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PubMed | Lewis Sigler Institute for Integrative Genomics, University of Washington, Roswell Park Cancer Institute and Central University of Tamil Nadu
Type: | Journal: Oncotarget | Year: 2017

Progression of prostate cancer (PC) to castration-recurrent growth (CRPC) remains dependent on sustained expression and transcriptional activity of the androgen receptor (AR). A major mechanism contributing to CRPC progression is through the direct phosphorylation and activation of AR by Src-family (SFK) and ACK1 tyrosine kinases. However, the AR-dependent transcriptional networks activated by Src during CRPC progression have not been elucidated. Here, we show that activated Src (Src527F) induces androgen-independent growth in human LNCaP cells, concomitant with its ability to induce proliferation/survival genes normally induced by dihydrotestosterone (DHT) in androgen-dependent LNCaP and VCaP cells. Src induces additional gene signatures unique to CRPC cell lines, LNCaP-C4-2 and CWR22Rv1, and to CRPC LuCaP35.1 xenografts. By comparing the Src-induced AR-cistrome and/or transcriptome in LNCaP to those in CRPC and LuCaP35.1 tumors, we identified an 11-gene Src-regulated CRPC signature consisting of AR-dependent, AR binding site (ARBS)-associated genes whose expression is altered by DHT in LNCaP[Src527F] but not in LNCaP cells. The differential expression of a subset (DPP4, BCAT1, CNTNAP4, CDH3) correlates with earlier PC metastasis onset and poorer survival, with the expression of BCAT1 required for Src-induced androgen-independent proliferation. Lastly, Src enhances AR binding to non-canonical ARBS enriched for FOXO1, TOP2B and ZNF217 binding motifs; cooperative AR/TOP2B binding to a non-canonical ARBS was both Src- and DHT-sensitive and correlated with increased levels of Src-induced phosphotyrosyl-TOP2B. These data suggest that CRPC progression is facilitated via Src-induced sensitization of AR to intracrine androgen levels, resulting in the engagement of canonical and non-canonical ARBS-dependent gene signatures.

PubMed | Lewis Sigler Institute for Integrative Genomics, Ben - Gurion University of the Negev, Lewis University and Harvard University
Type: Journal Article | Journal: Proceedings of the National Academy of Sciences of the United States of America | Year: 2014

The ParABS system mediates chromosome segregation and plasmid partitioning in many bacteria. As part of the partitioning mechanism, ParB proteins form a nucleoprotein complex at parS sites. The biophysical basis underlying ParB-DNA complex formation and localization remains elusive. Specifically, it is unclear whether ParB spreads in 1D along DNA or assembles into a 3D protein-DNA complex. We show that a combination of 1D spreading bonds and a single 3D bridging bond between ParB proteins constitutes a minimal model for a condensed ParB-DNA complex. This model implies a scaling behavior for ParB-mediated silencing of parS-flanking genes, which we confirm to be satisfied by experimental data from P1 plasmids. Furthermore, this model is consistent with experiments on the effects of DNA roadblocks on ParB localization. Finally, we show experimentally that a single parS site is necessary and sufficient for ParB-DNA complex formation in vivo. Together with our model, this suggests that ParB binding to parS triggers a conformational switch in ParB that overcomes a nucleation barrier. Conceptually, the combination of spreading and bridging bonds in our model provides a surface tension ensuring the condensation of the ParB-DNA complex, with analogies to liquid-like compartments such as nucleoli in eukaryotes.

Mora T.,Lewis Sigler Institute for Integrative Genomics | Mora T.,CNRS ENS Statistical Physics Laboratory | Bai F.,Osaka University | Che Y.-S.,Osaka University | And 4 more authors.
Physical Biology | Year: 2011

By analyzing 30 min, high-resolution recordings of single Escherichia coli flagellar motors in the physiological regime, we show that two main properties of motor switching - the mean clockwise and mean counter-clockwise interval durations - vary significantly. When we represent these quantities on a two-dimensional plot for several cells, the data do not fall on a one-dimensional curve, as expected with a single control parameter, but instead spread in two dimensions, pointing to motor individuality. The largest variations are in the mean counter-clockwise interval, and are attributable to variations in the concentration of the internal signaling molecule CheY-P. In contrast, variations in the mean clockwise interval are interpreted in terms of motor individuality. We argue that the sensitivity of the mean counter-clockwise interval to fluctuations in CheY-P is consistent with an optimal strategy of run and tumble. The concomittent variability in mean run length may allow populations of cells to better survive in rapidly changing environments by 'hedging their bets'. © 2011 IOP Publishing Ltd.

Lim S.F.,Princeton University | Ryu W.S.,Lewis Sigler Institute for Integrative Genomics | Austin R.H.,Princeton University
Optics Express | Year: 2010

The effects of the nanocrystal size on the emission spectra and decay rates of upconverting hexagonal NaYF4:Yb,Er nanocrystals are investigated. The influence of nanocrystal size is represented in terms of the surface area/volume ratio (SA/Vol). Our results show that a small nanocrystal size, or large SA/Vol ratio increases the decay rate, in particular, the green luminescence decay rate varies linearly with the SA/Vol ratio. © 2009 Optical Society of America.

Ghersi D.,Lewis Sigler Institute for Integrative Genomics | Singh M.,Lewis Sigler Institute for Integrative Genomics | Singh M.,Princeton University
Bioinformatics | Year: 2014

The chemical structures of biomolecules, whether naturally occurring or synthetic, are composed of functionally important building blocks. Given a set of small molecules - for example, those known to bind a particular protein - computationally decomposing them into chemically meaningful fragments can help elucidate their functional properties, and may be useful for designing novel compounds with similar properties. Here we introduce molBLOCKS, a suite of programs for breaking down sets of small molecules into fragments according to a predefined set of chemical rules, clustering the resulting fragments, and uncovering statistically enriched fragments. Among other applications, our software should be a great aid in large-scale chemical analysis of ligands binding specific targets of interest. © 2014 The Author 2014.

Seltzer M.J.,Johns Hopkins University | Bennett B.D.,Lewis Sigler Institute for Integrative Genomics | Joshi A.D.,Johns Hopkins University | Gao P.,Johns Hopkins University | And 8 more authors.
Cancer Research | Year: 2010

Mutation at the R132 residue of isocitrate dehydrogenase 1 (IDH1), frequently found in gliomas and acute myelogenous leukemia, creates a neoenzyme that produces 2-hydroxyglutarate (2-HG) from α-ketoglutarate (α-KG). We sought to therapeutically exploit this neoreaction in mutant IDH1 cells that require α-KG derived from glutamine. Glutamine is converted to glutamate by glutaminase and further metabolized to α-KG. Therefore, we inhibited glutaminase with siRNA or the small molecule inhibitor bis-2-(5-phenylacetamido- 1,2,4-thiadiazol-2-yl)ethyl sulfide (BPTES) and found slowed growth of glioblastoma cells expressing mutant IDH1 compared with those expressing wild-type IDH1. Growth suppression of mutant IDH1 cells by BPTES was rescued by adding exogenous α-KG. BPTES inhibited glutaminase activity, lowered glutamate and α-KG levels, and increased glycolytic intermediates while leaving total 2-HG levels unaffected. The ability to selectively slow growth in cells with IDH1 mutations by inhibiting glutaminase suggests a unique reprogramming of intermediary metabolism and a potential therapeutic strategy. ©2010 AACR.

Osterfield M.,Lewis Sigler Institute for Integrative Genomics | Du X.,Princeton University | Schupbach T.,Howard Hughes Medical Institute | Wieschaus E.,Lewis Sigler Institute for Integrative Genomics | And 3 more authors.
Developmental Cell | Year: 2013

Morphogenesis of the respiratory appendages on eggshells of Drosophila species provides a powerful experimental system for studying how cell sheets give rise to complex three-dimensional structures. In Drosophila melanogaster, each of the two tubular eggshell appendages is derived from a primordium comprising two distinct cell types. Using live imaging and three-dimensional image reconstruction, we demonstrate that the transformation of this two-dimensional primordium into a tube involves out-of-plane bending followed by a sequence of spatially ordered cell intercalations. These morphological transformations correlate with the appearance of complementary distributions of myosin and Bazooka in the primordium. These distributions suggest that a two-dimensional pattern of line tensions along cell-cell edges on the apical side of the epithelium is sufficient to produce the observed changes in morphology. Computational modeling shows that this mechanism could explain the main features of tissue deformation and cell rearrangements observed during three-dimensional morphogenesis. © 2013 Elsevier Inc.

Fletcher A.G.,University of Oxford | Osterfield M.,Lewis Sigler Institute for Integrative Genomics | Baker R.E.,University of Oxford | Shvartsman S.Y.,Lewis Sigler Institute for Integrative Genomics | Shvartsman S.Y.,Princeton University
Biophysical Journal | Year: 2014

The dynamic behavior of epithelial cell sheets plays a central role during numerous developmental processes. Genetic and imaging studies of epithelial morphogenesis in a wide range of organisms have led to increasingly detailed mechanisms of cell sheet dynamics. Computational models offer a useful means by which to investigate and test these mechanisms, and have played a key role in the study of cell-cell interactions. A variety of modeling approaches can be used to simulate the balance of forces within an epithelial sheet. Vertex models are a class of such models that consider cells as individual objects, approximated by two-dimensional polygons representing cellular interfaces, in which each vertex moves in response to forces due to growth, interfacial tension, and pressure within each cell. Vertex models are used to study cellular processes within epithelia, including cell motility, adhesion, mitosis, and delamination. This review summarizes how vertex models have been used to provide insight into developmental processes and highlights current challenges in this area, including progressing these models from two to three dimensions and developing new tools for model validation. © 2014 Biophysical Society.

Xu X.,Duke University | Kumar N.,University of Massachusetts Boston | Krishnan A.,Lewis Sigler Institute for Integrative Genomics | Kulkarni R.V.,University of Massachusetts Boston
Proceedings of the IEEE Conference on Decision and Control | Year: 2013

The process of transcription has been intensively studied for several decades, however there is still much to learn about the underlying biochemcial processes. Recent advances in single-molecule techniques have provided new experimental data that highlights the role of transcriptional pausing in the regulation of gene expression. In some cases, it has been shown that transcriptional pauses are rate-limiting stochastic processes, thus a quantitative understanding requires stochastic modeling of the underlying processes. We propose a coarsegrained stochastic model to analyze the dwell-time distribution for transcriptional pausing. The proposed kinetic scheme can also be used to model transcriptional initiation and to analyze the corresponding noise in gene expression. We obtain analytical solutions which can provide useful insights into current and future experiments focusing on time-resolved single-molecule studies of transcriptional pausing and noise in gene expression. ©2013 IEEE.

Chikina M.D.,Mount Sinai School of Medicine | Troyanskaya O.G.,Lewis Sigler Institute for Integrative Genomics
Bioinformatics | Year: 2012

Motivation: ChIPseq is rapidly becoming a common technique for investigating protein-DNA interactions. However, results from individual experiments provide a limited understanding of chromatin structure, as various chromatin factors cooperate in complex ways to orchestrate transcription. In order to quantify chromtain interactions, it is thus necessary to devise a robust similarity metric applicable to ChIPseq data. Unfortunately, moving past simple overlap calculations to give statistically rigorous comparisons of ChIPseq datasets often involves arbitrary choices of distance metrics, with significance being estimated by computationally intensive permutation tests whose statistical power may be sensitive to non-biological experimental and post-processing variation. Results: We show that it is in fact possible to compare ChIPseq datasets through the efficient computation of exact P-values for proximity. Our method is insensitive to non-biological variation in datasets such as peak width, and can rigorously model peak location biases by evaluating similarity conditioned on a restricted set of genomic regions (such as mappable genome or promoter regions). Applying our method to the well-studied dataset of Chen et al. (2008), we elucidate novel interactions which conform well with our biological understanding. By comparing ChIPseq data in an asymmetric way, we are able to observe clear interaction differences between cofactors such as p300 and factors that bind DNA directly. © The Author 2012. Published by Oxford University Press. All rights reserved.

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