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Kangabam R, Sahoo S, Ghosh A, Roy R, Silla Y, Misra N, Suar M. Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery. Comput Biol Med 2021; 128:104158. [PMID: 33301953 PMCID: PMC7705366 DOI: 10.1016/j.compbiomed.2020.104158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has affected 215 countries and territories around the world with 60,187,347 coronavirus cases and 17,125,719 currently infected patients confirmed as of the November 25, 2020. Currently, many countries are working on developing new vaccines and therapeutic drugs for this novel virus strain, and a few of them are in different phases of clinical trials. The advancement in high-throughput sequence technologies, along with the application of bioinformatics, offers invaluable knowledge on genomic characterization and molecular pathogenesis of coronaviruses. Recent multi-disciplinary studies using bioinformatics methods like sequence-similarity, phylogenomic, and computational structural biology have provided an in-depth understanding of the molecular and biochemical basis of infection, atomic-level recognition of the viral-host receptor interaction, functional annotation of important viral proteins, and evolutionary divergence across different strains. Additionally, various modern immunoinformatic approaches are also being used to target the most promiscuous antigenic epitopes from the SARS-CoV-2 proteome for accelerating the vaccine development process. In this review, we summarize various important computational tools and databases available for systematic sequence-structural study on coronaviruses. The features of these public resources have been comprehensively discussed, which may help experimental biologists with predictive insights useful for ongoing research efforts to find therapeutics against the infectious COVID-19 disease.
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Affiliation(s)
- Rajiv Kangabam
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Susrita Sahoo
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Arpan Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Riya Roy
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Yumnam Silla
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006, India
| | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Mrutyunjay Suar
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India.
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Das Kangabam R, Silla Y, Goswami G, Barooah M. Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes. Curr Genomics 2020; 21:512-524. [PMID: 33214767 PMCID: PMC7604743 DOI: 10.2174/1389202921999200716104355] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/28/2020] [Accepted: 05/30/2020] [Indexed: 01/22/2023] Open
Abstract
Background Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems. Objective The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis. Methods Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform. Results Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane. Conclusion The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.
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Affiliation(s)
- Rajiv Das Kangabam
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India; 2Advanced Computational and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat-785006, India; 3DBT North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India
| | - Yumnam Silla
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India; 2Advanced Computational and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat-785006, India; 3DBT North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India
| | - Gunajit Goswami
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India; 2Advanced Computational and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat-785006, India; 3DBT North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India
| | - Madhumita Barooah
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India; 2Advanced Computational and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat-785006, India; 3DBT North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, India
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Rani J, Silla Y, Borah K, Ramachandran S, Bajpai U. Repurposing of FDA-approved drugs to target MurB and MurE enzymes in Mycobacterium tuberculosis. J Biomol Struct Dyn 2019; 38:2521-2532. [PMID: 31244382 DOI: 10.1080/07391102.2019.1637280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 01/12/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is one amongst the top 10 causes of death worldwide. The growing rise in antibiotic resistance compounded with slow and expensive drug discovery has further aggravated the situation. 'Drug repurposing' is a promising approach where known drugs are examined for a new indication. In the present study, we have attempted to identify drugs that could target MurB and MurE enzymes involved in the muramic acid synthesis pathway (Mur Pathway) in Mtb. FDA-approved drugs from two repositories i.e. Drug Bank (1932 drugs) and e-LEA3D (1852 drugs) were screened against these proteins. Several criteria were applied to study the protein-drug interactions and the consensus drugs were further studied by molecular dynamics (MD) simulation. Our study found Sulfadoxine (-7.3 kcal/mol) and Pyrimethamine (-7.8 kcal/mol) to show stable interaction with MurB while Lifitegrast (-10.5 kcal/mol) and Sildenafil (-9.1 kcal/mol) showed most reliable interaction with MurE. Furthermore, binding free energy (ΔGbind), RMSD and RMSF data and the number of hydrogen bonds corroborated the stability of interactions and hence these drugs for repurposing should be explored further.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.,G. N. Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Yumnam Silla
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Kasmika Borah
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Srinivasan Ramachandran
- G. N. Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
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Silla Y, Varshney S, Ray A, Basak T, Zinellu A, Sabareesh V, Carru C, Sengupta S. Hydrolysis of homocysteine thiolactone results in the formation of Protein-Cys-S-S-homocysteinylation. Proteins 2019; 87:625-634. [PMID: 30869815 DOI: 10.1002/prot.25681] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/31/2019] [Accepted: 02/17/2019] [Indexed: 11/07/2022]
Abstract
An increased level of homocysteine, a reactive thiol amino acid, is associated with several complex disorders and is an independent risk factor for cardiovascular disease. A majority (>80%) of circulating homocysteine is protein bound. Homocysteine exclusively binds to protein cysteine residues via thiol disulfide exchange reaction, the mechanism of which has been reported. In contrast, homocysteine thiolactone, the cyclic thioester of homocysteine, is believed to exclusively bind to the primary amine group of lysine residue leading to N-homocysteinylation of proteins and hence studies on binding of homocysteine thiolactone to proteins thus far have only focused on N-homocysteinylation. Although it is known that homocysteine thiolactone can hydrolyze to homocysteine at physiological pH, surprisingly the extent of S-homocysteinylation during the exposure of homocysteine thiolactone with proteins has never been looked into. In this study, we clearly show that the hydrolysis of homocysteine thiolactone is pH dependent, and at physiological pH, 1 mM homocysteine thiolactone is hydrolysed to ~0.71 mM homocysteine within 24 h. Using albumin, we also show that incubation of HTL with albumin leads to a greater proportion of S-homocysteinylation (0.41 mol/mol of albumin) than N-homocysteinylation (0.14 mol/mol of albumin). S-homocysteinylation at Cys34 of HSA on treatment with homocysteine thiolactone was confirmed using LC-MS. Further, contrary to earlier reports, our results indicate that there is no cross talk between the cysteine attached to Cys34 of albumin and homocysteine attached to lysine residues.
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Affiliation(s)
- Yumnam Silla
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, Delhi, India
| | - Swati Varshney
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, Delhi, India
| | - Arjun Ray
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, Delhi, India
| | - Trayambak Basak
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, Delhi, India
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Varatharajan Sabareesh
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Quality Control Unit, University Hospital of Sassari (AOU Sassari), Sassari, Italy
| | - Shantanu Sengupta
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, Delhi, India
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Borah K, Sharma S, Silla Y. Structural bioinformatics-based identification of putative plant based lead compounds for Alzheimer Disease Therapy. Comput Biol Chem 2019; 78:359-366. [DOI: 10.1016/j.compbiolchem.2018.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/25/2018] [Indexed: 12/19/2022]
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Nongthombam GS, Borah K, Muinao T, Silla Y, Pal M, Deka Boruah HP, Boruah RC. Synthesis of D-Ring Annulated Pyridosteroids from β-Formyl Enamides and Their Biological Evaluations. ACS Comb Sci 2019; 21:11-27. [PMID: 30576125 DOI: 10.1021/acscombsci.8b00140] [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] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein, we report the synthesis of a novel class of substituted androst[17,16- b]pyridines (pyridosteroids) from the reaction of β-formyl enamides with alkynes in high yields. The optimized reaction protocol was extended to acyclic and cyclic β-formyl enamides to afford nonsteroidal pyridines. Cell survival assay of all compounds were carried against prostate cancer PC-3 cells wherein 3-hydroxy-5-en-2',3'-dicarbethoxy-androst[17,16- b]pyridine showed the highest cytotoxic activity. Phase contrast microscopy and flow cytometry studies exhibited marked morphological features characteristic of apoptosis in 3-hydroxy-5-en-2',3'-dicarbethoxy-androst[17,16- b]pyridine and abiraterone treated PC-3 cells. The treatment of 3-hydroxy-5-en-2',3'-dicarbethoxy-androst[17,16- b]pyridine induces G2/M phase cell cycle arrest in prostate cancer PC-3 cells. Enhancement of apoptotic inductions of PC-3 cells by 3-hydroxy-5-en-2',3'-dicarbethoxy-androst[17,16- b]pyridine and abiraterone through the activation of caspases-6, -7, and -8 pathways were supported by qRT-PCR. In silico study of the compound 3-hydroxy-5-en-2',3'-dicarbethoxy-androst[17,16- b]pyridine showed stable and promising interaction with the key caspase proteins. Our studies revealed that the pyridosteroid 3-hydroxy-5-en-2',3'-dicarbethoxy-androst[17,16- b]pyridine, bearing pyridine-2,3-dicarbethoxy pharmacophore, facilitated initiation of caspase-8 and activates downstream effectors caspase-6 and caspase-7 and thereby triggering apoptosis of PC-3 cancer cells.
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Affiliation(s)
- Geetmani Singh Nongthombam
- Chemical Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
| | - Kasmika Borah
- Biological Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
| | - Thingreila Muinao
- Biological Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
| | - Yumnam Silla
- Biological Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
| | - Mintu Pal
- Biological Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
| | - Hari Prasanna Deka Boruah
- Biological Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
| | - Romesh Chandra Boruah
- Chemical Science and Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India 785006
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Gogoi B, Gogoi D, Silla Y, Kakoti BB, Bhau BS. Network pharmacology-based virtual screening of natural products from Clerodendrum species for identification of novel anti-cancer therapeutics. Mol BioSyst 2017; 13:406-416. [DOI: 10.1039/c6mb00807k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the present work, latest network pharmacological approach has been used for the screening of natural anticancer compounds from Clerodendrum species.
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Affiliation(s)
- Barbi Gogoi
- Plant Genomic Laboratory
- Medicinal Aromatic & Economic Plants (MAEP) Group
- Biological Sciences & Technology Division (BSTD)
- CSIR-North East Institute of Science and Technology
- Jorhat-785006
| | - Dhrubajyoti Gogoi
- DBT-BIF
- Centre for Biotechnology and Bioinformatics
- Dibrugarh University
- Dibrugarh
- India
| | - Yumnam Silla
- Biotechnology Group
- Biological Sciences & Technology Division (BSTD)
- CSIR-North East Institute of Science and Technology
- Jorhat-785006
- India
| | | | - Brijmohan Singh Bhau
- Plant Genomic Laboratory
- Medicinal Aromatic & Economic Plants (MAEP) Group
- Biological Sciences & Technology Division (BSTD)
- CSIR-North East Institute of Science and Technology
- Jorhat-785006
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Shrivastava P, Navratna V, Silla Y, Dewangan RP, Pramanik A, Chaudhary S, Rayasam G, Kumar A, Gopal B, Ramachandran S. Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues. Sci Rep 2016; 6:30827. [PMID: 27501775 PMCID: PMC4977564 DOI: 10.1038/srep30827] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/11/2016] [Indexed: 11/09/2022] Open
Abstract
The Mycobacterium tuberculosis dihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (α-KPA) showed maximum inhibition of 88% and IC50 of 21 μM in the presence of pyruvate (500 μM) and ASA (400 μM). Competition experiments with pyruvate and ASA revealed competition of α-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1 °C Tm shift of Mtb-rDapA upon binding α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å(2) are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA.
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Affiliation(s)
- Priyanka Shrivastava
- Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, New Delhi 110025, India
| | - Vikas Navratna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Yumnam Silla
- Biotechnology Group (BIF center), Biological Science & Technology Division (BSTD), CSIR-North-East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Rikeshwer P. Dewangan
- Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India
| | - Atreyi Pramanik
- Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India
| | - Sarika Chaudhary
- Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India
| | - GeethaVani Rayasam
- Open Source Drug Discovery Unit (OSDD), CSIR-IGIB, New Delhi, 110001, India
| | - Anuradha Kumar
- Open Source Drug Discovery Unit (OSDD), CSIR-IGIB, New Delhi, 110001, India
| | | | - Srinivasan Ramachandran
- Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, New Delhi 110025, India
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Talwar P, Silla Y, Grover S, Gupta M, Agarwal R, Kushwaha S, Kukreti R. Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. BMC Genomics 2014; 15:199. [PMID: 24628925 PMCID: PMC4028079 DOI: 10.1186/1471-2164-15-199] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [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: 07/01/2013] [Accepted: 02/21/2014] [Indexed: 01/28/2023] Open
Abstract
Background Alzheimer’s disease (AD) is one of the leading genetically complex and heterogeneous disorder that is influenced by both genetic and environmental factors. The underlying risk factors remain largely unclear for this heterogeneous disorder. In recent years, high throughput methodologies, such as genome-wide linkage analysis (GWL), genome-wide association (GWA) studies, and genome-wide expression profiling (GWE), have led to the identification of several candidate genes associated with AD. However, due to lack of consistency within their findings, an integrative approach is warranted. Here, we have designed a rank based gene prioritization approach involving convergent analysis of multi-dimensional data and protein-protein interaction (PPI) network modelling. Results Our approach employs integration of three different AD datasets- GWL,GWA and GWE to identify overlapping candidate genes ranked using a novel cumulative rank score (SR) based method followed by prioritization using clusters derived from PPI network. SR for each gene is calculated by addition of rank assigned to individual gene based on either p value or score in three datasets. This analysis yielded 108 plausible AD genes. Network modelling by creating PPI using proteins encoded by these genes and their direct interactors resulted in a layered network of 640 proteins. Clustering of these proteins further helped us in identifying 6 significant clusters with 7 proteins (EGFR, ACTB, CDC2, IRAK1, APOE, ABCA1 and AMPH) forming the central hub nodes. Functional annotation of 108 genes revealed their role in several biological activities such as neurogenesis, regulation of MAP kinase activity, response to calcium ion, endocytosis paralleling the AD specific attributes. Finally, 3 potential biochemical biomarkers were found from the overlap of 108 AD proteins with proteins from CSF and plasma proteome. EGFR and ACTB were found to be the two most significant AD risk genes. Conclusions With the assumption that common genetic signals obtained from different methodological platforms might serve as robust AD risk markers than candidates identified using single dimension approach, here we demonstrated an integrated genomic convergence approach for disease candidate gene prioritization from heterogeneous data sources linked to AD. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-199) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Mall Road, Delhi 110 007, India.
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Silla Y, Chandamouli B, Maiti S, Sengupta S. A Single Nucleotide Polymorphism in Transcobalamin II (I5V) Induces Structural Changes in the Protein As Revealed by Molecular Modeling Studies. Biochemistry 2011; 50:1396-402. [DOI: 10.1021/bi101095g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yumnam Silla
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi, India
| | | | - Souvik Maiti
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi, India
- National Chemical Laboratory (CSIR), Dr. Homi Bhabha Road, Pune, India
| | - Shantanu Sengupta
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi, India
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