Showing papers by "Muneesh Tewari published in 2009"

Limitations and possibilities of small RNA digital gene expression profiling.

Abstract: 1. Li, H., Ruan, J. & Durbin, R. Genome Res. 18, 1851–1858 (2008) 2. Hormozdiari, F. et al. Genome Res. (in the press). 3. Korbel, J.O. et al. Genome Biol. 10, R23 (2009). 4. Lee, S., Cheran, E. & Brudno, M. Bioinformatics 24, i59–i67 (2008). 5. Mills, R.E. et al. Genome Res. 16, 1182–1190 (2006). 6. Bentley, D.R. et al. Nature 456, 53–59 (2008). 7. Kidd, J.M. et al. Nature 453, 56–64 (2008). Gaussian distribution with mean μ and standard deviation σ where

Empirically-controlled mapping of the Caenorhabditis elegans protein-protein interactome network

Abstract: High-throughput yeast two-hybrid screening is used to generate the largest C. elegans interactome resource available thus far. Using an empirical quality control framework presented in Venkatesan et al., also online, the data set is evaluated for quality and is used to estimate the total size of the worm interactome. To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards. We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of ∼10,000 × ∼10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at ∼116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins.

Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.

Abstract: Background MicroRNAs (miRNAs) are small regulatory RNAs that are implicated in cancer pathogenesis and have recently shown promise as blood-based biomarkers for cancer detection. Epithelial ovarian cancer is a deadly disease for which improved outcomes could be achieved by successful early detection and enhanced understanding of molecular pathogenesis that leads to improved therapies. A critical step toward these goals is to establish a comprehensive view of miRNAs expressed in epithelial ovarian cancer tissues as well as in normal ovarian surface epithelial cells.

Multiple Integrated Copies and High-Level Production of the Human Retrovirus XMRV (Xenotropic Murine Leukemia Virus-Related Virus) from 22Rv1 Prostate Carcinoma Cells

Abstract: The human retrovirus XMRV (xenotropic murine leukemia virus-related virus) is associated with prostate cancer, most frequently in humans with a defect in the antiviral defense protein RNase L, suggesting a role for XMRV in prostate carcinogenesis. However, XMRV has not been found in prostate carcinoma cells. Here we show that 22Rv1 prostate carcinoma cells produce high-titer virus that is nearly identical in properties and sequence to XMRV isolated by others and consist primarily of a single clone of cells with at least 10 integrated copies of XMRV, warranting further study of a possible role for XMRV integration in carcinogenesis.

Evaluation of the 8q24 Prostate Cancer Risk Locus and MYC Expression

Abstract: Polymorphisms at 8q24 are robustly associated with prostate cancer risk. The risk variants are located in non-protein coding regions and their mechanism has not been fully elucidated. To further dissect the function of this locus, we tested two hypotheses: i) unannotated microRNAs are transcribed in the region, and that ii) this region is a cis-acting enhancer. Using next generation sequencing, 8q24 risk regions were interrogated for known and novel microRNAs (miRNAs) in histologically normal radical prostatectomy (RP) tissue. We also evaluated the association between the risk variants and transcript levels of multiple genes, focusing on the proto-oncogene, MYC. RNA expression was measured in histologically normal and tumor tissue from 280 RP specimens (from 234 European American and 46 African American patients), and paired germline DNA from each individual was genotyped for six 8q24 risk SNPs. No evidence was found for significant miRNA transcription within 8q24 prostate cancer risk loci. Likewise, no convincing association between distal RNA expression and risk allele status was detected in either histologically normal or tumor tissue. To our knowledge, this is one of the first and largest studies to directly assess miRNA in this region and to systematically measure MYC expression levels in prostate tissue in relation to inherited risk variants. These data will help to direct the future study of this risk locus.

Quality Assessment and Data Analysis for microRNA Expression Arrays

Abstract: MicroRNAs are small (~22nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. However, microarray profiling of microRNA expression raises a number of data analytic challenges that must be addressed in order to obtain reliable results. We introduce here a universal reference microRNA reagent set as well as a series of nonhuman spiked-in synthetic microRNA controls, and demonstrate their use for quality control and between-array normalization of microRNA expression data. We also introduce diagnostic plots designed to assess and compare various normalization methods. We anticipate that the reagents and analytic approach presented here will be useful for improving the reliability of microRNA microarray experiments.

Use of extracellular rna to measure disease

Abstract: Stable, extracellular microRNAs and methods for isolating and identifying such microRNAs from a body fluid are provided. The extracellular microRNAs isolated from a bodily fluid of a subject can be used to measure disease and provide sensitive, efficient, and non invasive methods for the detection of disease, including cancer. The extracellular microRNAs can be used to develop new therapeutics for the treatment of disease, including cancer. The examples illustrate diagnosis of prostate and ovarian cancer and differential expression of miR-100, miR-135b, miR-141, miR-148a, miR-200a, miR-200c, miR-210, miR-222, miR-375, miR-425-Sp and miR-429.

Epigenetic silencing of mir-342 in colorectal cancer

Abstract: Novel tools and methods for the detection and treatment of colorectal cancer are provided. Expression of miR-342 and/or EVL are reduced or absent in colorectal cancer, due to methylation-induced silencing. Detection of specific methylation of the EVL gene is provided as a method for detecting the presence or risk of colorectal cancer. Therapeutic administration of miR-342 and/or EVL and/or administration of demethylation agents to restore activity of miR- 342 and EVL are provided as methods for treating or preventing colorectal cancer.

Photonic Crystal Optical Tweezers

Abstract: Non-invasive optical manipulation of particles has emerged as a powerful and versatile tool for biological study and nanotechnology. In particular, trapping and rotation of cells, cell nuclei and sub-micron particles enables unique functionality for various applications such as tissue engineering, cancer research and nanofabrication. We propose and demonstrate a purely optical approach to rotate and align particles using the interaction of polarized light with photonic crystal nanostructures to generate enhanced trapping force. With a weakly focused laser beam we observed efficient trapping and transportation of polystyrene beads with sizes ranging from 10 um down to 190 nm as well as cancer cell nuclei. In addition, we demonstrated alignment of non-spherical particles using a 1-D photonic crystal structure. Bacterial cells were trapped, rotated and aligned with optical intensity as low as 17 uW/um^2. Finite-difference time domain (FDTD) simulations of the optical near-field and far-field above the photonic crystal nanostructure reveal the origins for the observed results. This approach can be extended to using 2-D photonic crystal nanostructures for full rotation control.

Enhanced trapping and rotation of sub-micron particles and cells through nanostructures

Abstract: In this work we propose and demonstrate the use of 1D photonic crystals to achieve both enhanced trapping forces and unique functionality, namely the ability to rotate and align particles using purely optical means Particles as small as 190 nm can be trapped effectively, and bacteria cells can be rotated with an intensity as low as 17 µW/µm2