MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG.

Summary: MetaboNetworks is a tool to create custom sub-networks in Matlab using main reaction pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes and can be used to explore transgenomic interactions, for example mammalian and bacterial associations. It calculates the shortest path between a set of metabolites (e.g. biomarkers from a metabonomic study) and plots the connectivity between metabolites as links in a network graph. The resulting graph can be edited and explored interactively. Furthermore, nodes and edges in the graph are linked to the Kyoto Encyclopaedia of Genes and Genomes compound and reaction pair web pages. Availability and implementation: MetaboNetworks is available from http://www.mathworks.com/matlabcentral/fileexchange/42684. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Zinc transporter HKE4 as a new target in antihormone resistance of breast cancer

Background Oestrogen receptor-positive breast cancers develop resistance to anti-oestrogens by utilising alternative growth factor pathways as observed in our tamoxifen-resistant cell line (TAMR). These include EGFR, IGF1-R and Src signalling as well as increased growth and invasion. Zinc is elevated in breast cancer tissue and has been demonstrated to activate certain growth factor signalling pathways. We have tested the expression level of members of the LIV-1 family of zinc influx transporters and discovered that HKE4 (SLC39A7, ZIP7), previously shown by us capable of increasing the intracellular zinc levels, has increased expression in TAMR. We have therefore investigated whether the development of the more aggressive phenotype observed in our TAMR cells, including activation of these signalling pathways as well as increased growth and invasion, is due to an increase of intracellular zinc and as a direct result of increased expression of HKE4. Methods All nine members of the LIV-1 subfamily of ZIP transporters were measured in our model of tamoxifen-resistant breast cancer using Affymetrix arrays. Zinc-induced activation of growth factor signalling pathway components was investigated by western blot and/or fluorescent microscopy. Short-term (15-min) treatments with 20 μM zinc included ionophore, whereas long-term (hours/days) did not. Recombinant LIV-1 family members with a V5 tag were expressed using pcDNA3.1/V5-His-TOPO vector, and siRNA (Dharmacon smartpools with relevant controls) was used to reduce endogenous expression. Results HKE4 (SLC39A7), a ZIP transporter from the LIV-1 subfamily, was discovered to be elevated in TAMR cells by Affymetrix analysis and confirmed by PCR and western blot. We have observed that our TAMR cells have a twofold increase in intracellular zinc compared with wild-type cells, using the zinc-specific fluorescent dye Newport Green. Short-term zinc treatment of TAMR cells activates the signalling pathways implicated in antihormone-resistant proliferation and is reduced by both the zinc chelator TPEN and the Src kinase inhibitor SU6556. The same effects are observed after longer term (6 days) zinc treatment with additional increases in cell growth and invasion through Matrigel. Since we have previously demonstrated that HKE4 is capable of increasing intracellular zinc in cells and, more recently, that these TAMR have elevated intracellular zinc levels, we have tested the hypothesis that elevated HKE4 expression is directly responsible for the aggressive phenotype observed in our TAMR cells. Reducing HKE4 levels by siRNA demonstrated a role for this molecule in driving the zinc-induced activation of multiple signalling pathways. In the presence of siRNA for HKE4, the previously observed zinc-induced activation of EGFR, Src, and IGF1-R was eradicated and the EGF-stimulated activation was also decreased. Additionally, we have demonstrated the converse by transfecting recombinant HKE4 into wild-type cells and/or treating them with zinc to observe the activation of these signalling pathways and increases in invasive capability. Interestingly, we have observed a similar role of HKE4 in our model of faslodex-resistant breast cancer. Conclusion The presented results propose that HKE4, a member of the LIV-1 subfamily of ZIP transporters, is directly involved in the activation of the aggressive phenotype observed with the development of antihormone resistance, and as such is a potential new target for the prevention of resistance to antihormones in breast cancer progression

Recruitment of insulin receptor substrate-1 by erbB3 impacts on IGF-IR signalling in oestrogen receptor-positive breast cancer cells

Insulin-like growth factor receptor (IGF-IR) signalling classically involves phosphorylation of insulin receptor substrate-1 (IRS-1) to recruit key down-stream signalling pathways effecting breast cancer cell proliferation and survival. Recently, we have shown a further capacity for IRS-1 to associate with the epidermal growth factor receptor (EGFR/erbB1), with activation of EGFR promoting recruitment and phosphorylation of IRS-1 in an oestrogen receptor (ER)-positive tamoxifen-resistant breast cancer cell line. In this study, we examined recruitment of IRS-1 by another member of the erbB receptor family, erbB3, in three ER-positive breast cancer cell lines. Our studies revealed an interaction between erbB3 and IRS-1 in MCF-7, T47D and BT474 cells with HRGβ1 treatment significantly enhancing this recruitment and promoting IRS-1 phosphorylation at tyrosine (Y) 612, a specific phosphoinositide 3-kinase (PI3K) binding site. IRS-1 appears to play a key role in erbB3 signalling in MCF-7 and T47D cells as its knockdown using siRNA greatly impaired HRGβ1 signalling via PI3K/AKT in these cell lines. This novel interaction may have clinical relevance as immunohistochemical analysis of ER-positive breast cancer patient samples revealed IRS-1 Y612 expression positively correlated with total erbB3, p-AKT and Ki67 expression. Importantly, we found that recruitment of IRS-1 by erbB3 impaired IRS-1 recruitment by IGF-IR in both MCF-7 and T47D cells, whilst blockade of IGF-1R enhanced erbB3/IRS-1 interaction and sensitised both cell lines to HRGβ1. Consequently, blockade of erbB3 signalling enhanced the effects of IGF-IR inhibition in these cells. In conclusion, these and previous findings suggest that IRS-1 can be recruited to IGF-1R, EGFR and erbB3 in ER-positive breast cancer cells and this may provide an adaptive resistance mechanism when these receptors are targeted individually. Consequently co-targeting of IGF-IR and erbB receptors may prove to be a more effective strategy for the treatment of ER-positive breast cancer

The Children’s Attention Project: A community-based longitudinal study of children with ADHD and non-ADHD controls.

NHMR

Assessing availability and greenhouse gas emissions of lignocellulosic biomass feedstock supply – case study for a catchment in England

© 2019 Society of Chemical Industry and John Wiley & Sons, Ltd.Feedstocks from lignocellulosic biomass (LCB) include crop residues and dedicated per¬ennial biomass crops. The latter are often considered superior in terms of climate change mitigation potential. Uncertainty remains over their availability as feedstocks for biomass provision and the net greenhouse gas emissions (GHG) during crop production. Our objective was to assess the optimal land allocation to wheat and Miscanthus in a specific case study located in England, to increase bio¬mass availability, improve the carbon balance (and reduce the consequent GHG emissions), and mini¬mally constrain grain production losses from wheat. Using soil and climate variables for a catchment in east England, biomass yields and direct nitrogen emissions were simulated with validated process-based models. A ‘Field to up-stream factory gate’ life-cycle assessment was conducted to estimate indirect management-related GHG emissions. Results show that feedstock supply from wheat straw can be supplemented beneficially with LCB from Miscanthus grown on selected low-quality soils. In our study, 8% of the less productive arable land area was dedicated to Miscanthus, increasing total LCB provision by about 150%, with a 52% reduction in GHG emission per ton LCB delivered and only a minor effect on wheat grain production (−3%). In conclusion, even without considering the likely carbon sequestration in impoverished soils, agriculture should embrace the opportunities to provide the bioeconomy with LCB from dedicated, perennial crops.Peer reviewe

Fulvestrant-induced expression of ErbB3 and ErbB4 receptors sensitizes oestrogen receptor-positive breast cancer cells to heregulin β1

Introduction We have previously reported that induction of epidermal growth factor receptor and ErbB2 in response to antihormonal agents may provide an early mechanism to allow breast cancer cells to evade the growth-inhibitory action of such therapies and ultimately drive resistant cell growth. More recently, the other two members of the ErbB receptor family, ErbB3 and ErbB4, have been implicated in antihormone resistance in breast cancer. In the present study, we have investigated whether induction of ErbB3 and/or ErbB4 may provide an alternative resistance mechanism to antihormonal action in a panel of four oestrogen receptor (ER)-positive breast cancer cell lines. Methods MCF-7, T47D, BT474 and MDAMB361 cell lines were exposed to fulvestrant (100 nM) for seven days, and effects on ErbB3/4 expression and signalling, as well as on cell growth, were assessed. Effects of heregulin β1 (HRGβ1) were also examined in the absence and presence of fulvestrant to determine the impact of ER blockade on the capacity of this ErbB3/4 ligand to promote signalling and cell proliferation. Results Fulvestrant potently reduced ER expression and transcriptional activity and significantly inhibited growth in MCF-7, T47D, BT474 and MDAMB361 cells. However, alongside this inhibitory activity, fulvestrant also consistently induced protein expression and activity of ErbB3 in MCF-7 and T47D cells and ErbB4 in BT474 and MDAMB361 cell lines. Consequently, fulvestrant treatment sensitised all cell lines to the actions of the ErbB3/4 ligand HRGβ1 with enhanced ErbB3/4-driven signalling activity, reexpression of cyclin D1 and significant increases in cell proliferation being observed when compared to untreated cells. Indeed, in T47D and MDAMB361 HRGβ1 was converted from a ligand having negligible or suppressive growth activity into one that potently promoted cell proliferation. Consequently, fulvestrant-mediated growth inhibition was completely overridden by HRGβ1 in all four cell lines. Conclusions These findings suggest that although antihormones such as fulvestrant may have potent acute growth-inhibitory activity in ER-positive breast cancer cells, their ability to induce and sensitise cells to growth factors may serve to reduce and ultimately limit their inhibitory activity