VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

BACKGROUND

VirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We apply our method to dissect the regulation of estrogen receptor-alpha activation in breast cancer to identify potential co-regulators of the estrogen receptor's transcriptional response.

RESULTS

VULCAN analysis of estrogen receptor activation in breast cancer highlights the key components of the estrogen receptor complex alongside a novel interaction with GRHL2. We demonstrate that GRHL2 is recruited to a subset of estrogen receptor binding sites and regulates transcriptional output, as evidenced by changes in estrogen receptor-associated eRNA expression and stronger estrogen receptor binding at active enhancers after GRHL2 knockdown.

CONCLUSIONS

Our findings provide new insight into the role of GRHL2 in regulating eRNA transcription as part of estrogen receptor signaling. These results demonstrate VULCAN, available from Bioconductor, as a powerful predictive tool.

Search for the Production of a Long-Lived Neutral Particle Decaying within the ATLAS Hadronic Calorimeter in Association with a Z Boson from pp Collisions at sqrt[s]=13 TeV

This Letter presents a search for the production of a long-lived neutral particle (Z_{d}) decaying within the ATLAS hadronic calorimeter, in association with a standard model (SM) Z boson produced via an intermediate scalar boson, where Z→ℓ^{+}ℓ^{-} (ℓ=e, μ). The data used were collected by the ATLAS detector during 2015 and 2016 pp collisions with a center-of-mass energy of sqrt[s]=13  TeV at the Large Hadron Collider and correspond to an integrated luminosity of 36.1±0.8  fb^{-1}. No significant excess of events is observed above the expected background. Limits on the production cross section of the scalar boson times its decay branching fraction into the long-lived neutral particle are derived as a function of the mass of the intermediate scalar boson, the mass of the long-lived neutral particle, and its cτ from a few centimeters to one hundred meters. In the case that the intermediate scalar boson is the SM Higgs boson, its decay branching fraction to a long-lived neutral particle with a cτ approximately between 0.1 and 7 m is excluded with a 95% confidence level up to 10% for m_{Z_{d}} between 5 and 15 GeV.

Combination of the Searches for Pair-Produced Vectorlike Partners of the Third-Generation Quarks at sqrt[s]=13 TeV with the ATLAS Detector

A combination of the searches for pair-produced vectorlike partners of the top and bottom quarks in various decay channels (T→Zt/Wb/Ht, B→Zb/Wt/Hb) is performed using 36.1  fb^{-1} of pp collision data at sqrt[s]=13  TeV with the ATLAS detector at the Large Hadron Collider. The observed data are found to be in good agreement with the standard model background prediction in all individual searches. Therefore, combined 95% confidence-level upper limits are set on the production cross section for a range of vectorlike quark scenarios, significantly improving upon the reach of the individual searches. Model-independent limits are set assuming the vectorlike quarks decay to standard model particles. A singlet T is excluded for masses below 1.31 TeV and a singlet B is excluded for masses below 1.22 TeV. Assuming a weak isospin (T,B) doublet and |V_{Tb}|≪|V_{tB}|, T and B masses below 1.37 TeV are excluded.

Observation of Centrality-Dependent Acoplanarity for Muon Pairs Produced via Two-Photon Scattering in Pb+Pb Collisions at sqrt[s_{NN}]=5.02 TeV with the ATLAS Detector

This Letter presents a measurement of γγ→μ^{+}μ^{-} production in Pb+Pb collisions recorded by the ATLAS detector at the Large Hadron Collider at sqrt[s_{NN}]=5.02  TeV with an integrated luminosity of 0.49  nb^{-1}. The azimuthal angle and transverse momentum correlations between the muons are measured as a function of collision centrality. The muon pairs are produced from γγ through the interaction of the large electromagnetic fields of the nuclei. The contribution from background sources of muon pairs is removed using a template fit method. In peripheral collisions, the muons exhibit a strong back-to-back correlation consistent with previous measurements of muon pair production in ultraperipheral collisions. The angular correlations are observed to broaden significantly in central collisions. The modifications are qualitatively consistent with rescattering of the muons while passing through the hot matter produced in the collision.

Search for Resonant and Nonresonant Higgs Boson Pair Production in the bb[over ¯]τ^{+}τ^{-} Decay Channel in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

A search for resonant and nonresonant pair production of Higgs bosons in the bb[over ¯]τ^{+}τ^{-} final state is presented. The search uses 36.1  fb^{-1} of pp collision data with sqrt[s]=13  TeV recorded by the ATLAS experiment at the LHC in 2015 and 2016. Decays of the τ-lepton pairs with at least one τ lepton decaying to final states with hadrons and a neutrino are considered. No significant excess above the expected background is observed in the data. The cross-section times branching ratio for nonresonant Higgs boson pair production is constrained to be less than 30.9 fb, 12.7 times the standard model expectation, at 95% confidence level. The data are also analyzed to probe resonant Higgs boson pair production, constraining a model with an extended Higgs sector based on two doublets and a Randall-Sundrum bulk graviton model. Upper limits are placed on the resonant Higgs boson pair production cross-section times branching ratio, excluding resonances X in the mass range 305  GeV<m_{X}<402  GeV in the simplified hMSSM minimal supersymmetric model for tanβ=2 and excluding bulk Randall-Sundrum gravitons G_{KK} in the mass range 325  GeV<m_{G_{KK}}<885  GeV for k/M[over ¯]_{Pl}=1.

Probing the Quantum Interference between Singly and Doubly Resonant Top-Quark Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

This Letter presents a normalized differential cross-section measurement in a fiducial phase-space region where interference effects between top-quark pair production and associated production of a single top quark with a W boson and a b-quark are significant. Events with exactly two leptons (ee, μμ, or eμ) and two b-tagged jets that satisfy a multiparticle invariant mass requirement are selected from 36.1  fb^{-1} of proton-proton collision data taken at sqrt[s]=13  TeV with the ATLAS detector at the LHC in 2015 and 2016. The results are compared with predictions from simulations using various strategies for the interference. The standard prescriptions for interference modeling are significantly different from each other but are within 2σ of the data. State-of-the-art predictions that naturally incorporate interference effects provide the best description of the data in the measured region of phase space most sensitive to these effects. These results provide an important constraint on interference models and will guide future model development and tuning.

Measurement of the Soft-Drop Jet Mass in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

Jet substructure observables have significantly extended the search program for physics beyond the standard model at the Large Hadron Collider. The state-of-the-art tools have been motivated by theoretical calculations, but there has never been a direct comparison between data and calculations of jet substructure observables that are accurate beyond leading-logarithm approximation. Such observables are significant not only for probing the collinear regime of QCD that is largely unexplored at a hadron collider, but also for improving the understanding of jet substructure properties that are used in many studies at the Large Hadron Collider. This Letter documents a measurement of the first jet substructure quantity at a hadron collider to be calculated at next-to-next-to-leading-logarithm accuracy. The normalized, differential cross section is measured as a function of log_{10}ρ^{2}, where ρ is the ratio of the soft-drop mass to the ungroomed jet transverse momentum. This quantity is measured in dijet events from 32.9  fb^{-1} of sqrt[s]=13  TeV proton-proton collisions recorded by the ATLAS detector. The data are unfolded to correct for detector effects and compared to precise QCD calculations and leading-logarithm particle-level Monte Carlo simulations.

Search for Low-Mass Dijet Resonances Using Trigger-Level Jets with the ATLAS Detector in pp Collisions at sqrt[s]=13 TeV

Searches for dijet resonances with sub-TeV masses using the ATLAS detector at the Large Hadron Collider can be statistically limited by the bandwidth available to inclusive single-jet triggers, whose data-collection rates at low transverse momentum are much lower than the rate from standard model multijet production. This Letter describes a new search for dijet resonances where this limitation is overcome by recording only the event information calculated by the jet trigger algorithms, thereby allowing much higher event rates with reduced storage needs. The search targets low-mass dijet resonances in the range 450-1800 GeV. The analyzed data set has an integrated luminosity of up to 29.3  fb^{-1} and was recorded at a center-of-mass energy of 13 TeV. No excesses are found; limits are set on Gaussian-shaped contributions to the dijet mass distribution from new particles and on a model of dark-matter particles with axial-vector couplings to quarks.

Search for the Decay of the Higgs Boson to Charm Quarks with the ATLAS Experiment

A direct search for the standard model Higgs boson decaying to a pair of charm quarks is presented. Associated production of the Higgs and Z bosons, in the decay mode ZH→ℓ^{+}ℓ^{-}cc[over ¯] is studied. A data set with an integrated luminosity of 36.1  fb^{-1} of pp collisions at sqrt[s]=13TeV recorded by the ATLAS experiment at the LHC is used. The H→cc[over ¯] signature is identified using charm-tagging algorithms. The observed (expected) upper limit on σ(pp→ZH)×B(H→cc[over ¯]) is 2.7 (3.9_{-1.1}^{+2.1}) pb at the 95% confidence level for a Higgs boson mass of 125 GeV, while the standard model value is 26 fb.

Search for a Structure in the B_{s}^{0}π^{±} Invariant Mass Spectrum with the ATLAS Experiment

A search for the narrow structure, X(5568), reported by the D0 Collaboration in the decay sequence X→B_{s}^{0}π^{±}, B_{s}^{0}→J/ψϕ, is presented. The analysis is based on a data sample recorded with the ATLAS detector at the LHC corresponding to 4.9  fb^{-1} of pp collisions at 7 TeV and 19.5  fb^{-1} at 8 TeV. No significant signal was found. Upper limits on the number of signal events, with properties corresponding to those reported by D0, and on the X production rate relative to B_{s}^{0} mesons, ρ_{X}, were determined at 95% confidence level. The results are N(X)<382 and ρ_{X}<0.015 for B_{s}^{0} mesons with transverse momenta above 10 GeV, and N(X)<356 and ρ_{X}<0.016 for transverse momenta above 15 GeV. Limits are also set for potential B_{s}^{0}π^{±} resonances in the mass range 5550 to 5700 MeV.

Search for High-Mass Resonances Decaying to τν in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

A search for high-mass resonances decaying to τν using proton-proton collisions at sqrt[s]=13  TeV produced by the Large Hadron Collider is presented. Only τ-lepton decays with hadrons in the final state are considered. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 36.1  fb^{-1}. No statistically significant excess above the standard model expectation is observed; model-independent upper limits are set on the visible τν production cross section. Heavy W^{'} bosons with masses less than 3.7 TeV in the sequential standard model and masses less than 2.2-3.8 TeV depending on the coupling in the nonuniversal G(221) model are excluded at the 95% credibility level.

Search for Heavy Higgs Bosons A/H Decaying to a Top Quark Pair in pp Collisions at sqrt[s]=8 TeV with the ATLAS Detector

A search for heavy pseudoscalar (A) and scalar (H) Higgs bosons decaying into a top quark pair (tt[over ¯]) has been performed with 20.3  fb^{-1} of proton-proton collision data collected by the ATLAS experiment at the Large Hadron Collider at a center-of-mass energy sqrt[s]=8  TeV. Interference effects between the signal process and standard model tt[over ¯] production, which are expected to distort the signal shape from a single peak to a peak-dip structure, are taken into account. No significant deviation from the standard model prediction is observed in the tt[over ¯] invariant mass spectrum in final states with an electron or muon, large missing transverse momentum, and at least four jets. The results are interpreted within the context of a type-II two-Higgs-doublet model. Exclusion limits on the signal strength are derived as a function of the mass m_{A/H} and the ratio of the vacuum expectation values of the two Higgs fields, tanβ, for m_{A/H}>500  GeV.

Search for Dark Matter Produced in Association with a Higgs Boson Decaying to bb[over ¯] Using 36 fb^{-1} of pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

Several extensions of the standard model predict associated production of dark-matter particles with a Higgs boson. Such processes are searched for in final states with missing transverse momentum and a Higgs boson decaying to a bb[over ¯] pair with the ATLAS detector using 36.1  fb^{-1} of pp collisions at a center-of-mass energy of 13 TeV at the LHC. The observed data are in agreement with the standard model predictions and limits are placed on the associated production of dark-matter particles and a Higgs boson.

Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana

The Group VII Ethylene Responsive Factors (ERFs-VII) RAP2.2 and RAP2.12 have been mainly characterized with regard to their contribution as activators of fermentation in plants. However, transcriptional changes measured in conditions that stabilize these transcription factors exceed the mere activation of this biochemical pathway, implying additional roles performed by the ERF-VIIs in other processes. We evaluated gene expression in transgenic Arabidopsis lines expressing a stabilized form of RAP2.12, or hampered in ERF-VII activity, and identified genes affected by this transcriptional regulator and its homologs, including some involved in oxidative stress response, which are not universally induced under anaerobic conditions. The contribution of the ERF-VIIs in regulating this set of genes in response to chemically induced or submergence-stimulated mitochondria malfunctioning was found to depend on the plant developmental stage. A similar age-dependent mechanism also restrained ERF-VII activity upon the core-hypoxic genes, independently of the N-end rule pathway, which is accounted for the control of the anaerobic response. To conclude, this study shed new light on a dual role of ERF-VII proteins under submergence: as positive regulators of the hypoxic response and as repressors of oxidative-stress related genes, depending on the developmental stage at which plants are challenged by stress conditions.

Search for the Dimuon Decay of the Higgs Boson in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

A search for the dimuon decay of the Higgs boson was performed using data corresponding to an integrated luminosity of 36.1  fb^{-1} collected with the ATLAS detector in pp collisions at sqrt[s]=13  TeV at the Large Hadron Collider. No significant excess is observed above the expected background. The observed (expected) upper limit on the cross section times branching ratio is 3.0 (3.1) times the Standard Model prediction at the 95% confidence level for a Higgs boson mass of 125 GeV. When combined with the pp collision data at sqrt[s]=7  TeV and sqrt[s]=8  TeV, the observed (expected) upper limit is 2.8 (2.9) times the Standard Model prediction.

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.

Abstract LB-289: Computational detection of oncogene-centric pathway members

Elucidation of the full complement of members of oncogenic signaling pathways is critical for understanding dysregulated function in cancers. Our knowledge of experimentally verified human gene-regulatory networks and protein-protein interactions remains incomplete, thus limiting their use for predicting novel members of these critical pathways. We present a method that uses a machine learning approach to predict novel members of these aberrantly activated or inactivated pathways. We integrate predictions of protein-protein interactions, gene regulatory networks, post-translational modifications and co-segregation of mutational status and protein activity. This approach produces novel predictions for these pathways. For the Kras and EGFR pathway, these predictions are highly enriched for genes known to by synthetic lethal for these two pathways. Knockdown of top candidates derived from this approach decreased growth in a Kras-activated context, indicating their importance in Kras regulated pathways.

Citation Format: Joshua Broyde, David Simpson, Diana Murray, Alexander Lachmann, Federico M. Giorgi, Barry Honig, Alejandro E. Sweet-Cordero, Andrea Califano. Computational detection of oncogene-centric pathway members [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-289. doi:10.1158/1538-7445.AM2017-LB-289

Search for triboson [Formula: see text] production in pp collisions at [Formula: see text] [Formula: see text] with the ATLAS detector

This paper reports a search for triboson [Formula: see text] production in two decay channels ([Formula: see text] and [Formula: see text] with [Formula: see text]) in proton-proton collision data corresponding to an integrated luminosity of 20.3 [Formula: see text] at a centre-of-mass energy of 8 [Formula: see text] with the ATLAS detector at the Large Hadron Collider. Events with exactly three charged leptons, or two leptons with the same electric charge in association with two jets, are selected. The total number of events observed in data is consistent with the Standard Model (SM) predictions. The observed 95% confidence level upper limit on the SM [Formula: see text] production cross section is found to be 730 fb with an expected limit of 560 fb in the absence of SM [Formula: see text] production. Limits are also set on WWWW anomalous quartic gauge couplings.

Measurement of the Inelastic Proton-Proton Cross Section at sqrt[s]=13 TeV with the ATLAS Detector at the LHC

This Letter presents a measurement of the inelastic proton-proton cross section using 60  μb^{-1} of pp collisions at a center-of-mass energy sqrt[s] of 13 TeV with the ATLAS detector at the LHC. Inelastic interactions are selected using rings of plastic scintillators in the forward region (2.07<|η|<3.86) of the detector. A cross section of 68.1±1.4  mb is measured in the fiducial region ξ=M_{X}^{2}/s>10^{-6}, where M_{X} is the larger invariant mass of the two hadronic systems separated by the largest rapidity gap in the event. In this ξ range the scintillators are highly efficient. For diffractive events this corresponds to cases where at least one proton dissociates to a system with M_{X}>13  GeV. The measured cross section is compared with a range of theoretical predictions. When extrapolated to the full phase space, a cross section of 78.1±2.9  mb is measured, consistent with the inelastic cross section increasing with center-of-mass energy.

Correction: Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information

[This corrects the article DOI: 10.1371/journal.pone.0109569.].

Search for Higgs and Z Boson Decays to ϕγ with the ATLAS Detector

A search for the decays of the Higgs and Z bosons to a ϕ meson and a photon is performed with a pp collision data sample corresponding to an integrated luminosity of 2.7  fb^{-1} collected at sqrt[s]=13  TeV with the ATLAS detector at the LHC. No significant excess of events is observed above the background, and 95% confidence level upper limits on the branching fractions of the Higgs and Z boson decays to ϕγ of 1.4×10^{-3} and 8.3×10^{-6}, respectively, are obtained.

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

Identifying the multiple dysregulated oncoproteins that contribute to tumorigenesis in a given patient is crucial for developing personalized treatment plans. However, accurate inference of aberrant protein activity in biological samples is still challenging as genetic alterations are only partially predictive and direct measurements of protein activity are generally not feasible. To address this problem we introduce and experimentally validate a new algorithm, VIPER (Virtual Inference of Protein-activity by Enriched Regulon analysis), for the accurate assessment of protein activity from gene expression data. We use VIPER to evaluate the functional relevance of genetic alterations in regulatory proteins across all TCGA samples. In addition to accurately inferring aberrant protein activity induced by established mutations, we also identify a significant fraction of tumors with aberrant activity of druggable oncoproteins—despite a lack of mutations, and vice-versa. In vitro assays confirmed that VIPER-inferred protein activity outperforms mutational analysis in predicting sensitivity to targeted inhibitors.

Observation of Long-Range Elliptic Azimuthal Anisotropies in sqrt[s]=13 and 2.76 TeV pp Collisions with the ATLAS Detector

ATLAS has measured two-particle correlations as a function of the relative azimuthal angle, Δϕ, and pseudorapidity, Δη, in sqrt[s]=13 and 2.76 TeV pp collisions at the LHC using charged particles measured in the pseudorapidity interval |η|<2.5. The correlation functions evaluated in different intervals of measured charged-particle multiplicity show a multiplicity-dependent enhancement at Δϕ∼0 that extends over a wide range of Δη, which has been referred to as the "ridge." Per-trigger-particle yields, Y(Δϕ), are measured over 2<|Δη|<5. For both collision energies, the Y(Δϕ) distribution in all multiplicity intervals is found to be consistent with a linear combination of the per-trigger-particle yields measured in collisions with less than 20 reconstructed tracks, and a constant combinatoric contribution modulated by cos(2Δϕ). The fitted Fourier coefficient, v_{2,2}, exhibits factorization, suggesting that the ridge results from per-event cos(2ϕ) modulation of the single-particle distribution with Fourier coefficients v_{2}. The v_{2} values are presented as a function of multiplicity and transverse momentum. They are found to be approximately constant as a function of multiplicity and to have a p_{T} dependence similar to that measured in p+Pb and Pb+Pb collisions. The v_{2} values in the 13 and 2.76 TeV data are consistent within uncertainties. These results suggest that the ridge in pp collisions arises from the same or similar underlying physics as observed in p+Pb collisions, and that the dynamics responsible for the ridge has no strong sqrt[s] dependence.

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

Summary: The accurate reconstruction of gene regulatory networks from large scale molecular profile datasets represents one of the grand challenges of Systems Biology. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) represents one of the most effective tools to accomplish this goal. However, the initial Fixed Bandwidth (FB) implementation is both inefficient and unable to deal with sample sets providing largely uneven coverage of the probability density space. Here, we present a completely new implementation of the algorithm, based on an Adaptive Partitioning strategy (AP) for estimating the Mutual Information. The new AP implementation (ARACNe-AP) achieves a dramatic improvement in computational performance (200× on average) over the previous methodology, while preserving the Mutual Information estimator and the Network inference accuracy of the original algorithm. Given that the previous version of ARACNe is extremely demanding, the new version of the algorithm will allow even researchers with modest computational resources to build complex regulatory networks from hundreds of gene expression profiles.

Availability and Implementation: A JAVA cross-platform command line executable of ARACNe, together with all source code and a detailed usage guide are freely available on Sourceforge (http://sourceforge.net/projects/aracne-ap). JAVA version 8 or higher is required.

Contact:califano@c2b2.columbia.edu

Supplementary information:Supplementary data are available at Bioinformatics online.

Measurement of the ZZ Production Cross Section in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

The ZZ production cross section in proton-proton collisions at 13 TeV center-of-mass energy is measured using 3.2  fb^{-1} of data recorded with the ATLAS detector at the Large Hadron Collider. The considered Z boson candidates decay to an electron or muon pair of mass 66-116 GeV. The cross section is measured in a fiducial phase space reflecting the detector acceptance. It is also extrapolated to a total phase space for Z bosons in the same mass range and of all decay modes, giving 16.7_{-2.0}^{+2.2}(stat)+0.9/-0.7(syst)+1.0/-0.7(lumi)  pb. The results agree with standard model predictions.

Detection and removal of spatial bias in multiwell assays

MOTIVATION

Multiplex readout assays are now increasingly being performed using microfluidic automation in multiwell format. For instance, the Library of Integrated Network-based Cellular Signatures (LINCS) has produced gene expression measurements for tens of thousands of distinct cell perturbations using a 384-well plate format. This dataset is by far the largest 384-well gene expression measurement assay ever performed. We investigated the gene expression profiles of a million samples from the LINCS dataset and found that the vast majority (96%) of the tested plates were affected by a significant 2D spatial bias.

RESULTS

Using a novel algorithm combining spatial autocorrelation detection and principal component analysis, we could remove most of the spatial bias from the LINCS dataset and show in parallel a dramatic improvement of similarity between biological replicates assayed in different plates. The proposed methodology is fully general and can be applied to any highly multiplexed assay performed in multiwell format.

CONTACT

ac2248@columbia.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Determination of the Ratio of b-Quark Fragmentation Fractions f(s)/f(d) in pp Collisions at √s=7 TeV with the ATLAS Detector

With an integrated luminosity of 2.47  fb(-1) recorded by the ATLAS experiment at the LHC, the exclusive decays B(s)(0)→J/ψϕ and B(d)(0)→J/ψK(*0) of B mesons produced in pp collisions at √s=7  TeV are used to determine the ratio of fragmentation fractions f(s)/f(d). From the observed B(s)(0)→J/ψϕ and B(d)(0)→J/ψK(*0) yields, the quantity (f(s)/f(d))[B(B(s)(0)→J/ψϕ)/B(B(d)(0)→J/ψK(*0))] is measured to be 0.199±0.004(stat)±0.008(syst). Using a recent theory prediction for [B(B(s)(0)→J/ψϕ)/B(B(d)(0)→J/ψK(*0))] yields (f(s)/f(d))=0.240±0.004(stat)±0.010(syst)±0.017(th). This result is based on a new approach that provides a significant improvement of the world average.

Abstract PR13: Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors

Activated KRAS interacts directly and indirectly with numerous downstream effector pathways that are still elusive or poorly characterized. Furthermore, it has become clear over the past few years that the KRAS regulatory gene network (interactome) is highly cell-context dependent and thus tumor specific. We sought to computationally elucidate novel KRAS effectors, modulators, and interactors in Lung Adenocarcinomas (LUAD) and Colon Adenocarcinomas (COAD) by integrating computational and biochemical reverse engineering methods. Specifically, results from ARACNe and MINDy based analysis of KRAS networks were combined with Protein-protein interaction (PPI) predictions based on the PrePPI algorithm. These algorithms detect, respectively, transcriptional, post-translational, and protein-protein interactions respectively. The MARINa/VIPER algorithm was used to analyze the networks resulting from these analyses to identify key modulators and effectors of KRAS activity, including modulators harboring genetic alterations that phenocopy aberrant KRAS activity. In addition, we collaborated with the Jackson (Stanford) and Vidal (Harvard) labs to include high-throughput tandem affinity mass spectrometry data and yeast 2 hybrid screens in these analyses. Validation of computationally inferred effectors, using pooled shRNA silencing assays in primary lung cancer cells isolated from a KrasLSL/p53f/f mouse model of LUAD validated novel genes as likely KRASmut effectors and putative synthetic lethal genes. At least two hairpins against RNF43, E4F1, HMCN1, MYO9A, RHOT2, SETD1B and MAP3K2 scored in this assay. These results suggest that KRAS network analyses using computational methods can identify novel members of the KRAS interactome.

Citation Format: Joshua Broyde, David Simpson, David A. Wah, Federico M. Giorgi, Donald Petrey, Mariano J. Alvarez, Antonina Silkov, Alexander Lachmann, David E. Hill, Marc Vidal, Peter Jackson, Barry Honig, Alejandro Sweet-Cordero, Andrea Califano. Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR13.

Search for Dark Matter in Events with Missing Transverse Momentum and a Higgs Boson Decaying to Two Photons in pp Collisions at sqrt[s]=8 TeV with the ATLAS Detector

Results of a search for new phenomena in events with large missing transverse momentum and a Higgs boson decaying to two photons are reported. Data from proton-proton collisions at a center-of-mass energy of 8 TeV and corresponding to an integrated luminosity of 20.3 fb^{-1} have been collected with the ATLAS detector at the LHC. The observed data are well described by the expected standard model backgrounds. Upper limits on the cross section of events with large missing transverse momentum and a Higgs boson candidate are also placed. Exclusion limits are presented for models of physics beyond the standard model featuring dark-matter candidates.

Measurements of the Total and Differential Higgs Boson Production Cross Sections Combining the H→γγ and H→ZZ^{*}→4ℓ Decay Channels at sqrt[s]=8 TeV with the ATLAS Detector

Measurements of the total and differential cross sections of Higgs boson production are performed using 20.3  fb^{-1} of pp collisions produced by the Large Hadron Collider at a center-of-mass energy of sqrt[s]=8  TeV and recorded by the ATLAS detector. Cross sections are obtained from measured H→γγ and H→ZZ^{*}→4ℓ event yields, which are combined accounting for detector efficiencies, fiducial acceptances, and branching fractions. Differential cross sections are reported as a function of Higgs boson transverse momentum, Higgs boson rapidity, number of jets in the event, and transverse momentum of the leading jet. The total production cross section is determined to be σ_{pp→H}=33.0±5.3 (stat)±1.6 (syst)  pb. The measurements are compared to state-of-the-art predictions.

Search for a Heavy Neutral Particle Decaying to eμ, eτ, or μτ in pp Collisions at sqrt[s]=8 TeV with the ATLAS Detector

This Letter presents a search for a heavy neutral particle decaying into an opposite-sign different-flavor dilepton pair, e^{±}μ^{∓}, e^{±}τ^{∓}, or μ^{±}τ^{∓} using 20.3  fb^{-1} of pp collision data at sqrt[s]=8  TeV collected by the ATLAS detector at the LHC. The numbers of observed candidate events are compatible with the standard model expectations. Limits are set on the cross section of new phenomena in two scenarios: the production of ν[over ˜]_{τ} in R-parity-violating supersymmetric models and the production of a lepton-flavor-violating Z^{'} vector boson.

Evidence of Wγγ Production in pp Collisions at sqrt[s]=8 TeV and Limits on Anomalous Quartic Gauge Couplings with the ATLAS Detector

This Letter reports evidence of triple gauge boson production pp→W(ℓν)γγ+X, which is accessible for the first time with the 8 TeV LHC data set. The fiducial cross section for this process is measured in a data sample corresponding to an integrated luminosity of 20.3  fb^{-1}, collected by the ATLAS detector in 2012. Events are selected using the W boson decay to eν or μν as well as requiring two isolated photons. The measured cross section is used to set limits on anomalous quartic gauge couplings in the high diphoton mass region.

Search for a new resonance decaying to a W or Z boson and a Higgs boson in the [Formula: see text] final states with the ATLAS detector

A search for a new resonance decaying to a W or Z boson and a Higgs boson in the [Formula: see text] final states is performed using 20.3 fb[Formula: see text] of pp collision data recorded at [Formula: see text] 8 TeV with the ATLAS detector at the Large Hadron Collider. The search is conducted by examining the WH / ZH invariant mass distribution for a localized excess. No significant deviation from the Standard Model background prediction is observed. The results are interpreted in terms of constraints on the Minimal Walking Technicolor model and on a simplified approach based on a phenomenological Lagrangian of Heavy Vector Triplets.

Search for Scalar Charm Quark Pair Production in pp Collisions at sqrt[s]=8 TeV with the ATLAS Detector

The results of a dedicated search for pair production of scalar partners of charm quarks are reported. The search is based on an integrated luminosity of 20.3  fb^{-1} of pp collisions at sqrt[s]=8  TeV recorded with the ATLAS detector at the LHC. The search is performed using events with large missing transverse momentum and at least two jets, where the two leading jets are each tagged as originating from c quarks. Events containing isolated electrons or muons are vetoed. In an R-parity-conserving minimal supersymmetric scenario in which a single scalar-charm state is kinematically accessible, and where it decays exclusively into a charm quark and a neutralino, 95% confidence-level upper limits are obtained in the scalar-charm-neutralino mass plane such that, for neutralino masses below 200 GeV, scalar-charm masses up to 490 GeV are excluded.

Measurement of spin correlation in top-antitop quark events and search for top squark pair production in pp collisions at √s=8 TeV using the ATLAS detector

A measurement of spin correlation in tt[over ¯] production is presented using data collected with the ATLAS detector at the Large Hadron Collider in proton-proton collisions at a center-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 20.3  fb^{-1}. The correlation between the top and antitop quark spins is extracted from dilepton tt[over ¯] events by using the difference in the azimuthal angle between the two charged leptons in the laboratory frame. In the helicity basis the measured degree of correlation corresponds to A_{helicity}=0.38±0.04, in agreement with the standard model prediction. A search is performed for pair production of top squarks with masses close to the top quark mass decaying to predominantly right-handed top quarks and a light neutralino, the lightest supersymmetric particle. Top squarks with masses between the top quark mass and 191 GeV are excluded at the 95% confidence level.

Search for Higgs and Z Boson Decays to J/ψγ and ϒ(nS)γ with the ATLAS Detector

A search for the decays of the Higgs and Z bosons to J/ψγ and ϒ(nS)γ (n=1,2,3) is performed with pp collision data samples corresponding to integrated luminosities of up to 20.3  fb^{-1} collected at sqrt[s]=8  TeV with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above expected backgrounds and 95% C.L. upper limits are placed on the branching fractions. In the J/ψγ final state the limits are 1.5×10^{-3} and 2.6×10^{-6} for the Higgs and Z boson decays, respectively, while in the ϒ(1S,2S,3S)γ final states the limits are (1.3,1.9,1.3)×10^{-3} and (3.4,6.5,5.4)×10^{-6}, respectively.

Search for Higgs boson pair production in the γγbb[over ¯] final state using pp collision data at sqrt[s]=8 TeV from the ATLAS detector

Searches are performed for resonant and nonresonant Higgs boson pair production in the γγbb[over ¯] final state using 20  fb^{-1} of proton-proton collisions at a center-of-mass energy of 8 TeV recorded with the ATLAS detector at the CERN Large Hadron Collider. A 95% confidence level upper limit on the cross section times branching ratio of nonresonant production is set at 2.2 pb, while the expected limit is 1.0 pb. The difference derives from a modest excess of events, corresponding to 2.4 standard deviations from the background-only hypothesis. The limit observed in the search for a narrow X→hh resonance ranges between 0.7 and 3.5 pb as a function of the resonance mass.

Measurements of the Nuclear Modification Factor for Jets in Pb+Pb Collisions at √(s)NN]=2.76 TeV with the ATLAS detector

Measurements of inclusive jet production are performed in pp and Pb+Pb collisions at √(s)NN=2.76  TeV with the ATLAS detector at the LHC, corresponding to integrated luminosities of 4.0 and 0.14  nb(-1), respectively. The jets are identified with the anti-k(t) algorithm with R=0.4, and the spectra are measured over the kinematic range of jet transverse momentum 32<p(T)<500  GeV and absolute rapidity |y|<2.1 and as a function of collision centrality. The nuclear modification factor R(AA) is evaluated, and jets are found to be suppressed by approximately a factor of 2 in central collisions compared to pp collisions. The R(AA) shows a slight increase with p(T) and no significant variation with rapidity.

Abstract B34: A systems biology approach to elucidate novel drug targets in KRAS mutant tumors

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR09) of the Conference Proceedings.

Citation Format: David A. Wah, Federico M. Giorgi, Donald Petrey, Mariano J. Alvarez, Tonya Silkov, Josh Broyde, Gabrielle E. Rieckhof, Barry Honig, Andrea Califano. A systems biology approach to elucidate novel drug targets in KRAS mutant tumors. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr B34. doi: 10.1158/1557-3125.RASONC14-B34

Abstract PR09: A systems biology approach to elucidate novel drug targets in KRAS mutant tumors

Mutations of RAS GTPase family oncogenes affect more than 20% of human cancers. Of the three major RAS isoforms (HRAS, KRAS, and NRAS), KRAS is the most frequently mutated, affecting 57% of pancreatic adenocarcinomas, 33% of colorectal cancers, 17% of lung adenocarcinomas, and many other tumor subtypes. Most RAS mutations abrogate its GTPase activity, thus activating aberrant downstream signals associated with worst prognosis and tumor resistance to both chemotoxic and targeted therapy. Therapies against RAS have failed, in part, because of our limited understanding of RAS-mediated signal transduction pathways. Therefore, we hypothesize that the systematic and complete dissection of RAS relevant regulatory interactions can help elucidate druggable mechanisms to abrogate its aberrant activity or elicit synthetic lethality in RAS mutated tumors. Here, we have employed computational systems biology approaches to begin to dissect KRAS regulatory pathways. Specifically, we reverse-engineered a cell context specific KRAS regulatory network from TCGA transcriptome-wide expression data. The KRAS regulatory network was used to predict KRAS activation levels across all colon and lung adenocarcinoma samples available in TCGA in order to generate a patient-by-patient estimate of KRAS activity. Genome-wide somatic mutations and copy-number variations were then tested for significant association with the predicted KRAS activity. Consistent with known KRAS biology, samples harboring KRAS or BRAF activating mutations were significantly associated with increased KRAS activity. However, we also observed that mutations in the DEAD box helicase DDX6 and the Glycolipid Transfer-domain protein GLTPD2 to be significantly associated, suggesting that these proteins may be involved in KRAS pathways. We dissected the effects of KRAS mutations on the activity of all transcription factors, identifying those more closely activated or repressed in a KRAS-specific context. KRAS is activated by its own mutations, along with known KRAS interactors, such as SOS1 and RAPGEF6. Interestingly, we found that these activating KRAS mutations significantly correlate with increased activities of the Rho-associated kinases ROCK1 and ROCK2. Moreover, the protein-protein interaction database PrePPI predicts KRAS to homodimerize, and surprisingly, to interact with ROCK1/2 through a new PPI interface. We are currently confirming these results through biochemical and biophysical analyses.

This abstract is also presented as Poster B34.

Citation Format: David A. Wah, Federico M. Giorgi, Donald Petrey, Mariano J. Alvarez, Tonya Silkov, Josh Broyde, Gabrielle E. Rieckhof, Barry Honig, Andrea Califano. A systems biology approach to elucidate novel drug targets in KRAS mutant tumors. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr PR09. doi: 10.1158/1557-3125.RASONC14-PR09

Observation of an excited Bc(±) meson state with the ATLAS detector

A search for excited states of the Bc(±) meson is performed using 4.9  fb(-1) of 7 TeV and 19.2  fb(-1) of 8 TeV pp collision data collected by the ATLAS experiment at the LHC. A new state is observed through its hadronic transition to the ground state, with the latter detected in the decay Bc(±)→J/ψπ(±). The state appears in the m(Bc(±)π(+)π(-))-m(Bc(±))-2m(π(±)) mass difference distribution with a significance of 5.2 standard deviations. The mass of the observed state is 6842±4±5  MeV, where the first error is statistical and the second is systematic. The mass and decay of this state are consistent with expectations for the second S-wave state of the Bc(±) meson, Bc(±)(2S).

Measurement of the [Formula: see text] production cross-section using [Formula: see text] events with [Formula: see text]-tagged jets in [Formula: see text] collisions at [Formula: see text] and 8 TeV with the ATLAS detector

The inclusive top quark pair ([Formula: see text]) production cross-section [Formula: see text] has been measured in proton-proton collisions at [Formula: see text] and [Formula: see text] with the ATLAS experiment at the LHC, using [Formula: see text] events with an opposite-charge [Formula: see text] pair in the final state. The measurement was performed with the 2011 7 TeV dataset corresponding to an integrated luminosity of 4.6 [Formula: see text] and the 2012 8 TeV dataset of 20.3 [Formula: see text]. The numbers of events with exactly one and exactly two [Formula: see text]-tagged jets were counted and used to simultaneously determine [Formula: see text] and the efficiency to reconstruct and [Formula: see text]-tag a jet from a top quark decay, thereby minimising the associated systematic uncertainties. The cross-section was measured to be: [Formula: see text]where the four uncertainties arise from data statistics, experimental and theoretical systematic effects, knowledge of the integrated luminosity and of the LHC beam energy. The results are consistent with recent theoretical QCD calculations at next-to-next-to-leading order. Fiducial measurements corresponding to the experimental acceptance of the leptons are also reported, together with the ratio of cross-sections measured at the two centre-of-mass energies. The inclusive cross-section results were used to determine the top quark pole mass via the dependence of the theoretically predicted cross-section on [Formula: see text] giving a result of [Formula: see text][Formula: see text] GeV. By looking for an excess of [Formula: see text] production with respect to the QCD prediction, the results were also used to place limits on the pair-production of supersymmetric top squarks [Formula: see text] with masses close to the top quark mass, decaying via [Formula: see text] to predominantly right-handed top quarks and a light neutralino [Formula: see text], the lightest supersymmetric particle. Top squarks with masses between the top quark mass and 177 GeV are excluded at the 95 % confidence level.

Measurement of the [Formula: see text] production cross-section using [Formula: see text] events with [Formula: see text]-tagged jets in [Formula: see text] collisions at [Formula: see text] and 8 TeV with the ATLAS detector

The inclusive top quark pair ([Formula: see text]) production cross-section [Formula: see text] has been measured in proton-proton collisions at [Formula: see text] and [Formula: see text] with the ATLAS experiment at the LHC, using [Formula: see text] events with an opposite-charge [Formula: see text] pair in the final state. The measurement was performed with the 2011 7 TeV dataset corresponding to an integrated luminosity of 4.6 [Formula: see text] and the 2012 8 TeV dataset of 20.3 [Formula: see text]. The numbers of events with exactly one and exactly two [Formula: see text]-tagged jets were counted and used to simultaneously determine [Formula: see text] and the efficiency to reconstruct and [Formula: see text]-tag a jet from a top quark decay, thereby minimising the associated systematic uncertainties. The cross-section was measured to be: [Formula: see text]where the four uncertainties arise from data statistics, experimental and theoretical systematic effects, knowledge of the integrated luminosity and of the LHC beam energy. The results are consistent with recent theoretical QCD calculations at next-to-next-to-leading order. Fiducial measurements corresponding to the experimental acceptance of the leptons are also reported, together with the ratio of cross-sections measured at the two centre-of-mass energies. The inclusive cross-section results were used to determine the top quark pole mass via the dependence of the theoretically predicted cross-section on [Formula: see text] giving a result of [Formula: see text][Formula: see text] GeV. By looking for an excess of [Formula: see text] production with respect to the QCD prediction, the results were also used to place limits on the pair-production of supersymmetric top squarks [Formula: see text] with masses close to the top quark mass, decaying via [Formula: see text] to predominantly right-handed top quarks and a light neutralino [Formula: see text], the lightest supersymmetric particle. Top squarks with masses between the top quark mass and 177 GeV are excluded at the 95 % confidence level.

Search for scalar diphoton resonances in the mass range 65-600 GeV with the ATLAS detector in pp collision data at √s=8 TeV

A search for scalar particles decaying via narrow resonances into two photons in the mass range 65-600 GeV is performed using 20.3  fb(-1) of √s 8 TeV pp collision data collected with the ATLAS detector at the Large Hadron Collider. The recently discovered Higgs boson is treated as a background. No significant evidence for an additional signal is observed. The results are presented as limits at the 95% confidence level on the production cross section of a scalar boson times branching ratio into two photons, in a fiducial volume where the reconstruction efficiency is approximately independent of the event topology. The upper limits set extend over a considerably wider mass range than previous searches.

Inferring protein modulation from gene expression data using conditional mutual information

Systematic, high-throughput dissection of causal post-translational regulatory dependencies, on a genome wide basis, is still one of the great challenges of biology. Due to its complexity, however, only a handful of computational algorithms have been developed for this task. Here we present CINDy (Conditional Inference of Network Dynamics), a novel algorithm for the genome-wide, context specific inference of regulatory dependencies between signaling protein and transcription factor activity, from gene expression data. The algorithm uses a novel adaptive partitioning methodology to accurately estimate the full Condition Mutual Information (CMI) between a transcription factor and its targets, given the expression of a signaling protein. We show that CMI analysis is optimally suited to dissecting post-translational dependencies. Indeed, when tested against a gold standard dataset of experimentally validated protein-protein interactions in signal transduction networks, CINDy significantly outperforms previous methods, both in terms of sensitivity and precision.

Evidence for electroweak production of W±W±jj in pp collisions at sqrt[s] = 8 TeV with the ATLAS detector

This Letter presents the first study of W(±)W(±)jj, same-electric-charge diboson production in association with two jets, using 20.3 fb(-1) of proton-proton collision data at sqrt[s] = 8  TeV recorded by the ATLAS detector at the Large Hadron Collider. Events with two reconstructed same-charge leptons (e(±)e(±), e(±)μ(±), and μ(±)μ(±)) and two or more jets are analyzed. Production cross sections are measured in two fiducial regions, with different sensitivities to the electroweak and strong production mechanisms. First evidence for W(±)W(±)jj production and electroweak-only W(±)W(±)jj production is observed with a significance of 4.5 and 3.6 standard deviations, respectively. The measured production cross sections are in agreement with standard model predictions. Limits at 95% confidence level are set on anomalous quartic gauge couplings.

CEBPA-regulated lncRNAs, new players in the study of acute myeloid leukemia

CCAAT/enhancer-binding protein-α (CEBPA) is a critical regulator of myeloid differentiation. Disruption of CEBPA function contributes to the development of acute myeloid leukemia (AML). CEBPA regulates a large number of protein coding genes of which several were shown to contribute to CEBPA function. In this study, we expand the analysis of CEBPA transcriptional targets to the newly identified class of long non-coding RNAs. We show that lncRNAs are a main component of the transcriptional program driven by C/EBPα and that many of these are also induced during granulocytic differentiation of AML cell lines supporting their relevance in proliferation arrest and differentiation.

Measurements of four-lepton production at the Z resonance in pp collisions at sqrt[s] = 7 and 8 TeV with ATLAS

Measurements of four-lepton (4ℓ, ℓ=e,μ) production cross sections at the Z resonance in pp collisions at the LHC with the ATLAS detector are presented. For dilepton and four-lepton invariant mass regions m(ℓ+ℓ(-)) > 5 GeV and 80<m(4ℓ) < 100 GeV, the measured cross sections are 76 ± 18(stat) ± 4(syst) ± 1.4(lumi) fb and 107 ± 9(stat) ± 4(syst) ± 3.0(lumi) fb at sqrt[s] = 7 and 8 TeV, respectively. By subtracting the nonresonant 4ℓ production contributions and normalizing with Z → μ(+)μ(-) events, the branching fraction for the Z boson decay to 4ℓ is determined to be (3.20 ± 0.25(stat) ± 0.13(syst)) × 10(-6), consistent with the standard model prediction.

Search for quantum black hole production in high-invariant-mass lepton+jet final states using pp collisions at √s=8 TeV and the ATLAS detector

This Letter presents a search for quantum black-hole production using 20.3 fb-1 of data collected with the ATLAS detector in pp collisions at the LHC at √s = 8 TeV. The quantum black holes are assumed to decay into a final state characterized by a lepton (electron or muon) and a jet. In either channel, no event with a lepton-jet invariant mass of 3.5 TeV or more is observed, consistent with the expected background. Limits are set on the product of cross sections and branching fractions for the lepton+jet final states of quantum black holes produced in a search region for invariant masses above 1 TeV. The combined 95% confidence level upper limit on this product for quantum black holes with threshold mass above 3.5 TeV is 0.18 fb. This limit constrains the threshold quantum black-hole mass to be above 5.3 TeV in the model considered.

Search for dark matter in events with a hadronically decaying W or Z boson and missing transverse momentum in pp collisions at √s=8 TeV with the ATLAS detector

A search is presented for dark matter pair production in association with a W or Z boson in pp collisions representing 20.3  fb(-1) of integrated luminosity at √s=8  TeV using data recorded with the ATLAS detector at the Large Hadron Collider. Events with a hadronic jet with the jet mass consistent with a W or Z boson, and with large missing transverse momentum are analyzed. The data are consistent with the standard model expectations. Limits are set on the mass scale in effective field theories that describe the interaction of dark matter and standard model particles, and on the cross section of Higgs production and decay to invisible particles. In addition, cross section limits on the anomalous production of W or Z bosons with large missing transverse momentum are set in two fiducial regions.