indexed: 02/07/2023] Open
Abstract
Background Acute viral hepatitis E (AVH-E) can often result in acute liver failure (ALF) during pregnancy. microRNAs serve as mediators in drug induced liver failure. We investigated their role as a biomarker in predicting ALF due to HEV (ALF-E). Methods We performed next generation sequencing and subsequent validation studies in PBMCs of pregnant (P) self limiting AVH-E, ALF due to HEV (ALF-E) and compared with AVH-E in non-pregnant (NP) females and healthy controls. Findings Eleven microRNAs were significantly expressed in response to HEV infection; importantly, miR- 431, 654, 1468 and 4435, were distinctly expressed in pregnant self-limiting AVH-E and healthy females (p = 0.0005), but not in ALF-E. Sixteen exclusive microRNAs differentiated ALF-E from self limiting AVH-E in pregnant females. miR-450b which affects cellular proliferation and metabolic processes through RNF20 and SECB was predominanlty upregulated and correlated with poor outcome (ROC 0.958, p = 0.001). Interpretation Our results reveal that a specific microRNA profile can predict fatality in ALF-E in pregnancy. These microRNAs could be exploited as prognostic biomarkers and help in the development of new therapeutic interventions.
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Affiliation(s)
- Nirupma Trehanpati
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | - Rashi Sehgal
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | - Sharda Patra
- Departrment of Gynaecology and Obstetrics, Lady Harding Medical College, New Delhi, India
| | - Ashish Vyas
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | | | - Ritu Khosla
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | - Arshi Khanam
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | - Guresh Kumar
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | - Rakhi Maiwall
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gayatri Ramakrishna
- Laboratory Of Molecular Immunology, Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences New Delhi, India
| | - Shyam Kottilil
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland, Baltimore, MD 21201, USA
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
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33
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Ray U, Roy Chowdhury S, Vasudevan M, Bankar K, Roychoudhury S, Roy SS. Gene regulatory networking reveals the molecular cue to lysophosphatidic acid-induced metabolic adaptations in ovarian cancer cells. Mol Oncol 2017; 11:491-516. [PMID: 28236660 PMCID: PMC5527468 DOI: 10.1002/1878-0261.12046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 11/15/2016] [Revised: 01/25/2017] [Accepted: 02/15/2017] [Indexed: 12/15/2022] Open
Abstract
Extravasation and metastatic progression are two main reasons for the high mortality rate associated with cancer. The metastatic potential of cancer cells depends on a plethora of metabolic challenges prevailing within the tumor microenvironment. To achieve higher rates of proliferation, cancer cells reprogram their metabolism, increasing glycolysis and biosynthetic activities. Just why this metabolic reprogramming predisposes cells towards increased oncogenesis remains elusive. The accumulation of myriad oncolipids in the tumor microenvironment has been shown to promote the invasiveness of cancer cells, with lysophosphatidic acid (LPA) being one such critical factor enriched in ovarian cancer patients. Cellular bioenergetic studies confirm that oxidative phosphorylation is suppressed and glycolysis is increased with long exposure to LPA in ovarian cancer cells compared with non‐transformed epithelial cells. We sought to uncover the regulatory complexity underlying this oncolipid‐induced metabolic perturbation. Gene regulatory networking using RNA‐Seq analysis identified the oncogene ETS‐1 as a critical mediator of LPA‐induced metabolic alterations for the maintenance of invasive phenotype. Moreover, LPA receptor‐2 specific PtdIns3K‐AKT signaling induces ETS‐1 and its target matrix metalloproteases. Abrogation of ETS‐1 restores cellular bioenergetics towards increased oxidative phosphorylation and reduced glycolysis, and this effect was reversed by the presence of LPA. Furthermore, the bioenergetic status of LPA‐treated ovarian cancer cells mimics hypoxia through induction of hypoxia‐inducible factor‐1α, which was found to transactivate ets‐1. Studies in primary tumors generated in syngeneic mice corroborated the in vitro findings. Thus, our study highlights the phenotypic changes induced by the pro‐metastatic factor ETS‐1 in ovarian cancer cells. The relationship between enhanced invasiveness and metabolic plasticity further illustrates the critical role of metabolic adaptation of cancer cells as a driver of tumor progression. These findings reveal oncolipid‐induced metabolic predisposition as a new mechanism of tumorigenesis and propose metabolic inhibitors as a potential approach for future management of aggressive ovarian cancer.
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Affiliation(s)
- Upasana Ray
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Shreya Roy Chowdhury
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | | | - Kiran Bankar
- Bionivid Technology Private Limited, Bangalore, India
| | | | - Sib Sankar Roy
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
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34
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Khosla R, Rastogi A, Ramakrishna G, Pamecha V, Mukhopadhyay A, Vasudevan M, Sarin SK, Trehanpati N. EpCAM+ Liver Cancer Stem-Like Cells Exhibiting Autocrine Wnt Signaling Potentially Originate in Cirrhotic Patients. Stem Cells Transl Med 2017; 6:807-818. [PMID: 28176469 PMCID: PMC5442787 DOI: 10.1002/sctm.16-0248] [Citation(s) in RCA: 23] [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: 05/20/2016] [Revised: 08/18/2016] [Accepted: 09/30/2016] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is believed to originate from cancer stem cells (CSCs). While epithelial cell adhesion molecule (EpCAM) is a marker of normal hepatic stem cells (HSCs), EpCAM+ cells from HCC behave like CSCs. Since HCC mostly develops on a cirrhotic background, we sought to determine whether CSC‐like EpCAM+ cells exist in patients with advanced cirrhosis. Both flow cytometry and immunohistochemistry showed that frequency of EpCAM+ cells in advanced cirrhosis was increased as compared to control. To determine whether increased EpCAM population in advanced cirrhosis harbors any CSC‐like cells, we compared molecular and functional features of EpCAM+ cells from advanced cirrhosis (Ep+CIR; n = 20) with EpCAM+ cells from both HCC (Ep+HCC; n = 20) and noncancerous/noncirrhotic (control) (Ep+NSC; n = 7) liver tissues. Ep+CIRs displayed similarity with Ep+HCC cells including upregulated expression of stemness and Notch pathway genes, enhanced self‐renewal in serial spheroid assay and generation of subcutaneous tumors in nonobese diabetic/severe combined immunodeficiency mice. Moreover, transcriptome and miRNome of Ep+CIRs appeared closer to that of Ep+HCC cells than Ep+NSCs. Interestingly, more than 50% micro RNAs (miRNAs) and transcripts specifically expressed in Ep+HCCs were also expressed in Ep+CIRs. However, none of Ep+NSC specific miRNAs and only 7% Ep+NSC specific transcripts were expressed in Ep+CIRs. Further, according to gene expression and in vitro Wnt inhibition analysis, autocrine Wnt signaling appeared to be a distinct feature of Ep+CIR and Ep+HCC cells, which was absent from Ep+NSCs. EpCAM+ cells in advanced cirrhosis possibly include a population of CSC‐like cells which can be explored for early diagnosis of HCC development. Stem Cells Translational Medicine2017;6:807–818
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Affiliation(s)
- Ritu Khosla
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Archana Rastogi
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gayatri Ramakrishna
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Viniyendra Pamecha
- Department of Liver Transplant and Hepato Pancreato Biliary Surgery, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Ashok Mukhopadhyay
- Stem Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | | | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nirupma Trehanpati
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
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Govindaraj V, Krishnagiri H, Chakraborty P, Vasudevan M, Rao AJ. Age-related changes in gene expression patterns of immature and aged rat primordial follicles. Syst Biol Reprod Med 2017; 63:37-48. [PMID: 28045561 DOI: 10.1080/19396368.2016.1267820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Women are born with millions of primordial follicles which gradually decrease with increasing age and this irreversible supply of follicles completely exhausts at menopause. The fertility capacity of women diminishes in parallel with aging. The mechanisms for reproductive aging are not fully understood. We have observed a decline in Brca1 mediated DNA repair in aging rat primordial follicles. To further understand the age-related molecular changes, we performed microarray gene expression analysis using total RNA extracted from immature (18 to 20 day old) and aged (400 to 450 day old) rat primordial follicles. The results of current microarray study revealed that there were 1,011 (>1.5 fold, p<0.05) genes differentially expressed between two groups in which 422 genes were up-regulated and 589 genes were down-regulated in aged rat primordial follicles compared to immature primordial follicles. The gene ontology and pathway analysis of differentially expressed genes revealed a critical biological function such as cell cycle, oocyte meiosis, chromosomal stability, transcriptional activity, DNA replication, and DNA repair were affected by age. This considerable difference in gene expression profiles may have an adverse influence on oocyte quality. Our data provide information on the processes that may contribute to aging and age-related decline in fertility.
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Affiliation(s)
| | | | | | | | - A Jagannadha Rao
- a Department of Biochemistry , Indian Institute of Science , Bangalore , India
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Vasudevan M, Johnston CD, Bastow TP, Lekmine G, Rayner JL, Nambi IM, Suresh Kumar G, Ravi Krishna R, Davis GB. Effect of compositional heterogeneity on dissolution of non-ideal LNAPL mixtures. J Contam Hydrol 2016; 194:10-16. [PMID: 27669377 DOI: 10.1016/j.jconhyd.2016.09.006] [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] [Received: 12/03/2015] [Revised: 09/09/2016] [Accepted: 09/17/2016] [Indexed: 06/06/2023]
Abstract
The extent of dissolution of petroleum hydrocarbon fuels into groundwater depends greatly on fuel composition. Petroleum fuels can consist of thousands of compounds creating different interactions within the non-aqueous phase liquid (NAPL), thereby affecting the relative dissolution of the components and hence a groundwater plume's composition over long periods. Laboratory experiments were conducted to study the variability in the effective solubilities and activity coefficients for common constituents of gasoline fuels (benzene, toluene, p-xylene and 1,2,4-trimethylbenzene) (BTX) in matrices with an extreme range of molar volumes and chemical affinities. Four synthetic mixtures were investigated comprising BTX with the bulk of the NAPL mixtures made up of either, ethylbenzene (an aromatic like BTX with similar molar volume); 1,3,5-trimethylbenzene (an aromatic with a greater molar volume); n-hexane (an aliphatic with a low molar volume); and n-decane (an aliphatic with a high molar volume). Equilibrium solubility values for the constituents were under-predicted by Raoult's law by up to 30% (higher experimental concentrations) for the mixture with n-hexane as a filler and over-predicted by up to 12% (lower experimental concentrations) for the aromatic mixtures with ethylbenzene and 1,3,5-trimethylbenzene as fillers. Application of PP-LFER (poly-parameter linear free energy relationship) model for non-ideal mixtures also resulted in poor correlation between experimentally measured and predicted concentrations, indicating that differences in chemical affinities can be the major cause of deviation from ideal behavior. Synthetic mixtures were compared with the dissolution behavior of fresh and naturally weathered unleaded gasoline. The presence of lighter aliphatic components in the gasoline had a profound effect on estimating effective solubility due to chemical affinity differences (estimated at 0.0055 per percentage increase in the molar proportion of aliphatic) as well as reduced molar volumes (estimated at -0.0091 in the activity coefficient per unit increase in molar volume, mL/mol). Previously measured changes in activity coefficients due to natural weathering of 0.25 compares well to 0.27 calculated here based on changes in the chemical affinity and molar volumes. The study suggests that the initial estimation of the composition of a fuel is crucial in evaluating dissolution processes due to ideal and non-ideal dissolution, and in predicting long term dissolution trends and the longevity of NAPL petroleum plume risks.
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Affiliation(s)
- M Vasudevan
- Department of Civil Engineering, Bannari Amman Institute of Technology, Sathyamangalam, Erode, India.
| | - C D Johnston
- CSIRO Land and Water, Private Bag No. 5, Wembley, WA 6913, Australia; School of Earth and Environment, The University of Western Australia, Nedlands, WA, Australia
| | - T P Bastow
- CSIRO Land and Water, Private Bag No. 5, Wembley, WA 6913, Australia
| | - G Lekmine
- CSIRO Land and Water, Private Bag No. 5, Wembley, WA 6913, Australia
| | - J L Rayner
- CSIRO Land and Water, Private Bag No. 5, Wembley, WA 6913, Australia
| | - I M Nambi
- Environmental and Water Resources Engineering Division, Department of Civil Engineering, Indian Institute of Technology, Madras, India.
| | - G Suresh Kumar
- Petroleum Engineering Program, Department of Ocean Engineering, Indian Institute of Technology, Madras, India.
| | - R Ravi Krishna
- Department of Chemical Engineering, Indian Institute of Technology, Madras, India.
| | - G B Davis
- CSIRO Land and Water, Private Bag No. 5, Wembley, WA 6913, Australia; School of Earth and Environment, The University of Western Australia, Nedlands, WA, Australia.
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Selvi RB, Swaminathan A, Chatterjee S, Shanmugam MK, Li F, Ramakrishnan GB, Siveen KS, Chinnathambi A, Zayed ME, Alharbi SA, Basha J, Bhat A, Vasudevan M, Dharmarajan A, Sethi G, Kundu TK. Inhibition of p300 lysine acetyltransferase activity by luteolin reduces tumor growth in head and neck squamous cell carcinoma (HNSCC) xenograft mouse model. Oncotarget 2016; 6:43806-18. [PMID: 26517526 PMCID: PMC4791268 DOI: 10.18632/oncotarget.6245] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 05/22/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023] Open
Abstract
Chromatin acetylation is attributed with distinct functional relevance with respect to gene expression in normal and diseased conditions thereby leading to a topical interest in the concept of epigenetic modulators and therapy. We report here the identification and characterization of the acetylation inhibitory potential of an important dietary flavonoid, luteolin. Luteolin was found to inhibit p300 acetyltransferase with competitive binding to the acetyl CoA binding site. Luteolin treatment in a xenografted tumor model of head and neck squamous cell carcinoma (HNSCC), led to a dramatic reduction in tumor growth within 4 weeks corresponding to a decrease in histone acetylation. Cells treated with luteolin exhibit cell cycle arrest and decreased cell migration. Luteolin treatment led to an alteration in gene expression and miRNA profile including up-regulation of p53 induced miR-195/215, let7C; potentially translating into a tumor suppressor function. It also led to down-regulation of oncomiRNAs such as miR-135a, thereby reflecting global changes in the microRNA network. Furthermore, a direct correlation between the inhibition of histone acetylation and gene expression was established using chromatin immunoprecipitation on promoters of differentially expressed genes. A network of dysregulated genes and miRNAs was mapped along with the gene ontology categories, and the effects of luteolin were observed to be potentially at multiple levels: at the level of gene expression, miRNA expression and miRNA processing.
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Affiliation(s)
- Ruthrotha B Selvi
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
| | - Amrutha Swaminathan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
| | - Snehajyoti Chatterjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Feng Li
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gowsica B Ramakrishnan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
| | | | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - M Emam Zayed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Jeelan Basha
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
| | - Akshay Bhat
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
| | | | - Arunasalam Dharmarajan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Curtin University, Bentley, Western Australia, Australia
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia.,School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Curtin University, Bentley, Western Australia, Australia
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Jakkur, Bangalore, India
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Gharat SA, Parmar S, Tambat S, Vasudevan M, Shaw BP. Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes. PLoS One 2016; 11:e0163485. [PMID: 27682829 PMCID: PMC5040429 DOI: 10.1371/journal.pone.0163485] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 05/30/2016] [Accepted: 09/10/2016] [Indexed: 01/02/2023] Open
Abstract
Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.
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Affiliation(s)
- Sachin Ashruba Gharat
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Shaifaly Parmar
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Subodh Tambat
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Madavan Vasudevan
- Bionivid Technology Private Limited, 3rd Floor, 4C-209, 4th Cross, Near New Horizon College, Kasturi Nagar, Bangalore, 560043, Karnataka, India
| | - Birendra Prasad Shaw
- Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
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Bharathy N, Suriyamurthy S, Rao VK, Ow JR, Lim HJ, Chakraborty P, Vasudevan M, Dhamne CA, Chang KTE, Min VLK, Kundu TK, Taneja R. P/CAF mediates PAX3-FOXO1-dependent oncogenesis in alveolar rhabdomyosarcoma. J Pathol 2016; 240:269-281. [PMID: 27453350 DOI: 10.1002/path.4773] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 12/29/2022]
Abstract
Alveolar rhabdomyosarcoma (ARMS) is an aggressive paediatric cancer of skeletal muscle with poor prognosis. A PAX3-FOXO1 fusion protein acts as a driver of malignancy in ARMS by disrupting tightly coupled but mutually exclusive pathways of proliferation and differentiation. While PAX3-FOXO1 is an attractive therapeutic target, no current treatments are designed to block its oncogenic activity. The present work shows that the histone acetyltransferase P/CAF (KAT2B) is overexpressed in primary tumours from ARMS patients. Interestingly, in fusion-positive ARMS cell lines, P/CAF acetylates and stabilizes PAX3-FOXO1 rather than MyoD, a master regulator of muscle differentiation. Silencing P/CAF, or pharmacological inhibition of its acetyltransferase activity, down-regulates PAX3-FOXO1 levels concomitant with reduced proliferation and tumour burden in xenograft mouse models. Our studies identify a P/CAF-PAX3-FOXO1 signalling node that promotes oncogenesis and may contribute to MyoD dysfunction in ARMS. This work exemplifies the therapeutic potential of targeting chromatin-modifying enzymes to inhibit fusion oncoproteins that are a frequent event in sarcomas. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Narendra Bharathy
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sudha Suriyamurthy
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vinay Kumar Rao
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jin Rong Ow
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Huey Jin Lim
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Payal Chakraborty
- Bionivid Technology Pvt Ltd, 401-4 AB Cross, 1st Main, Kasturi Nagar, Bangalore, India
| | - Madavan Vasudevan
- Bionivid Technology Pvt Ltd, 401-4 AB Cross, 1st Main, Kasturi Nagar, Bangalore, India
| | | | | | - Victor Lee Kwan Min
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tapas K Kundu
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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40
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Subramanian N, Srimany A, Kanwar JR, Kanwar RK, Akilandeswari B, Rishi P, Khetan V, Vasudevan M, Pradeep T, Krishnakumar S. Nucleolin-aptamer therapy in retinoblastoma: molecular changes and mass spectrometry-based imaging. Mol Ther Nucleic Acids 2016; 5:e358. [PMID: 27574784 PMCID: PMC5023409 DOI: 10.1038/mtna.2016.70] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/21/2016] [Indexed: 12/17/2022]
Abstract
Retinoblastoma (RB) is an intraocular childhood tumor which, if left untreated, leads to blindness and mortality. Nucleolin (NCL) protein which is differentially expressed on the tumor cell surface, binds ligands and regulates carcinogenesis and angiogenesis. We found that NCL is over expressed in RB tumor tissues and cell lines compared to normal retina. We studied the effect of nucleolin-aptamer (NCL-APT) to reduce proliferation in RB tumor cells. Aptamer treatment on the RB cell lines (Y79 and WERI-Rb1) led to significant inhibition of cell proliferation. Locked nucleic acid (LNA) modified NCL-APT administered subcutaneously (s.c.) near tumor or intraperitoneally (i.p.) in Y79 xenografted nude mice resulted in 26 and 65% of tumor growth inhibition, respectively. Downregulation of inhibitor of apoptosis proteins, tumor miRNA-18a, altered serum cytokines, and serum miRNA-18a levels were observed upon NCL-APT treatment. Desorption electrospray ionization mass spectrometry (DESI MS)-based imaging of cell lines and tumor tissues revealed changes in phosphatidylcholines levels upon treatment. Thus, our study provides proof of concept illustrating NCL-APT-based targeted therapeutic strategy and use of DESI MS-based lipid imaging in monitoring therapeutic responses in RB.
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Affiliation(s)
- Nithya Subramanian
- Department of Nanobiotechnology, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, India.,Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (NLIMBR), School of Medicine (SoM), Centre for Molecular and Medical Research (C-MMR), Faculty of Health, Deakin University, Geelong, Australia
| | - Amitava Srimany
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Jagat R Kanwar
- Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (NLIMBR), School of Medicine (SoM), Centre for Molecular and Medical Research (C-MMR), Faculty of Health, Deakin University, Geelong, Australia
| | - Rupinder K Kanwar
- Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (NLIMBR), School of Medicine (SoM), Centre for Molecular and Medical Research (C-MMR), Faculty of Health, Deakin University, Geelong, Australia
| | - Balachandran Akilandeswari
- Department of Nanobiotechnology, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, India
| | - Pukhraj Rishi
- Department of Ocular Oncology and Vitreo Retina, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Vikas Khetan
- Department of Ocular Oncology and Vitreo Retina, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | | | - Thalappil Pradeep
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Subramanian Krishnakumar
- Department of Nanobiotechnology, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, India.,L&T Ocular Pathology Department, Vision Research Foundation, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Chennai, India
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41
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Banerjee A, Sanyal S, Dutta S, Chakraborty P, Das PP, Jana K, Vasudevan M, Das C, Dasgupta D. The plant alkaloid chelerythrine binds to chromatin, alters H3K9Ac and modulates global gene expression. J Biomol Struct Dyn 2016; 35:1491-1499. [PMID: 27494525 DOI: 10.1080/07391102.2016.1188154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.
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Affiliation(s)
- Amrita Banerjee
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Sulagna Sanyal
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Shreyasi Dutta
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Payal Chakraborty
- b Genome Informatics Research Group , Bionivid Technology Pvt Ltd. , Bangalore 560043 , India
| | - Prajna Paramita Das
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Kuladip Jana
- c Division of Molecular Medicine, Centre for Translational Animal Research , Bose Institute , P 1/12, C. I. T. Road, Scheme - VIIM, Kolkata 700054 , India
| | - Madavan Vasudevan
- b Genome Informatics Research Group , Bionivid Technology Pvt Ltd. , Bangalore 560043 , India
| | - Chandrima Das
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Dipak Dasgupta
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
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42
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Vasudevan M, Nambi IM, Suresh Kumar G. Scenario-based modelling of mass transfer mechanisms at a petroleum contaminated field site-numerical implications. J Environ Manage 2016; 175:9-19. [PMID: 27017268 DOI: 10.1016/j.jenvman.2016.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 09/30/2015] [Revised: 02/28/2016] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
Knowledge about distribution of dissolved plumes and their influencing factors is essential for risk assessment and remediation of light non-aqueous phase liquid contamination in groundwater. Present study deals with the applicability of numerical model for simulating various hydro-geological scenarios considering non-uniform source distribution at a petroleum contaminated site in Chennai, India. The complexity associated with the hydrogeology of the site has limited scope for on-site quantification of petroleum pipeline spillage. The change in fuel composition under mass-transfer limited conditions was predicted by simultaneously comparing deviations in aqueous concentrations and activity coefficients (between Raoult's law and analytical approaches). The effects of source migration and weathering on the dissolution of major soluble fractions of petroleum fuel were also studied in relation to the apparent change in their activity coefficients and molar fractions. The model results were compared with field observations and found that field conditions were favourable for biodegradation, especially for the aromatic fraction (benzene and toluene (nearly 95% removal), polycyclic aromatic hydrocarbons (up to 65% removal) and xylene (nearly 45% removal). The results help to differentiate the effect of compositional non-ideality from rate-limited dissolution towards tailing of less soluble compounds (alkanes and trimethylbenzene). Although the effect of non-ideality decreased with distance from the source, the assumption of spatially varying residual saturation could effectively illustrate post-spill scenario by estimating the consequent decrease in mass transfer rate.
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Affiliation(s)
- M Vasudevan
- Department of Civil Engineering, Bannari Amman Institute of Technology, Sathyamangalam, Erode, India.
| | - Indumathi M Nambi
- Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India.
| | - G Suresh Kumar
- Department of Ocean Engineering, Indian Institute of Technology Madras, Chennai, India.
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43
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Singh V, Singh LC, Vasudevan M, Chattopadhyay I, Borthakar BB, Rai AK, Phukan RK, Sharma J, Mahanta J, Kataki AC, Kapur S, Saxena S. Esophageal Cancer Epigenomics and Integrome Analysis of Genome-Wide Methylation and Expression in High Risk Northeast Indian Population. OMICS: A Journal of Integrative Biology 2015; 19:688-99. [DOI: 10.1089/omi.2015.0121] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Virendra Singh
- National Institute of Pathology (ICMR), New Delhi, India
| | | | | | | | | | | | - Rup Kumar Phukan
- Regional Medical Research Centre (RMRC), Dibrugadh, Assam, India
| | | | - Jagadish Mahanta
- Regional Medical Research Centre (RMRC), Dibrugadh, Assam, India
| | | | - Sujala Kapur
- National Institute of Pathology (ICMR), New Delhi, India
| | - Sunita Saxena
- National Institute of Pathology (ICMR), New Delhi, India
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Bankar KG, Todur VN, Shukla RN, Vasudevan M. Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler. Genom Data 2015; 5:352-9. [PMID: 26484285 PMCID: PMC4583709 DOI: 10.1016/j.gdata.2015.07.012] [Citation(s) in RCA: 27] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 07/12/2015] [Indexed: 11/28/2022]
Abstract
Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.
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Affiliation(s)
- Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India
| | - Vivek Nagaraj Todur
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India
| | - Rohit Nandan Shukla
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India
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Kulkarni KK, Bankar KG, Shukla RN, Das C, Banerjee A, Dasgupta D, Vasudevan M. Global gene expression profiling data analysis reveals key gene families and biological processes inhibited by Mithramycin in sarcoma cell lines. Genom Data 2014; 3:8-14. [PMID: 26484141 PMCID: PMC4535529 DOI: 10.1016/j.gdata.2014.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/03/2023]
Abstract
The role of Mithramycin as an anticancer drug has been well studied. Sarcoma is a type of cancer arising from cells of mesenchymal origin. Though incidence of sarcoma is not of significant percentage, it becomes vital to understand the role of Mithramycin in controlling tumor progression of sarcoma. In this article, we have analyzed the global gene expression profile changes induced by Mithramycin in two different sarcoma lines from whole genome gene expression profiling microarray data. We have found that the primary mode of action of Mithramycin is by global repression of key cellular processes and gene families like phosphoproteins, kinases, alternative splicing, regulation of transcription, DNA binding, regulation of histone acetylation, negative regulation of gene expression, chromosome organization or chromatin assembly and cytoskeleton.
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Affiliation(s)
- Kirti K Kulkarni
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
| | - Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
| | - Rohit Nandan Shukla
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Amrita Banerjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Dipak Dasgupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
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46
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Venkatesan N, Deepa P, Vasudevan M, Khetan V, Reddy AM, Krishnakumar S. Integrated Analysis of Dysregulated miRNA-gene Expression in HMGA2-silenced Retinoblastoma Cells. Bioinform Biol Insights 2014; 8:177-91. [PMID: 25232279 PMCID: PMC4159370 DOI: 10.4137/bbi.s16958] [Citation(s) in RCA: 10] [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: 05/20/2014] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 12/29/2022] Open
Abstract
Retinoblastoma (RB) is a primary childhood eye cancer. HMGA2 shows promise as a molecule for targeted therapy. The involvement of miRNAs in genome-level molecular dys-regulation in HMGA2-silenced RB cells is poorly understood. Through miRNA expression microarray profiling, and an integrated array analysis of the HMGA2-silenced RB cells, the dysregulated miRNAs and the miRNA-target relationships were modelled. Loop network analysis revealed a regulatory association between the transcription factor (SOX5) and the deregulated miRNAs (miR-29a, miR-9*, miR-9-3). Silencing of HMGA2 deregulated the vital oncomirs (miR-7, miR-331, miR-26a, miR-221, miR-17~92 and miR-106b∼25) in RB cells. From this list, the role of the miR-106b∼25 cluster was examined further for its expression in primary RB tumor tissues (n = 20). The regulatory targets of miR-106b∼25 cluster namely p21 (cyclin-dependent kinase inhibitor) and BIM (pro-apoptotic gene) were elevated, and apoptotic cell death was observed, in RB tumor cells treated with the specific antagomirs of the miR-106b∼25 cluster. Thus, suppression of miR-106b∼25 cluster controls RB tumor growth. Taken together, HMGA2 mediated anti-tumor effect present in RB is, in part, mediated through the miR-106b∼25 cluster.
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Affiliation(s)
- Nalini Venkatesan
- Larsen and Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, India. ; Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Pr Deepa
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) - Pilani, Rajasthan, India
| | | | - Vikas Khetan
- Sri Bhagawan Mahavir Department of Vitreoretinal and Ocular Oncology, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Ashwin M Reddy
- Department of Ophthalmology, Barts Health NHS Trust, London, UK
| | - Subramanian Krishnakumar
- Larsen and Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
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Mruthyunjaya S, Parveen D, Shah RD, Manchanda R, Godbole R, Vasudevan M, Shastry P. Gene expression analysis of laminin-1-induced neurite outgrowth in human mesenchymal stem cells derived from bone marrow. J Biomed Mater Res A 2014; 103:746-61. [DOI: 10.1002/jbm.a.35221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/15/2014] [Accepted: 05/02/2014] [Indexed: 11/06/2022]
Affiliation(s)
- S. Mruthyunjaya
- National centre for Cell Science (NCCS); University of Pune; Ganeshkhind Pune 411007 India
| | - D. Parveen
- National centre for Cell Science (NCCS); University of Pune; Ganeshkhind Pune 411007 India
| | - Reecha D. Shah
- National centre for Cell Science (NCCS); University of Pune; Ganeshkhind Pune 411007 India
| | | | | | | | - Padma Shastry
- National centre for Cell Science (NCCS); University of Pune; Ganeshkhind Pune 411007 India
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48
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Nalini V, Segu R, Deepa PR, Khetan V, Vasudevan M, Krishnakumar S. Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis. Bioinform Biol Insights 2013; 7:289-306. [PMID: 24092970 PMCID: PMC3785389 DOI: 10.4137/bbi.s12494] [Citation(s) in RCA: 14] [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] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Management of Retinoblastoma (RB), a pediatric ocular cancer is limited by drug-resistance and drug-dosage related side effects during chemotherapy. Molecular de-regulation in post-chemotherapy RB tumors was investigated. MATERIALS AND METHODS cDNA microarray analysis of two post-chemotherapy and one pre-chemotherapy RB tumor tissues was performed, followed by Principle Component Analysis, Gene ontology, Pathway Enrichment analysis and Biological Analysis Network (BAN) modeling. The drug modulation role of two significantly up-regulated genes (p≤0.05) - Ect2 (Epithelial-cell-transforming-sequence-2), and PRAME (preferentially-expressed-Antigen-in-Melanoma) was assessed by qRT-PCR, immunohistochemistry and cell viability assays. RESULTS Differential up-regulation of 1672 genes and down-regulation of 2538 genes was observed in RB tissues (relative to normal adult retina), while 1419 genes were commonly de-regulated between pre-chemotherapy and post- chemotherapy RB. Twenty one key gene ontology categories, pathways, biomarkers and phenotype groups harboring 250 differentially expressed genes were dys-regulated (EZH2, NCoR1, MYBL2, RB1, STAMN1, SYK, JAK1/2, STAT1/2, PLK2/4, BIRC5, LAMN1, Ect2, PRAME and ABCC4). Differential molecular expressions of PRAME and Ect2 in RB tumors with and without chemotherapy were analyzed. There was neither up- regulation of MRP1, nor any significant shift in chemotherapeutic IC50, in PRAME over-expressed versus non-transfected RB cells. CONCLUSION Cell cycle regulatory genes were dys-regulated post-chemotherapy. Ect2 gene was expressed in response to chemotherapy-induced stress. PRAME does not contribute to drug resistance in RB, yet its nuclear localization and BAN information, points to its possible regulatory role in RB.
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Affiliation(s)
- Venkatesan Nalini
- Larsen and Toubro Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, India. ; Birla Institute of Technology and Science (BITS), Pilani, India
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Sharma S, Verma S, Vasudevan M, Samanta S, Thakur JK, Kulshreshtha R. The interplay of HuR and miR-3134 in regulation of AU rich transcriptome. RNA Biol 2013; 10:1283-90. [PMID: 23823647 DOI: 10.4161/rna.25482] [Citation(s) in RCA: 22] [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] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs and AU Rich element (ARE)-mediated degradation of transcripts are thought to be two independent means of gene regulation at the post-transcriptional level. However, since their site of action is the same (3'UTR of mRNA), there exists a high probability that specific miRNAs may bind to AREs and, thus, interact with ARE-binding proteins (ARE-BPs) to regulate transcript levels. In this study, we have characterized AREs as potential targets of hsa-miR-3134. An analysis of the global gene expression profile of breast cancer cell line MCF7 overexpressing miR-3134 revealed the presence of at least one AUUUA element in the 3'-UTRs of 63% of miR-3134 regulated protein coding genes. Quantitative RT-PCR or 3'UTR luciferase assays show that miR-3134 mediates an up to 4-8-fold increase in the levels of ARE bearing transcripts-SOX9, VEGFA, and EGFR, while mutated miR-3134 shows a decreased effect. The miR-3134-mediated increase in transcript levels was unaffected by treatment with transcription inhibitor (actinomycin D), indicating that miR-3134 enhances transcript stability. To investigate a possible interplay between miR-3134 and a prototype ARE-BP, HuR, we compared their overexpression transcriptome profiles. Interestingly, up to 80% of miR-3134-regulated genes were also regulated by HuR. Overexpression studies of HuR alone or in combination with miR-3134 shows that wt miR-3134 but not a mutated miR-3134 promotes stabilization of HuR-regulated transcripts SOX9, VEGFA, and EGFR as confirmed by qRT-PCR or RNA-immunoprecipitation experiments. Overall, this report suggests that collaboration between ARE-binding microRNAs and ARE-binding proteins could be a general mechanism of 3'-UTR mediated regulation of gene expression in human cells.
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Affiliation(s)
- Shivani Sharma
- Department of Biochemical Engineering and Biotechnology; Indian Institute of Technology; Delhi, India
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50
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Modak R, Basha J, Bharathy N, Maity K, Mizar P, Bhat AV, Vasudevan M, Rao VK, Kok WK, Natesh N, Taneja R, Kundu TK. Probing p300/CBP associated factor (PCAF)-dependent pathways with a small molecule inhibitor. ACS Chem Biol 2013; 8:1311-23. [PMID: 23570531 DOI: 10.1021/cb4000597] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PCAF (KAT2B) belongs to the GNAT family of lysine acetyltransferases (KAT) and specifically acetylates the histone H3K9 residue and several nonhistone proteins. PCAF is also a transcriptional coactivator. Due to the lack of a PCAF KAT-specific small molecule inhibitor, the exclusive role of the acetyltransferase activity of PCAF is not well understood. Here, we report that a natural compound of the hydroxybenzoquinone class, embelin, specifically inhibits H3Lys9 acetylation in mice and inhibits recombinant PCAF-mediated acetylation with near complete specificity in vitro. Furthermore, using embelin, we have identified the gene networks that are regulated by PCAF during muscle differentiation, further highlighting the broader regulatory functions of PCAF in muscle differentiation in addition to the regulation via MyoD acetylation.
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Affiliation(s)
- Rahul Modak
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Jeelan Basha
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Narendra Bharathy
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Koustav Maity
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Pushpak Mizar
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Akshay V. Bhat
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Madavan Vasudevan
- Bionivid Technology [P] Ltd, 401 - 4 AB Cross, 1st Main, Kasturi Nagar,
East of NGEF, Bangalore, India 560043
| | - Vinay Kumar Rao
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Wai Kay Kok
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Nagashayana Natesh
- Central Government Health Scheme
Dispensary Number 3, Basavanagudi, Bangalore, India
| | - Reshma Taneja
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Tapas K. Kundu
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
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