IU Indianapolis ScholarWorks :: Browsing by Author "Perumal, Narayanan B."

Browsing by Author "Perumal, Narayanan B."

Now showing 1 - 7 of 7

DACS-DB: An Annotation and Dissemination Model for Disease Associated Cytokine SNPs
(2011-10-19) Bhushan, Sushant; Perumal, Narayanan B.; Mahoui, Malika; Skaar, Todd
Cytokines mediate crucial functions in innate and adaptive immunity. They play valuable roles in immune cell growth and lineage specification, and are associated with various disease pathologies. A large number of low, medium and high throughput studies have implicated association of single nucleotide polymorphisms (SNPs) in cytokine genes with diseases. A preponderance of such experiments have not shown any causality of an identified SNP to the associated disease. Instead, they have identified statistically significant SNP-disease associations; hence, it is likely that some of these cytokine gene variants may directly or indirectly cause the disease phenotype(s). To fill this knowledge gap and derive study parameters for cytokine SNP-disease causality relationships, we have designed and developed the Disease Associated Cytokine SNP Database (DACS-DB). DACS-DB has data on 456 cytokine genes, approximately 61,000 SNPs, and 891 SNP-associated diseases. In DACS-DB, among other attributes, we present functional annotation, and heterozygosity allele frequency for the SNPs, and literature-validated SNP association for diseases. Users of the DB can run queries such as the ones to find disease-associated SNPs in a cytokine gene, and all the SNPs involved in a disease. We have developed a web front end (available at http://www.iupui.edu/~cytosnp) to disseminate this information for immunologists, biomedical researchers, and other interested biological researchers. Since there is no such comprehensive collection of disease associated cytokine SNPs, this DB will be vital to understanding the role of cytokine SNPs as markers in disease, and, more importantly, in causality to disease thus helping to identify drug targets for common inflammatory diseases. Due to the presence of rich annotations, the DACS-DB can be a good source for building a tool for the prediction of the "disease association potential (DAP)" of a given SNP. In a preliminary effort to devise such a methodology for DAP prediction, we have applied a support vector machine (SVM) to classify SNPs. Employing the SNP attributes of function class, heterozygosity value, and heterozygosity standard error, 864 SNPs were classified into two classes, "disease" and "non-disease". The SVM returned a classification of these SNPs into the disease and non-disease classes with an accuracy of 74%. By modifying various SNP and disease attributes in the training data sets, such a predictive algorithm can be extrapolated to identify potential disease associated SNPs among newly sequenced cytokine variations. In the long run, this approach can provide a means for future gene variation based therapeutic regimens.
Functional characterization of a genetic polymorphism in the promoter of the ESR2 gene
(Springer, 2012-04) Philips, Santosh; Richter, Alexandra; Oesterreich, Steffi; Rae, James M.; Flockhart, David A.; Perumal, Narayanan B.; Skaar, Todd C.
The ESR2 gene encodes the estrogen receptor beta protein. Several studies have shown that genetic variants in the ESR2 gene are associated with a variety of clinical phenotypes. However, very little is known about the functional significance of ESR2 genetic variants. We used a bioinformatics approach to identify regions of the ESR2 promoter that is evolutionarily conserved across the genomes of several species. We resequenced 1.6 kb of the ESR2 gene which included 0.8 kb of the promoter, 0.3 kb of exon ON, and 0.5 kb of the following intron. We identified five single-nucleotide polymorphisms (SNPs) in the ESR2 promoter and one SNP in the intron. Phase analysis indicated that the SNPs likely exist in 11 different haplotypes. Three of the SNPs (rs8008187, rs3829768, rs35036378) were predicted to alter transcription factor binding sites in the ESR2 promoter. All three were detected only in African American subjects. The rs35036378 SNP was in the TATA box and was highly conserved across species. ESR2 promoter reporter assays in LNCaP and SKBR3 cell lines showed that the variant construct containing the rs35036378 SNP allele had approximately 50% less activity relative to the wild-type construct. We conclude that the rs35036378 SNP appears to cause a reduced promoter activity of the ESR2 gene.
FUNCTIONAL GENOMICS STUDY TO UNDERSTAND THE ROLE OF SEROTONIN IN MOUSE EMBRYONIC STEM CELLS
(2011-10-19) Nagari, Anusha; Perumal, Narayanan B.; Panicker, Mitradas M.; Zhou, Yaoqi; Pradhan, Meeta
Serotonin (5-hydroxytryptamine, 5-HT) is a monoamine neurotransmitter that is synthesized from the amino acid L-tryptophan and is reported to localize in mitochondria of embryonic stem cells. Even before its role as a neurotransmitter in mature brain was discovered, 5-HT has been shown to play an important role in regulating brain development. However, there is a lack of knowledge about the downstream target genes regulated by serotonin in embryonic stem (ES) cells. Towards this end, our study helps in understanding transcriptional regulatory mechanisms of 5-HT responsive genes in ES cells. By combining the gene expression data with motif prediction algorithms, literature validation and comparison with public domain data, gene targets specific to endogenous or exogenous 5-HT in ES cells were identified. By performing one-way ANOVA, and volcano plots using GeneSpring software, we identified 44 5-HT induced and 29 5-HT suppressed genes, likely to be transcriptionally regulated by 4 & 2 TFs respectively. Motif enrichment analysis on these target genes using MotifScanner revealed that the transcription factor TFAP2A plays a key role in regulating the expression of 5-HT responsive genes. Furthermore, by comparing our dataset with published expression profiles of ES cells, we observed a number of 5-HT responsive target genes showing enrichment in ES cells. Genes such as Nanog, Slc38a5, Hoxb1 and Eif2s1 from this analysis have been observed to be components of ‘stemness’ phenotypes reported in literature. Functional annotation of the 5-HT responsive genes identified gene ontologies such as regulation of translation in response to stress and energy derivation by oxidation, suggesting a regulatory role for 5-HT in mitochondrial functions of ES cells. Additionally, enrichment of other biological process terms such as development of various parts of nervous system, cell adhesion, and apoptosis suggests that 5-HT target genes may play an important role in ES cell differentiation. Our study implemented a new combinatorial approach for identifying gene regulatory mechanisms involved in 5-HT responsive genes and proposed potential mediatory role for serotonin in ES cell differentiation and growth. Thus, this study provides potential 5-HT target genes in ES cells for biological validation.
Implementation of a Laboratory Information Management System To Manage Genomic Samples
(2013-09-05) Witty, Derick; Merchant, Mahesh; Perumal, Narayanan B.; Turpin, Joseph
A Laboratory Information Management Systems (LIMS) is designed to manage laboratory processes and data. It has the ability to extend the core functionality of the LIMS through configuration tools and add-on modules to support the implementation of complex laboratory workflows. The purpose of this project is to demonstrate how laboratory data and processes from a complex workflow can be implemented using a LIMS. Genomic samples have become an important part of the drug development process due to advances in molecular testing technology. This technology evaluates genomic material for disease markers and provides efficient, cost-effective, and accurate results for a growing number of clinical indications. The preparation of the genomic samples for evaluation requires a complex laboratory process called the precision aliquotting workflow. The precision aliquotting workflow processes genomic samples into precisely created aliquots for analysis. The workflow is defined by a set of aliquotting scheme attributes that are executed based on scheme specific rules logic. The aliquotting scheme defines the attributes of each aliquot based on the achieved sample recovery of the genomic sample. The scheme rules logic executes the creation of the aliquots based on the scheme definitions. LabWare LIMS is a Windows® based open architecture system that manages laboratory data and workflow processes. A LabWare LIMS model was developed to implement the precision aliquotting workflow using a combination of core functionality and configured code.
Intrinsic disorder in protein products of newborn genes
(2011-10-19) K., S.; Romero, Pedro; Perumal, Narayanan B.; Dunker, Keith
There are many mechanisms for the creation of new genes. In this study, the newborn genes i.e. de novo genes are the genes that are created from scratch. These are created by two mechanisms, polymerization (de novo genes produced from non-coding regions) and overprinting (de novo genes produced from overlapping frames). Rancurel et al has found that de novo genes in overlapping coding regions tend to be more disordered than their ancestral counterparts. It was suggested that it is natural for the newborn genes to be disordered, as it must be very difficult for newborn genes to obtain order at such an early stage, so that the structure is only developed after the evolutionary development. The two hypotheses tested in this study state (1) that genes generated de novo will have a tendency to be disordered, and (2) this tendency is due to a natural inclination of these genes to be disordered at birth. The origin and evolution of some de novo coding regions have been studied in detail. We analyzed genes reported in literature that have been produced de novo; either by overprinting or by polymerization, and their tendency for disorder was evaluated using the VSL2 disorder predictor. The de novo coding regions produced by both ways indeed shows a tendency towards disorder, which supports hypothesis 1. For hypothesis 2 to be tested on a larger dataset the exonic and intronic materials of two human chromosomes were studied and the tendency for disorder was assessed for any new peptide sequence arising from the translation of non-coding sequences arising from introns and exons (overlapping frames). It was shown that the tendency of disorder for protein products of newborn genes arising from introns were not inclined towards being ordered or disordered, but they can become disordered by evolution. The new exonic material created from the existing exons tends to be more disordered when translated, and this tendency does not seem to be dependent upon the disorder content of the original exons. This difference could be a consequence of the fact that the overlapping frames of coding sequences have indirectly been subjected to evolutionary pressure along with the original exon, whereas intronic sequences do not seem to have this constraint, but the exact nature of this discrepancy needs further study to be explained. The tendency of disorder in the existing new exons seems to be higher than the artificial exons (generated in this study). We conclude that the intrinsic disorder in the protein products of de novo genes is selected by the evolution rather than an initial condition. Thus, the newborn genes were not born disordered.
Intrinsic Disorder in Transcription Factors
(2005-08) Liu, Jiangang (Al); Perumal, Narayanan B.
Reported evidence suggested that high abundance of intrinsic disorder in eukaryotic genomes in comparison to bacteria and archaea may reflect the greater need for disorder-associated signaling and transcriptional regulation in nucleated cells. The major advantage of intrinsically disordered proteins or disordered regions is their inherent plasticity for molecular recognition, and this advantage promotes disordered proteins or disordered regions in binding their targets with high specificity and low affinity and with numerous partners. Although several well-characterized examples of intrinsically disordered proteins in transcriptional regulation have been reported and the biological functions associated with their corresponding structural properties have been examined, so far no specific systematic analysis of intrinsically disordered proteins has been reported. To test for a generalized prevalence of intrinsic disorder in transcriptional regulation, we first used the Predictor Of Natural Disorder Regions (PONDR VL-XT) to systematically analyze the intrinsic disorder in three Transcription Factor (TF) datasets (TFSPTRENR25, TFSPNR25, TFNR25) and two control sets (PDBs25 and RandomACNR25). PONDR VL-XT predicts regions of ≥30 consecutive disordered residues for 94.13%, 85.19%, 82.63%, 54.51%, and 18.64% of the proteins from TFNR25, TFSPNR25, TFSPTRENR25, RandomACNR25, and PDBs25, respectively, indicating significant abundance of intrinsic disorder in TFs as compared to the two control sets. We then used Cumulative Distribution Function (CDF) and charge-hydropathy plots to further confirm this propensity for intrinsic disorder in TFs. The amino acid compositions results showed that the three TF datasets differed significantly 5 from the two control sets. All three TF datasets were substantially depleted in order-promoting residues such as W, F, I, Y, and V, and significantly enriched in disorder-promoting residues such as Q, S, and P. H and C were highly over-represented in TF datasets because nearly a half of TFs contain several zinc-fingers and the most popular type of zinc-finger is C2H2. High occurrence of proline and glutamine in these TF datasets suggests that these residues might contribute to conformational flexibility needed during the process of binding by co-activators or repressors during transcriptional activation or repression. The data for disorder predictions on TF domains showed that the AT-hooks and basic regions of DNA Binding Domains (DBDs) were highly disordered (the overall disorder scores are 99% and 96% respectively). The C2H2 zinc-fingers were predicted to be highly ordered; however, the longer the zinc finger linkers, the higher the predicted magnitude of disorder. Overall, the degree of disorder in TF activation regions was much higher than that in DBDs. Our studies also confirmed that the degree of disorder was significantly higher in eukaryotic TFs than in prokaryotic TFs, and the results reflected the fact that the eukaryotes have well-developed elaborated gene transcription mechanism, and such a system is in great need of TF flexibility. Taken together, our data suggests that intrinsically disordered TFs or partially unstructured regions in TFs play key roles in transcriptional regulation, where folding coupled to binding is a common mechanism.
Role of ovarian cancer-initiating cells in high-grade serous ovarian carcinogenesis
(2012-03-20) Jadhav, Rohit; Zhou, Yaoqi; Nephew, Kenneth P.; Li, Lang; Shen, Changyu; Perumal, Narayanan B.
A subpopulation of tumor cells known as ovarian cancer initiating cells (OCICs) have been shown to be the cells that propagate the tumor phenotype in ovarian cancer. Studies have showed that a very small population (100) of these cells is sufficient to induce a tumor phenotype; while a large quantity of tumor cells (5 X 105) are required to induce such a phenotype. In this study we studied the functional changes in genes expressed in the OCIC phenotype which were important for such efficient propagation of cancers. To enable this analysis, we generated mRNA expression and DNA methylation profiles of OCICs and compared them with those of tumor and normal ovarian surface epithelial cells. We identified four pathways which regulated most of the observed changes and were predicted to be important factors in distinguishing the OCICs from tumors and normal cells. The gene signatures for these pathways were analyzed by unsupervised clustering in order to determine the similarities of OCICs with respect to tumor and normal samples. We further believed that the OCICs can be used as indicators towards the genesis and progression of early events in the ovarian cancers. In light of this, we considered two hypotheses which are currently addressing the genesis of ovarian cancer. The first hypothesis proposed ovarian surface epithelial cells to be cells of origin of the ovarian cancer while the other proposed the fallopian tube cells to be contributing the cell of origin for these cancers. It is also believed that these two cells can be reciprocal cells of origin for the cancer phenotype. In order to test these hypotheses, we integrated the in-house dataset with a public domain fallopian tube gene expression data. The integration of the results obtained from these analyses provided better understanding of the early events in ovarian carcinogenesis.

Browsing by Author "Perumal, Narayanan B."

Results Per Page

Sort Options