Designing and recasting LHC analyses with MadAnalysis 5

We present an extension of the expert mode of the MadAnalysis 5 program dedicated to the design or reinterpretation of high-energy physics collider analyses. We detail the predefined classes, functions and methods available to the user and emphasize the most recent developments. The latter include the possible definition of multiple sub-analyses and a novel user-friendly treatment for the selection criteria. We illustrate this approach by two concrete examples: a CMS search for supersymmetric partners of the top quark and a phenomenological analysis targeting hadronically decaying monotop systems.Comment: 17 pages, 3 figures, 10 tables; version accepted by EPJ

Signs of Susy

After a brief introduction to 21st century fundamental physics suitable for the layman with a reasonable level of mathematical competence, I introduce the concept of unnaturalness in Standard Model electroweak symmetry breaking and Supersymmetry (Susy) as a potential solution. The optimally natural situation in Susy in light of the 2012 discovery of a Higgs boson is derived, namely that of almost maximal mixing, with the scalar top partners almost as light as can be. The discovery is also interpreted numerically in terms of the Next-to-Minimal Supersymmetric Standard Model, with greater emphasis placed on the visibility of the Higgs boson at the observed mass, i.e. on signal strengths. I introduce simple models of gauge-mediated Susy breaking (GMSB), and how their generalisation leads to a richer parameter space. I then investigate the role played by the mediation scale of GMSB: this is found to be as a control of the extent to which Yukawa couplings de-tune flavour-blind relations set by gauge couplings. Finally, issues relating to the discovery or exclusion of Susy at colliders are discussed. Bounds are derived for the masses of new particles from Large Hadron Collider searches for excesses of jets and missing energy without leptons, and compared to constraints arising from Higgs boson searches, for models of GMSB and the Constrained Minimal Supersymmetric Standard Model. I present a novel search strategy for new physics signatures with two neutral, stable particles, when such particles are produced by boosted decays. (Susy examples include models with light gravitinos, pseudo-goldstinos, singlinos or new photinos.) The method is shown to produce sharp mass peaks that enhance the visibility of the signal

Towards a public analysis database for LHC new physics searches using MadAnalysis 5

We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.Comment: 20 pages, 15 figures, 5 recast codes; version accepted by EPJC (Dec 22, 2014) including a new section with guidelines for the experimental collaborations as well as for potential contributors to the PAD; complementary information can be found at http://madanalysis.irmp.ucl.ac.be/wiki/PhysicsAnalysisDatabas

The role of BCA2 in receptor tyrosine kinase endocytosis and breast cancer

Breast Cancer Associated gene 2 (BCA2), is a little-studied E3 ligase that is overexpressed in 56% of all primary breast cancers and has been linked with increased cell proliferation and invasion in vitro. BCA2 has been implicated in EGFR degradation however there is conflicting evidence surrounding its function and effect on receptor biology. This project aimed to elucidate the role of BCA2 in EGFR endocytosis and downregulation and to determine its link with breast cancer survival. Data generated with online mRNA analysis tools indicated that high BCA2 levels were often associated with improved breast cancer prognosis. In silico studies also demonstrated that many genes coexpressed with BCA2 were regulators of membrane trafficking and suggested that BCA2 expression was repressed by HER2/EGFR/Ras signalling. Experimentally, it was shown that siRNA depletion of BCA2 led to increased EGFR protein levels while transient BCA2 overexpression reduced levels of the receptor. It was found that BCA2 overexpressing, EGF stimulated cells demonstrated reduced lysosomal degradation of both receptor and ligand. Associated with this, downstream EGFR signalling in BCA2 overexpressing cells was reduced in magnitude but prolonged in duration and ultimately cell viability was impaired. 3 These findings support a role for BCA2 in the endolysosomal system. In agreement with this it was shown that BCA2 overexpression inhibited the vesicle membrane association of Rab7, a regulator of late endocytosis and reported BCA2 interactor. Transferrin receptor levels and transferrin uptake were unaffected by BCA2 overexpression suggesting trafficking effects may be restricted to EGFR, a distinct class of receptor and/or to later (degradation) stages of endocytosis. This thesis provides a detailed exploration of BCA2 biology and presents evidence of a functional role for the protein in the endocytic regulation of EGFR. The mechanism/s underlying the complex relationship between BCA2 and breast cancer outcome have yet to be fully determined

The Role of BCA2 in the Endocytic Trafficking of EGFR and Significance as a Prognostic Biomarker in Cancer

Breast Cancer Associated gene 2 (BCA2) is an E3 ubiquitin ligase that is over-expressed in >50% of primary breast cancers, and has been shown to increase in vitro cell proliferation and invasion. The protein has been linked to alterations in EGFR degradation, however there is some dispute as to its role and influence on the biology of this receptor. Our work aimed to ascertain the role of BCA2 in EGFR endocytosis and down-regulation and to examine its links with breast cancer outcome. Data generated with the online expression analysis tool KM-Plotter showed that high BCA2 levels are associated with poor prognosis in ovarian, gastric and breast cancer, particularly HER2 over-expressing breast cancers. Experimentally, we demonstrate that over-expression of BCA2 induced a reduction in total EGFR levels. BCA2 over-expressing cells stimulated with EGF exhibited reduced lysosomal degradation of both this ligand and its receptor. Signalling downstream of EGFR in BCA2 over-expressing cells was characterized by a lower magnitude but increased duration. Our findings support a role for BCA2 in receptor endocytosis. Consistent with this we show that BCA2 over-expression reduces the level of vesicle-associated Rab7, a regulator of late endocytosis and documented interaction partner of BCA2. Levels of transferrin receptor and the uptake of transferrin were unaltered by over-expression of BCA2 indicating that trafficking changes may be limited to late endocytic sorting events. This report offers a thorough exploration of BCA2 biology and suggests a context-dependent role for the protein in the endocytic regulation of EGFR and as a prognostic biomarker in cancer

Strategic trastuzumab mediated crosslinking driving concomitant HER2 and HER3 endocytosis and degradation in breast cancer

Efficacious anticancer therapies for targeting plasma membrane receptors with antibody based therapeutics are often contingent on sufficient endocytic delivery of receptor and conjugate to lysosomes. This results in downregulation of receptor activity and, in the case of antibody-drug conjugates (ADCs), intracellular release of a drug payload. The oncogenic receptor HER2 is a priority therapeutic target in breast cancer. Known as an “endocytosis resistant” receptor, HER2 thwarts the receptor downregulating efficiency of the frontline treatment trastuzumab and reduces the potential of trastuzumab-based therapies such as trastuzumab-emtansine. We previously demonstrated that strategically inducing trastuzumab and HER2 crosslinking in breast cancer cells promoted endocytosis and lysosomal delivery of the HER2-trastuzumab complex, stimulating downregulation of the receptor. Here we reveal that HER3, but not EGFR, is also concomitantly downregulated with HER2 after crosslinking. This is accompanied by strong activation of MEK/ERK pathway that we show does not directly contribute to HER2/trastuzumab endocytosis. We show that crosslinking induced trastuzumab endocytosis occurs via clathrin-dependent and independent pathways and is an actin-dependent process. Detailed ultrastructural studies of the plasma membrane highlight crosslinking-specific remodelling of microvilli and induction of extensive ruffling. Investigations in a cell model of acquired trastuzumab resistance demonstrate, for the first time, that they are refractory to crosslinking induced HER2 endocytosis and downregulation. This implicates further arrest of HER2 internalisation in developing trastuzumab resistance. Overall our findings highlight the potential of receptor crosslinking as a therapeutic strategy for cancer while exposing the ability of cancer cells to develop resistance via endocytic mechanisms

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 10(4) and 10(5) copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 10(5) copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.Peer reviewe

A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination. with increased transmissibility and an unfamiliar molecular mechanism of virulence.Peer reviewe