Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations

Feasibility and Acceptability of a Healthy Nordic Diet Intervention for the Treatment of Depression: A Randomized Controlled Pilot Trial

Healthy diet interventions have been shown to improve depressive symptoms, but thereis a need for randomized controlled trials (RCTs) that are double blind and investigate biologicalmechanisms. The primary objectives of this randomized controlled pilot trial were to test thepalatability of the meals and the acceptability of the intervention in preparation for an 8-week RCTin the future, which will investigate whether a healthy Nordic diet improves depressive symptomsin individuals with major depressive disorder, and associated biological mechanisms. Depressed(n = 10) and non-depressed (n = 6) women and men were randomized to receive either a healthyNordic diet (ND) or a control diet (CD) for 8 days. Participants were blinded to their diet allocationand the study hypotheses. Health questionnaires were completed before and after the interventionand, throughout the study, questionnaires assessed participants’ liking for the meals, their sensoryproperties, adherence, and open-ended feedback. In the ND group, 75% of participants consumedonly the provided foods, as instructed, compared to 50% of CD participants. The meals of both diets,on average, received good ratings for liking and sensory properties, though the ND ratings weresomewhat higher. Overall, results were positive and informative, indicating that the planned RCTwill be feasible and well-accepted, with some proposed modifications

Subcellular Partitioning of Protein Tyrosine Phosphatase 1B to the Endoplasmic Reticulum and Mitochondria Depends Sensitively on the Composition of Its Tail Anchor

<div><p>The canonical protein tyrosine phosphatase PTP1B is an important regulator of diverse cellular signaling networks. PTP1B has long been thought to exert its influence solely from its perch on the endoplasmic reticulum (ER); however, an additional subpopulation of PTP1B has recently been detected in mitochondria extracted from rat brain tissue. Here, we show that PTP1B’s mitochondrial localization is general (observed across diverse mammalian cell lines) and sensitively dependent on the transmembrane domain length, C-terminal charge and hydropathy of its short (≤35 amino acid) tail anchor. Our electron microscopy of specific DAB precipitation revealed that PTP1B localizes via its tail anchor to the outer mitochondrial membrane (OMM), with fluorescence lifetime imaging microscopy establishing that this OMM pool contributes to the previously reported cytoplasmic interaction of PTP1B with endocytosed epidermal growth factor receptor. We additionally examined the mechanism of PTP1B’s insertion into the ER membrane through heterologous expression of PTP1B’s tail anchor in wild-type yeast and yeast mutants of major conserved ER insertion pathways: In none of these yeast strains was ER targeting significantly impeded, providing in vivo support for the hypothesis of spontaneous membrane insertion (as previously demonstrated in vitro). Further functional elucidation of the newly recognized mitochondrial pool of PTP1B will likely be important for understanding its complex roles in cellular responses to external stimuli, cell proliferation and diseased states.</p></div

Effects of Dietary Fibres on Acute Indomethacin-Induced Intestinal Hyperpermeability in the Elderly: A Randomised Placebo Controlled Parallel Clinical Trial

The effect of dietary fibres on intestinal barrier function has not been well studied, especially in the elderly. We aimed to investigate the potential of the dietary fibres oat beta-glucan and wheat arabinoxylan to strengthen the intestinal barrier function and counteract acute non-steroid anti-inflammatory drug (indomethacin)-induced hyperpermeability in the elderly. A general population of elderly subjects (&amp;gt;= 65 years,n= 49) was randomised to a daily supplementation (12g/day) of oat beta-glucan, arabinoxylan or placebo (maltodextrin) for six weeks. The primary outcome was change in acute indomethacin-induced intestinal permeability from baseline, assessed by an in vivo multi-sugar permeability test. Secondary outcomes were changes from baseline in: gut microbiota composition, systemic inflammatory status and self-reported health. Despite a majority of the study population (85%) showing a habitual fibre intake below the recommendation, no significant effects on acute indomethacin-induced intestinal hyperpermeability in vivo or gut microbiota composition were observed after six weeks intervention with either dietary fibre, compared to placebo.Funding Agencies|European UnionEuropean Union (EU) [289517]; Bo Rydin foundation [F0514]</p

Mitochondrial localization of endogenous PTP1B in multiple mammalian cell lines.

<p>Mammalian cells were fixed with PFA and immunostained for endogenous PTP1B using an anti-PTP1B (Ab-1) mouse monoclonal primary antibody (Calbiochem) and a chicken anti-mouse secondary antibody conjugated with Alexa488 (Invitrogen). Mitochondria were stained with MitoTracker Red CMXRos (Invitrogen). COS-7, BJ Fibroblast, HeLa, MCF7, MDCK and HepG2 cells were visualized with confocal microscopy. Representative mitochondria are marked with arrows. Mitochondrial targeting of PTP1B was easier to assess in the cells with a flatter morphology towards the top of the figure as compared with the more compact cells towards the bottom. Scale bars: 20 μm.</p

Tail anchor targeting is largely dictated by three different factors: TMD length, C-terminal charge and hydropathy.

<p>Our experimental localization results for different tail isoforms in COS-7 cells and yeast cells are summarized. We have shown that the wild-type localization of PTP1Btail to the mitochondria and ER (Mito/ER) is highly sensitive to changes in these three factors (see text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139429#pone.0139429.s008" target="_blank">S8 Fig</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139429#pone.0139429.s009" target="_blank">S9 Fig</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139429#pone.0139429.s010" target="_blank">S10 Fig</a>).</p

Systematic study of the potential pathways responsible for the subcellular targeting of the tail anchor of PTP1B in yeast.

<p>We used an aggregate-formation assay to examine the impact of deletion of the various insertion pathway components in yeast. Aggregate formation in strains expressing tail anchors from Ysy6 and Sec22 upon deletion of the GET pathway component Get2 was used as a control. Comparing wild-type with Get2∆ deletion strains that expressed yemCitrine-Ysy6tail or yemCitrine-Sec22tail, we observed visible aggregates in a fraction of the Get2∆ cells that were consistent with previous findings (though the bulk of these proteins still managed to insert properly). We observed similar aggregates in cells expressing yemCitrine-PTP1Btail. Slightly more aggregates were observed in Get3∆ cells and significantly fewer in the Sgt2∆ cells of this strain. A strain in which both Get2 and Get1 were deleted was similar to the Get2∆ deletion strain. The green box indicates all strains in which one or more GET pathway components were deleted. Deletion of the α subunit of the SRP receptor (Srp101) led to a much larger cell phenotype (blue box), but no change in the ER and vacuolar partitioning of the PTP1B tail anchor. Deletion of Sec72 (yellow box), an essential factor of the Sec62/63 pathway, also did not alter the localization of the PTP1B tail anchor. Deletion of Sec72 in the Get2∆/Get1∆ strain did not further alter the localization of the PTP1B tail anchor beyond that observed in the Get2∆/Get1∆ strain. Finally, deletion of the chaperones Apj1 and Ydj1 (as well as the farnesyl transferase of Ydj1, Ram1) did not alter PTP1B’s subcellular localization (red box). The intensity scale shown at the bottom right and indicating photon counts/pixel is applicable to all images, as is the scale bar shown in the bottom right panel. Scale bar: 10 μm.</p

Wild-type and mutant PTP1B tail anchor isoforms examined in this study.

<p>See text for further description.</p

PTP1B localizes to the mitochondria in COS-7 cells.

<p>Confocal images of COS-7 cells expressing mCitrine-PTP1B along with the mitochondrial marker Tom20-mTagBFP. The mCitrine-PTP1B chimera localized to the general ER (arrowhead) and at a higher local concentration to the mitochondria (arrow). Scale bar: 20 μm.</p