Targeting the Triple-Negative Breast Cancer Kinome with Chemical Proteomics

Kinases are members of a large dynamic and cooperative signaling network, which senses inhibition of key nodal kinases and induces compensatory responses that offset pharmacological intervention. Combination therapies that target multiple growth- and survival promoting kinases are proving to be a better strategy for successful cancer therapy. What is lacking is the ability to measure whole kinome activity and to assess kinome adaptation and resistance to targeted therapies. We have developed a chemical proteomics approach that couples kinase affinity capture with quantitative mass spectrometry, providing a systems biology platform to profile global kinome activity in cancer cells, GEMM tumors and patient biopsies. Our chemical proteomic approach captures the majority of the expressed kinome estimated by RNA-seq and detects altered kinome activity profiles in response to stimulus or kinase inhibitors. Kinases from all major kinome subfamilies are captured with a large percentage representing the understudied kinome. Applying this technology, we discovered previously undefined activation of tyrosine and serine/threonine kinases in breast cancer cell lines in response to targeted inhibitors against MEK or EGFR that are currently undergoing clinical trials. Combined kinome activity assessment using chemical proteomics and RNAi synthetic lethal screens predicted a specific kinase inhibitor combination therapy. The combination therapy gave apoptosis and tumor regression in a breast cancer GEMM, where single agents were largely ineffective. The relevance of kinome reprogramming to patient triple-negative breast cancer was confirmed by the investigation of MEK inhibitor-treated patient samples from a window trial established in conjunction with GlaxoSmithKline. However, differential kinome responses were observed across intrinsic breast cancer subtypes, suggesting that broader approaches to targeting or preventing kinome reprogramming may be necessary to avert resistance to kinase inhibitor therapies. The findings presented here define a novel approach to determining kinome-based mechanisms of resistance to targeted therapies to suggest novel inhibitor combinations and strategies that may more effectively treat triple-negative breast cancer.Doctor of Philosoph

Preparing SME Suppliers for Sustainable Local Authority eProcurement

Public sector organisations are increasingly introducing eProcurement systems in order to improve the efficiency and effectiveness of their procurement processes. This clearly has implications for their suppliers, who are being asked to adopt eProcurement. For many SMEs, particularly small and micro businesses, this is proving a difficult challenge given their lack of eProcurement knowledge, as well as their resource shortages. It is at the Local Authority (LA) level that this situation is most problematic, as SMEs tend to supply more to local than central government. This paper presents the results of research undertaken with LAs and SMEs as part of the EPROC project. In particular, it provides insights into the level of eProcurement use and development in LAs in North West Europe, and illustrates how the introduction of eProcurement could have a negative impact on local economies and communities if LAs don’t help their SMEs to adopt eProcurement. The paper also reports on the findings of research conducted with SMEs in relation to the problems they’ve experienced in undertaking eProcurement with LAs, and details how some LAs are engaging with their local SMEs to help them become ‘eProcurement ready’. The research has demonstrated there is a need to bridge the knowledge gap between SME understanding and awareness of LA eProcurement developments on the one hand, and on the other, LA understanding of the typical eProcurement capabilities of their SME supplier base. To meet these needs, the EPROC project has developed separate eProcurement guides for SMEs and LAs

Parameter estimation in a spatial unit root autoregressive model

Spatial unilateral autoregressive model $X_{k,\ell}=\alpha X_{k-1,\ell}+\beta X_{k,\ell-1}+\gamma X_{k-1,\ell-1}+\epsilon_{k,\ell}$ is investigated in the unit root case, that is when the parameters are on the boundary of the domain of stability that forms a tetrahedron with vertices $(1,1,-1), \ (1,-1,1),\ (-1,1,1)$and$(-1,-1,-1)$. It is shown that the limiting distribution of the least squares estimator of the parameters is normal and the rate of convergence is$n$when the parameters are in the faces or on the edges of the tetrahedron, while on the vertices the rate is$n^{3/2}$.Comment: 47 pages, 1 figur

Subclinical cardiopulmonary dysfunction in stage 3 chronic kidney disease.

OBJECTIVE: Reduced exercise capacity is well documented in end-stage chronic kidney disease (CKD), preceded by changes in cardiac morphology in CKD stage 3. However, it is unknown whether subclinical cardiopulmonary dysfunction occurs in CKD stage 3 independently of heart failure. METHODS: Prospective observational cross-sectional study of exercise capacity assessed by cardiopulmonary exercise testing in 993 preoperative patients. Primary outcome was peak oxygen consumption (VO2peak). Anaerobic threshold (AT), oxygen pulse and exercise-evoked measures of autonomic function were analysed, controlling for CKD stage 3, age, gender, diabetes mellitus and hypertension. RESULTS: CKD stage 3 was present in 93/993 (9.97%) patients. Diabetes mellitus (RR 2.49 (95% CI 1.59 to 3.89); p<0.001), and hypertension (RR 3.20 (95% CI 2.04 to 5.03); p<0.001)) were more common in CKD stage 3. Cardiac failure (RR 0.83 (95% CI 0.30 to 2.24); p=0.70) and ischaemic heart disease (RR 1.40 (95% CI 0.97 to 2.02); p=0.09) were not more common in CKD stage 3. Patients with CKD stage 3 had lower predicted VO2peak (mean difference: 6% (95% CI 1% to 11%); p=0.02), lower peak heart rate (mean difference:9 bpm (95% CI 3 to 14); p=0.03)), lower AT (mean difference: 1.1 mL/min/kg (95% CI 0.4 to 1.7); p<0.001) and impaired heart rate recovery (mean difference: 4 bpm (95% CI 1 to 7); p<0.001)). CONCLUSIONS: Subclinical cardiopulmonary dysfunction in CKD stage 3 is common. This study suggests that maladaptive cardiovascular/autonomic dysfunction may be established in CKD stage 3, preceding pathophysiology reported in end-stage CKD

A Deep Chandra ACIS Study of NGC 4151. II. The Innermost Emission Line Region and Strong Evidence for Radio Jet-NLR Cloud Collision

We have studied the X-ray emission within the inner 150 pc radius of NGC 4151 by constructing high spatial resolution emission line images of OVII, OVIII, and NeIX. These maps show extended structures that are spatially correlated with the radio outflow and optical [OIII] emission. We find strong evidence for jet--gas cloud interaction, including morphological correspondences with regions of X-ray enhancement, peaks of near-infrared [FeII] emission, and optical clouds. In these regions, moreover, we find evidence of elevated NeIX/OVII ratios; the X-ray emission of these regions also exceeds that expected from nuclear photoionization. Spectral fitting reveals the presence of a collisionally ionized component. The thermal energy of the hot gas suggests that >0.1% of the estimated jet power is deposited into the host interstellar medium through interaction between the radio jet and the dense medium of the circum-nuclear region. We find possible pressure equilibrium between the collisionally ionized hot gas and the photoionized line-emitting cool clouds. We also obtain constraints on the extended iron and silicon fluorescent emission. Both lines are spatially unresolved. The upper limit on the contribution of an extended emission region to the Fe Kalpha emission is <5% of the total, in disagreement with a previous claim that 65% of the Fe Kalpha emission originates in the extended narrow line region.Comment: Accepted for publication in ApJ. 28 pages, 9 figure

Sympathetic autonomic dysfunction and impaired cardiovascular performance in higher risk surgical patients: implications for perioperative sympatholysis

OBJECTIVE: Recent perioperative trials have highlighted the urgent need for a better understanding of why sympatholytic drugs intended to reduce myocardial injury are paradoxically associated with harm (stroke, myocardial infarction). We hypothesised that following a standardised autonomic challenge, a subset of patients may demonstrate excessive sympathetic activation which is associated with exercise-induced ischaemia and impaired cardiac output. METHODS: Heart rate rise during unloaded pedalling (zero workload) prior to the onset of cardiopulmonary exercise testing (CPET) was measured in 2 observation cohorts of elective surgical patients. The primary outcome was exercise-evoked, ECG-defined ischaemia (>1 mm depression; lead II) associated with an exaggerated increase in heart rate (EHRR ≥12 bpm based on prognostic data for all-cause cardiac death in preceding epidemiological studies). Secondary outcomes included cardiopulmonary performance (oxygen pulse (surrogate for left ventricular stroke volume), peak oxygen consumption (VO2peak), anaerobic threshold (AT)) and perioperative heart rate. RESULTS: EHRR was present in 40.4-42.7% in both centres (n=232, n=586 patients). Patients with EHRR had higher heart rates perioperatively (p<0.05). Significant ST segment depression during CPET was more common in EHRR patients (relative risk 1.7 (95% CI 1.3 to 2.1); p<0.001). EHRR was associated with 11% (95%CI 7% to 15%) lower predicted oxygen pulse (p<0.0001), consistent with impaired left ventricular function. CONCLUSIONS: EHRR is common and associated with ECG-defined ischaemia and impaired cardiac performance. Perioperative sympatholysis may further detrimentally affect cardiac output in patients with this phenotype

Termination shocks and the extended X-ray emission in Mrk 78

Subarcsecond imaging of the X-ray emission in the type 2 active galactic nucleus (AGN) Mrk 78 with Chandra shows complex structure with spectral variations on scales from ∼200 pc to ∼2 kpc. Overall the X-ray emission is aligned E–W with the radio (3.6 cm) and narrow emission line region as mapped in [O III], with a marked E–W asymmetry. The eastern X-ray emission is mostly in a compact knot coincident with the location where the radio source is deflected, while the western X-ray emission forms a loop or shell ∼2 kpc from the nucleus with radius ∼0.7 kpc. There is suggestive evidence of shocks in both the eastern knot and the western arc. Both these positions coincide with large changes in the velocities of the [O III] outflow. We discuss possible reasons why the X-ray shocks on the western side occur ∼1 kpc farther out than on the eastern side. We estimate that the thermal energy injected by the shocks into the interstellar medium corresponds to 0.05%–0.6% of the AGN bolometric luminosity

Discovery of strongly blue shifted mid-infrared [NeIII] and [NeV] emission in ULIRGs

We report the discovery of blue shifted (delta(V) > 200 km/s) mid-infrared [NeIII] and/or [NeV] emission in 25 out of 82 ULIRGs (30% of our sample). The incidence of blue shifted [NeV] emission is even higher (59%) among the sources with a [NeV] detection -- the tell-tale signature of an active galactic nucleus (AGN). Sixteen ULIRGs in our sample, eleven of which are optically classified as AGN, have [NeIII] blue shifts above 200 km/s. A comparison of the line profiles of their 12.81um [NeII], 15.56um [NeIII] and 14.32um [NeV] lines reveals the ionization of the blue shifted gas to increase with blue shift, implying decelerating outflows in a stratified medium, photo-ionized by the AGN. The strong correlation of the line width of the [NeIII] line with the radio luminosity indicates that interaction of expanding radio jets with the dense ISM surrounding the AGN may explain the observed neon line kinematics for the strongest radio sources in this sample.Comment: Accepted for publication by ApJ Letters. 15 pages, 4 figure

Orbitofrontal and caudate volumes in cannabis users: a multi-site mega-analysis comparing dependent versus non-dependent users.

Cannabis (CB) use and dependence are associated with regionally specific alterations to brain circuitry and substantial psychosocial impairment.The objective of this study was to investigate the association between CB use and dependence, and the volumes of brain regions critically involved in goal-directed learning and behaviour-the orbitofrontal cortex (OFC) and caudate.In the largest multi-site structural imaging study of CB users vs healthy controls (HC), 140 CB users and 121 HC were recruited from four research sites. Group differences in OFC and caudate volumes were investigated between HC and CB users and between 70 dependent (CB-dep) and 50 non-dependent (CB-nondep) users. The relationship between quantity of CB use and age of onset of use and caudate and OFC volumes was explored.CB users (consisting of CB-dep and CB-nondep) did not significantly differ from HC in OFC or caudate volume. CB-dep compared to CB-nondep users exhibited significantly smaller volume in the medial and the lateral OFC. Lateral OFC volume was particularly smaller in CB-dep females, and reduced volume in the CB-dep group was associated with higher monthly cannabis dosage.Smaller medial OFC volume may be driven by CB dependence-related mechanisms, while smaller lateral OFC volume may be due to ongoing exposure to cannabinoid compounds. The results highlight a distinction between cannabis use and dependence and warrant examination of gender-specific effects in studies of CB dependence