Comparison of 2 cell-based phosphoprotein assays to support screening and development of an ALK inhibitor

Anaplastic lymphoma kinase (ALK) when expressed as a fusion protein with nucleophosmin (NPM) has been implicated as a driving oncogene in a subset of lymphomas. Recent reports of ALK expression in a number of other cancers have raised the possibility that an ALK inhibitor may benefit patients with these diseases as well. In a campaign to identify and develop a selective ALK inhibitor, 2 assays were devised to measure the phosphorylation of tyrosine residue 1604 of ALK (pY(1604) ALK). Amplified Luminescent Proximity Homogeneous Assay (AlphaScreen(?)) and phosflow platforms were used to detect modulation of pY(1604) ALK to determine the relative potency of a set of small-molecule inhibitors. Prior to making use of these assays in diverse settings, the authors attempted to ensure their equivalence with a direct comparison of their performance. The pY(1604) ALK assays correlated well both with each other and with assays of ALK enzyme activity or ALK-dependent cell proliferation. The AlphaScreen(?) assay was amenable to automation and enabled rapid, high-throughput compound assessment in an NPM-ALK-driven cell line, whereas the phosflow assay enabled the authors to characterize the activity of compounds with respect to their impact on targeted enzymes and pathways. Results show that both AlphaScreen(?) and phosflow ALK assays exhibited diverse characteristics that made them desirable for different applications but were determined to be equally sensitive and robust in the detection of inhibition of pY(1604) ALK.     

Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories

Understanding how novel functions evolve (genetic adaptation) is a critical goal of evolutionary biology. Among asexual organisms, genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion (epistasis). Non-linear interactions pose a formidable challenge for the computational prediction of mutation effects. Here we use the recent evolution of β-lactamase under antibiotic selection as a model for genetic adaptation. We build a network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence. Most often these pairs occur in the setting of more complex mutants. Focusing on extended-spectrum resistant sequences, we use network-theoretical tools to identify triple mutant trajectories of likely special significance for adaptation. We extrapolate evolutionary paths (n = 3) that increase resistance and that are longer than the units used to build the network (n = 2). These paths consist of a limited number of residue positions and are enriched for known triple mutant combinations that increase cefotaxime resistance. We find that the pairs of residues used to build the network frequently decrease resistance compared to their corresponding singlets. This is a surprising result, given that their coevolution suggests a selective advantage. Thus, β-lactamase adaptation is highly epistatic. Our method can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context. Our approach requires only sequence information, sufficient genetic diversity, and discrete selective pressures. Thus, it can be used to analyze recent evolutionary events, where coevolution analysis methods that use phylogeny or statistical coupling are not possible. Improving our ability to assess evolutionary trajectories will help predict the evolution of clinically relevant genes and aid in protein design.     

Divergent patrilineal signals in three Roma populations

Previous studies have revealed that the European Roma share close genetic, linguistic and cultural similarities with Indian populations despite their disparate geographical locations and divergent demographic histories. In this study, we report for the first time Y-chromosome distributions in three Roma collections residing in Belgrade, Vojvodina and Kosovo. Eighty-eight Y-chromosomes were typed for 14 SNPs and 17 STRs. The data were subsequently utilized for phylogenetic comparisons to pertinent reference collections available from the literature. Our results illustrate that the most notable difference among the three Roma populations is in their opposing distributions of haplogroups H and E. Although the Kosovo and Belgrade samples exhibit elevated levels of the Indian-specific haplogroup H-M69, the Vojvodina collection is characterized almost exclusively by haplogroup E-M35 derivatives, most likely the result of subsequent admixture events with surrounding European populations. Overall, the available data from Romani groups points to different levels of gene flow from local populations.     

Inhibitor of Apoptosis (IAP) survivin is indispensable for survival of HER2 gene-amplified breast cancer cells with primary resistance to HER1/2-targeted therapies

Primary resistance of HER2 gene-amplified breast carcinomas (BC) to HER-targeted therapies can be explained in terms of overactive HER2-independent downstream pro-survival pathways. We here confirm that constitutive overexpression of Inhibitor of Apoptosis (IAP) survivin is indispensable for survival of HER2-positive BC cells with intrinsic cross-resistance to multiple HER1/2 inhibitors. The IC₅₀ values for the HER1/2 Tyrosine Kinase Inhibitors (TKIs) gefitinib, erlotinib and lapatinib were up to 40-fold higher in trastuzumab-unresponsive JIMT-1 cells than in trastuzumab-naïve SKBR3 cells. ELISA-based and immunoblotting assays demonstrated that trastuzumab-refractory JIMT-1 cells constitutively expressed ∼4 times more survivin protein than trastuzumab-responsive SKBR3 cells. In response to trastuzumab, JIMT-1 cells accumulated ∼10 times more survivin than SKBR3 cells. HER1/2 TKIs failed to down-regulate survivin expression in JIMT-1 cells whereas equimolar doses of HER1/HER2 TKIs drastically depleted survivin protein in SKBR3 cells. ELISA-based detection of histone-associated DNA fragments confirmed that trastuzumab-refractory JIMT-1 cells were intrinsically protected against the apoptotic effects of HER1/2 TKIs. Of note, when we knocked-down survivin expression using siRNA and then added trastuzumab, cell proliferation and colony formation were completely suppressed in JIMT-1 cells. Our current findings may be extremely helpful to design successful combinatorial strategies aimed to circumvent the occurrence of de novo resistance to HER2-directed drugs using survivin antagonists.     

Exploring the role of transhumance drove roads on the conservation of ant diversity in Mediterranean agroecosystems

Drove roads are a major feature of Mediterranean countries, where this livestock management system has been practiced for centuries. In Spain, many drove roads have become completely or partially abandoned by herders, and transformed for other land uses. Yet, some major drove roads continue to be used for the passage of livestock, and might exert important effects on the conservation of biodiversity and ecosystem functions, particularly in highly transformed agricultural landscapes. In this study, we compare ant taxonomic and functional diversity on a drove road that is still used by transhumant livestock (the Conquense Drove Road) versus an abandoned road (the Murciana Drove Road). Ant species richness per trap and ant richness per sample unit were significantly higher on the used drove road compared to the abandoned drove road. The used drove road also had a positive edge effect on ant species diversity in adjacent croplands (both herbaceous crops and vineyards). Ant functional diversity was also higher on the used drove road. These results draw attention to the role of drove roads as ecologically unique systems and reservoirs of biodiversity, particularly within intensive agricultural landscapes. These effects, however, are largely dependent on maintaining livestock use.     

Sarcopenia y albúmina sanguínea: revisión sistemática con metaanálisis

Sarcopenia is characterized by loss of muscle mass during aging, which can have consequences for the individuals'' health. There are many ways to detect it, among them, with the use of blood biomarkers such as albumin, although the association between the two has not been confirmed yet.This review synthesizes the knowledge on the association between sarcopenia and serum albumin among elderly individuals through a systematic review and meta-analysis focused on the etiology and risk factors. We used the Joanna Briggs Institute software for the review and conducted a search in MEDLINE, Embase, CINAHL, and LILACS databases while two reviewers conducted an independent manual search. EpiDat, version 3.1 was used for the meta-analysis; mean differences with the albumin scores disaggregated by sarcopenia were analyzed by the random-effects model. The degree of heterogeneity was assessed with the DerSimonian and Laird Q test.We analyzed 630 articles and finally included 14 in the review. Higher blood albumin levels were found in the meta-analysis, which was statistically significant among the elderly adults who did not present sarcopenia compared to those who did. Although there are studies exploring the association between albumin and sarcopenia, there is a need to continue evaluating its association with biological markers and comparing them to verify which can be used to detect sarcopenia among the elderly.