Institute of Bioinformatics and Applied Biotechnology IBAB

Bangalore, India

Institute of Bioinformatics and Applied Biotechnology IBAB

Bangalore, India
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R. M.,SASTRA University | P. H.A.,Institute of Bioinformatics and Applied Biotechnology IBAB | Mahadevan V.,SASTRA University | Mahadevan V.,Institute of Bioinformatics and Applied Biotechnology IBAB
Journal of Biomolecular Structure and Dynamics | Year: 2017

Besides inactivating tumour suppressor activity in cells, mutations in p53 confer significant oncogenic functions and promote metastasis and resistance to anticancer therapy. A variety of therapies involving genetic and epigenetic signalling events regulate tumorogenesis and progression in such cases. Pharmacological interventions with HDAC inhibitors have shown promise in therapy. This work explores the changes in efficacy of the four HDAC inhibitors SAHA, MS-275, valproic acid and sodium butyrate on a panel of colon cancer cell lines – HCT116 (p53 wt), HCT116 p53-/-, HT29 and SW480 (with mutations in p53). Clonogenic assays, gene profiling and epigenetic expression done on these cells point to p53 dependent differential activity of the 4 HDAC inhibitors which also elevate methylation levels in p53 mutant cell lines. In silico modelling establishes the alterations in interactions that lead to such differential activity of valproic acid, one of the inhibitors considered for the work. Molecular Dynamic simulations carried out on the valproic acid complex ensure stability of the complex. This work establishes a p53 dependent epigenetic signalling mechanism triggered by HDAC inhibition expanding the scope of HDAC inhibitors in adjuvant therapy for p53 mutant tumours. © 2017 Informa UK Limited, trading as Taylor & Francis Group


Tammana D.,Institute of Bioinformatics and Applied Biotechnology IBAB | Tammana T.V.S.,Institute of Bioinformatics and Applied Biotechnology IBAB
Cytoskeleton | Year: 2017

Several nuclear and nucleic acid-binding proteins were detected in the proteomic analyses of ciliary fractions from various organisms. Yet very little is known about the role of these proteins in ciliogenesis and ciliary signaling. In an attempt to characterize the role of these nuclear proteins, we identified a hypothetical protein from Chlamydomonas reinhardtii, CrRuvBL1, which is homologous to human DNA helicase, HsRuvBL1. CrRuvBL1 localizes to flagella and nucleus in vegetative Chlamydomonas cells. It accumulates in the nucleus specifically during initial stages of flagellar assembly and cell division indicating its role in these processes. Mammalian counterpart of this protein, HsRuvBL1, was found to be present at the basal bodies and in the primary cilium of quiescent Retinal Pigment Epithelial (RPE1) cells. In interphase cells, HsRuvBL1 is present at centrioles while the protein localizes on spindle fibers, spindle poles and midbodies, which are important structures formed during different phases of cell division. Depletion of HsRuvBL1 by using siRNAs leads to complete loss of primary cilia in RPE1 cells. Together these results suggest that nuclear proteins play an important role in ciliogenesis. © 2017 Wiley Periodicals, Inc.


Bhagwat S.,National Health Research Institute | Dalvi V.,National Health Research Institute | Chandrasekhar D.,Institute of Bioinformatics and Applied Biotechnology IBAB | Matthew T.,Institute of Bioinformatics and Applied Biotechnology IBAB | And 7 more authors.
Fertility and Sterility | Year: 2014

Objective To determine the status of α-tubulin acetylation and of testis-specific acetylable α-tubulin isoforms in asthenozoospermia. Design Research study. Setting Research institute and an infertility clinic. Patient(s) 50 men with normal sperm parameters, and 50 men with asthenozoospermia. Intervention(s) None. Main Outcome Measure(s) Western blot analyses of α-tubulin, acetylated α-tubulin, and isoforms TUBA3C, TUBA4A, and TUBA8 in Percoll separated sperm and flow cytometry, real-time reverse-transcription polymerase chain reaction, and immunofluorescent localization. Result(s) A statistically significant decrease in the expression of acetylated α-tubulin in asthenozoosperm was seen with Western blot analysis, double immunostaining by direct immunofluorescence, and flow cytometric analysis. The transcript and protein of testis-specific acetylable α-tubulin isoform TUBA3C was decreased and TUBA4A was statistically significantly increased in asthenozoosperm as compared with normal spermatozoa. TUBA8 was reduced in asthenozoosperm. Similar observations were noted by indirect immunofluorescent localization. The potential transcription factors involved in the differential expression of TUBA4A and TUBA3C have been identified. Conclusion(s) Data suggest an association of α-tubulin acetylation with asthenozoospermia. Ours is the first report to demonstrate α-tubulin isoforms in sperm, implicating their role in motility. The differential expression of TUBA3C and TUBA4A suggests that tubulin acetylation may be governed by the isoform of α-tubulin that is expressed or silenced and that this in turn is transcriptionally controlled. © 2014 by American Society for Reproductive Medicine.


PubMed | National Health Research Institute, Institute of Bioinformatics and Applied Biotechnology IBAB and India; Shodhaka Life science Pvt.
Type: Journal Article | Journal: Fertility and sterility | Year: 2014

To determine the status of -tubulin acetylation and of testis-specific acetylable -tubulin isoforms in asthenozoospermia.Research study.Research institute and an infertility clinic.50 men with normal sperm parameters, and 50 men with asthenozoospermia.None.Western blot analyses of -tubulin, acetylated -tubulin, and isoforms TUBA3C, TUBA4A, and TUBA8 in Percoll separated sperm and flow cytometry, real-time reverse-transcription polymerase chain reaction, and immunofluorescent localization.A statistically significant decrease in the expression of acetylated -tubulin in asthenozoosperm was seen with Western blotanalysis, double immunostaining by direct immunofluorescence, and flow cytometric analysis. The transcript and protein of testis-specific acetylable -tubulin isoform TUBA3C was decreased and TUBA4A was statistically significantly increased in asthenozoosperm as compared with normal spermatozoa. TUBA8 was reduced in asthenozoosperm. Similar observations were noted by indirect immunofluorescent localization. The potential transcription factors involved in the differential expression of TUBA4A and TUBA3C have been identified.Data suggest an association of -tubulin acetylation with asthenozoospermia. Ours is the first report to demonstrate -tubulin isoforms in sperm, implicating their role in motility. The differential expression of TUBA3C and TUBA4A suggests that tubulin acetylation may be governed by the isoform of -tubulin that is expressed or silenced and that this in turn is transcriptionally controlled.


PubMed | National Health Research Institute and Institute of Bioinformatics and Applied Biotechnology IBAB
Type: Journal Article | Journal: Molecular and cellular biochemistry | Year: 2016

Cysteine-rich secretory protein 3 (CRISP-3) is upregulated in prostate cancer as compared to the normal prostate tissue. Higher expression of CRISP-3 has been linked to poor prognosis and hence it has been thought to act as a prognostic marker for prostate cancer. It is proposed to have a role in innate immunity but its role in prostate cancer is still unknown. In order to understand its function, its expression was stably knocked down in LNCaP cells. CRISP-3 knockdown did not affect cell viability but resulted in reduced invasiveness. Global gene expression changes upon CRISP-3 knockdown were identified by microarray analysis. Microarray data were quantitatively validated by evaluating the expression of seven candidate genes in three independent stable clones. Functional annotation of the differentially expressed genes identified cell adhesion, cell motility, and ion transport to be affected among other biological processes. Prostate-specific antigen (PSA, also known as Kallikrein 3) was the top most downregulated gene whose expression was also validated at protein level. Interestingly, expression of Annexin A1 (ANXA1), a known anti-inflammatory protein, was upregulated upon CRISP-3 knockdown. Re-introduction of CRISP-3 into the knockdown clone reversed the effect on invasiveness and also led to increased PSA expression. These results suggest that overexpression of CRISP-3 in prostate tumor may maintain higher PSA expression and lower ANXA1 expression. Our data also indicate that poor prognosis associated with higher CRISP-3 expression could be due to its role in cell invasion.


PubMed | Institute of Bioinformatics and Applied Biotechnology IBAB and DoS in Computer Science
Type: Journal Article | Journal: PloS one | Year: 2016

Exploring novel computational methods in making sense of biological data has not only been a necessity, but also productive. A part of this trend is the search for more efficient in silico methods/tools for analysis of promoters, which are parts of DNA sequences that are involved in regulation of expression of genes into other functional molecules. Promoter regions vary greatly in their function based on the sequence of nucleotides and the arrangement of protein-binding short-regions called motifs. In fact, the regulatory nature of the promoters seems to be largely driven by the selective presence and/or the arrangement of these motifs. Here, we explore computational classification of promoter sequences based on the pattern of motif distributions, as such classification can pave a new way of functional analysis of promoters and to discover the functionally crucial motifs. We make use of Position Specific Motif Matrix (PSMM) features for exploring the possibility of accurately classifying promoter sequences using some of the popular classification techniques. The classification results on the complete feature set are low, perhaps due to the huge number of features. We propose two ways of reducing features. Our test results show improvement in the classification output after the reduction of features. The results also show that decision trees outperform SVM (Support Vector Machine), KNN (K Nearest Neighbor) and ensemble classifier LibD3C, particularly with reduced features. The proposed feature selection methods outperform some of the popular feature transformation methods such as PCA and SVD. Also, the methods proposed are as accurate as MRMR (feature selection method) but much faster than MRMR. Such methods could be useful to categorize new promoters and explore regulatory mechanisms of gene expressions in complex eukaryotic species.


Hegde M.,Indian Institute of Science | Karki S.S.,KLE University | Thomas E.,Indian Institute of Science | Kumar S.,KLE University | And 5 more authors.
PLoS ONE | Year: 2012

Background: Levamisole, an imidazo(2,1-b)thiazole derivative, has been reported to be a potential antitumor agent. In the present study, we have investigated the mechanism of action of one of the recently identified analogues, 4a (2-benzyl-6-(49-fluorophenyl)-5-thiocyanato-imidazo[2,1-b][1,3,4]thiadiazole).Results: We have determined the IC50 value of 4a in many leukemic and breast cancer cell lines and found CEM cells most sensitive (IC50 5 mM). Results showed that 4a treatment leads to the accumulation of ROS. Western blot analysis showed upregulation of pro-apoptotic proteins t-BID and BAX, upon treatment with 4a. Besides, dose-dependent activation of p53 along with FAS, FAS-L, and cleavage of CASPASE-8 suggest that it induces death receptor mediated apoptotic pathway in CEM cells. More importantly, we observed a reduction in tumor growth and significant increase in survival upon oral administration of 4a (20 mg/kg, six doses) in mice. In comparison, 4a was found to be more potent than its parental analogue Levamisole based on both ex vivo and in vivo studies. Further, immunohistochemistry and western blotting studies indicate that 4a treatment led to abrogation of tumor cell proliferation and activation of apoptosis by the extrinsic pathway even in animal models.Conclusion: Thus, our results suggest that 4a could be used as a potent chemotherapeutic agent.Materials and Methods: ROS production and expression of various apoptotic proteins were measured following 4a treatment in leukemia cell lines. Tumor animal models were used to evaluate the effect of 4a in comparison with Levamisole on progression of breast adenocarcinoma and survival. Immunohistochemistry and western blotting studies were performed to understand the mechanism of 4a action both ex vivo and in vivo. © 2012 Hegde et al.


Somasagara R.R.,Indian Institute of Science | Hegde M.,Indian Institute of Science | Chiruvella K.K.,Indian Institute of Science | Musini A.,Indian Institute of Science | And 2 more authors.
PLoS ONE | Year: 2012

Background: The consumption of berry fruits, including strawberries, has been suggested to have beneficial effects against oxidative stress mediated diseases. Berries contain multiple phenolic compounds and secondary metabolites that contribute to their biological properties. Methodology/Principal Findings: Current study investigates the anticancer activity of the methanolic extract of strawberry (MESB) fruits in leukaemia (CEM) and breast cancer (T47D) cell lines ex vivo, and its cancer therapeutic and chemopreventive potential in mice models. Results of MTT, trypan blue and LDH assays suggested that MESB can induce cytotoxicity in cancer cells, irrespective of origin, in a concentration- and time-dependent manner. Treatment of mice bearing breast adenocarcinoma with MESB blocked the proliferation of tumor cells in a time-dependent manner and resulted in extended life span. Histological and immunohistochemical studies suggest that MESB treatment affected tumor cell proliferation by activating apoptosis and did not result in any side effects. Finally, we show that MESB can induce intrinsic pathway of apoptosis by activating p73 in breast cancer cells, when tumor suppressor gene p53 is mutated. Conclusions/Significance: The present study reveals that strawberry fruits possess both cancer preventive and therapeutic values and we discuss the mechanism by which it is achieved. © 2012 Somasagara et al.


Dey P.,Institute of Bioinformatics and Applied Biotechnology IBAB | Dey P.,Manipal University India | Panga V.,Institute of Bioinformatics and Applied Biotechnology IBAB | Panga V.,Manipal University India | Raghunathan S.,Institute of Bioinformatics and Applied Biotechnology IBAB
PLoS ONE | Year: 2016

In rheumatoid arthritis (RA), nitric oxide (NO) is implicated in inflammation, angiogenesis and tissue destruction. The enzyme inducible nitric oxide synthase (iNOS) is responsible for the localised over-production of NO in the synovial joints affected by RA. The pro- and antiinflammatory cytokines stimulate the synovial macrophages and the fibroblast-like synoviocytes to express iNOS. Therefore, the cytokine signalling network underlying the regulation of iNOS is essential to understand the pathophysiology of the disease. By using information from the literature, we have constructed, for the first time, the cytokine signalling network involved in the regulation of iNOS expression. Using the differential expression patterns obtained by re-analysing the microarray data on the RA synovium and the synovial macrophages available in the Gene Expression Omnibus (GEO) database, we aimed to establish the role played by the network genes towards iNOS regulation in the RA synovium. Our analysis reveals that the network genes belonging to interferon (IFN) and interleukin-10 (IL- 10) pathways are always up-regulated in the RA synovium whereas the genes which are part of the anti-inflammatorytransforming growth factor-beta (TGF-â) signalling pathway are mostly down-regulated.We observed a consistent up-regulation of the transcription factor signal transducers and activators of transcription 1 (STAT1) in the RA synovium and the macrophages. Interestingly, we found a consistent up-regulation of the iNOS interacting protein ras-related C3 botulinum toxin substrate 2 (RAC2) in the RA synovium as well as the macrophages. Importantly, we have constructed a model to explain the impact of IFN and IL-10 pathways on Rac2-iNOS interaction leading to over-production of NO and thereby causing chronic inflammation in the RA synovium. The interplay between STAT1 and RAC2 in the regulation of NO could have implications for the identification of therapeutic targets for RA. © 2016 Dey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


PubMed | Institute of Bioinformatics and Applied Biotechnology IBAB
Type: Journal Article | Journal: PloS one | Year: 2016

In rheumatoid arthritis (RA), nitric oxide (NO) is implicated in inflammation, angiogenesis and tissue destruction. The enzyme inducible nitric oxide synthase (iNOS) is responsible for the localised over-production of NO in the synovial joints affected by RA. The pro- and anti-inflammatory cytokines stimulate the synovial macrophages and the fibroblast-like synoviocytes to express iNOS. Therefore, the cytokine signalling network underlying the regulation of iNOS is essential to understand the pathophysiology of the disease. By using information from the literature, we have constructed, for the first time, the cytokine signalling network involved in the regulation of iNOS expression. Using the differential expression patterns obtained by re-analysing the microarray data on the RA synovium and the synovial macrophages available in the Gene Expression Omnibus (GEO) database, we aimed to establish the role played by the network genes towards iNOS regulation in the RA synovium. Our analysis reveals that the network genes belonging to interferon (IFN) and interleukin-10 (IL-10) pathways are always up-regulated in the RA synovium whereas the genes which are part of the anti-inflammatory transforming growth factor-beta (TGF-) signalling pathway are mostly down-regulated. We observed a consistent up-regulation of the transcription factor signal transducers and activators of transcription 1 (STAT1) in the RA synovium and the macrophages. Interestingly, we found a consistent up-regulation of the iNOS interacting protein ras-related C3 botulinum toxin substrate 2 (RAC2) in the RA synovium as well as the macrophages. Importantly, we have constructed a model to explain the impact of IFN and IL-10 pathways on Rac2-iNOS interaction leading to over-production of NO and thereby causing chronic inflammation in the RA synovium. The interplay between STAT1 and RAC2 in the regulation of NO could have implications for the identification of therapeutic targets for RA.

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