Fematrin-1 Is Involved in Fetomaternal Cell-to-Cell Fusion in Bovinae Placenta and Has Contributed to Diversity of Ruminant Placentation

During placentation, mammals employ different strategies for nourishing and supporting fetuses. Members of the Bovidae family, consisting of cloven-hoofed ruminants, utilize multiple maternal attachment points on the placenta, known as cotyledons, and hybrid cells, named trinucleate cells or syncytial plaques, made up of a fusion of fetal trophoblasts and maternal endometrial cells to provide essential hormones and maintain long gestation periods. These hybrid cells are unique to the Bovidae, as fetomaternal borders are clearly separated by syncytiotrophoblasts or epithelial cells in the placenta of other mammals. Recently, it was reported that Syncytin-Rum1 was inserted into ruminant genomes, including cattle and sheep, and was possibly involved in fetomaternal cell-to-cell fusion in both species. However, Syncytin-Rum1 alone is insufficient to explain the morphological diversity of the fetomaternal hybrids between Bovinae and Caprinae (i.e., trinucleate cells in Bovinae and syncytial plaques in Caprinae). Here we report that the bovine endogenous retrovirus K1 (BERV-K1) envelope, which we term Fematrin-1, was specifically expressed in binucleated trophoblasts throughout gestation in cattle and induced fusion with bovine endometrial cells in vitro at a significantly higher level than Syncytin-Rum1 under physiological conditions. Fematrin-1 was found to be integrated into intron 18 of FAT tumor suppressor homolog 2 (FAT2) about 18.3 to 25.4 million years ago and has been subject to purifying selection through the evolution of Bovinae. Phylogenetically, Fematrin-1 is distinct from Syncytin genes found in other mammalian species that form syncytiotrophoblasts. Our results suggest that the newly acquired endogenous retroelement has contributed to generating placentation diversity through ruminant evolution.     

NUDT15 polymorphism and NT5C2 and PRPS1 mutations influence thiopurine sensitivity in acute lymphoblastic leukaemia cells

In chemotherapy for childhood acute lymphoblastic leukaemia (ALL), maintenance therapy consisting of oral daily mercaptopurine and weekly methotrexate is important. NUDT15 variant genotype is reportedly highly associated with severe myelosuppression during maintenance therapy, particularly in Asian and Hispanic populations. It has also been demonstrated that acquired somatic mutations of the NT5C2 and PRPS1 genes, which are involved in thiopurine metabolism, are detectable in a portion of relapsed childhood ALL. To directly confirm the significance of the NUDT15 variant genotype and NT5C2 and PRPS1 mutations in thiopurine sensitivity of leukaemia cells in the intrinsic genes, we investigated 84 B-cell precursor-ALL (BCP-ALL) cell lines. Three and 14 cell lines had homozygous and heterozygous variant diplotypes of the NUDT15 gene, respectively, while 4 and 2 cell lines that were exclusively established from the samples at relapse had the NT5C2 and PRPS1 mutations, respectively. Both NUDT15 variant genotype and NT5C2 and PRPS1 mutations were significantly associated with DNA-incorporated thioguanine levels after exposure to thioguanine at therapeutic concentration. Considering the continuous exposure during the maintenance therapy, we evaluated in vitro mercaptopurine sensitivity after 7-day exposure. Mercaptopurine concentrations lethal to 50% of the leukaemia cells were comparable to therapeutic serum concentration of mercaptopurine. Both NUDT15 variant genotype and NT5C2 and PRPS1 mutations were significantly associated with mercaptopurine sensitivity in 83 BCP-ALL and 23 T-ALL cell lines. The present study provides direct evidence to support the general principle showing that both inherited genotype and somatically acquired mutation are crucially implicated in the drug sensitivity of leukaemia cells.     

Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes

HIV-1 subtype phylogeny is investigated using a previously developed computational model of natural amino acid site substitutions. This model, based on Boltzmann statistics and Metropolis kinetics, involves an order of magnitude fewer adjustable parameters than traditional substitution matrices and deals more effectively with the issue of protein site heterogeneity. When optimized for sequences of HIV-1 envelope (env) proteins from a few specific subtypes, our model is more likely to describe the evolutionary record for other subtypes than are methods using a single substitution matrix, even a matrix optimized over the same data. Pairwise distances are calculated between various probabilistic ancestral subtype sequences, and a distance matrix approach is used to find the optimal phylogenetic tree. Our results indicate that the relationships between subtypes B, C, and D and those between subtypes A and H may be closer than previously thought.     

Syntaxin4 interacting protein (synip) binds phosphatidylinositol (3,4,5) triphosphate

The insulin responsive Glut4 transport vesicles contain the v-SNARE protein Vamp2 that associate with the plasma membrane t-SNARE protein Syntaxin 4 to drive insulin-stimulated Glut4 translocation in skeletal muscle and adipocytes. The syntaxin 4 interacting protein (Synip) binds to syntaxin 4 in the basal state and dissociates in the insulin-stimulated state allowing for the subsequent binding of Vamp2 containing Glut4 vesicles and fusion with the plasma membrane. In this study, we have found that Synip binds phosphatidylinositol 3,4,5-triphosphate (PIP3), but not phosphatidylinositol 3 phosphate (PIP) or phosphatidylinositol 3,4-biphosphate (PIP2) through the Synip WW domain as deletion of this domain (Synip ΔWW) failed to bind PIP3. Over-expressed Synip ΔWW in 3T3L1 adipocytes reduced the basal levels of Glut4 at the plasma membrane with no effect on the binding to syntaxin 4 in vitro. Subcellular fractionation demonstrated that the amount of Synip ΔWW at the PM was decreased in response to insulin in 3T3L1 adipocytes whereas the amount of Synip WT increased. These data suggest that in the presence of insulin, the dissociated Synip remains anchored to the plasma membrane by binding to PIP3.     

Molecular Dynamics Study of High Temperature Phase-Separation in a H2O/N2 Mixture with Exp-6 Interactions

Abstract

Equimolar H₂O/N₂ fluid mixture was studied by molecular dynamics simulations for NVT ensemble. Calculations were performed with the modified Buckingham (exp-6) potentials at T = 2000 K. Particular attention was given to the phase separation at very high pressures relevant to a detonation environment. Calculations of pair correlation functions and local mole fractions clearly indicated the occurrence of the fluid separation into N₂-rich and H₂O-rich phase. The density at the phase boundary between homogeneous and inhomogeneous phase-separated state was determined to be p = 1.35 g/cm³ on the basis of the static cross correlation factor which is defined by the sum of the local mole fractions. The ratio of the self-diffusion coefficients of N₂ and H₂O at p < 1.35 g/cm³ was found to be approximately equal to the value predicted by the kinetic theory of the ideal gas, whereas the ratio was close to unity at the phase-separated state (p > 1.35 g/cm³). In addition, two distinctive behaviors of the system could be observed for the relaxation from the initial uniform mixture to the phase-separated fluid: at lower densities (1.35 < p < 2.0 g/cm³) the fluid mixture began to relax into the phase-separated system without obvious incubation time, while clear incubation period was associated for the separation at higher densities. During this incubation period, discontinuous jumps in the mean square displacements were found.     

Membrane-anchored ubiquitin ligase complex is required for the turnover of lysosomal membrane proteins

Cells must regulate the abundance and activity of numerous nutrient transporters in different organelle membranes to achieve nutrient homeostasis. As the recycling center and major storage organelle, lysosomes are essential for maintaining nutrient homeostasis. However, very little is known about mechanisms that govern the regulation of its membrane proteins. In this study, we demonstrated that changes of Zn²⁺ levels trigger the downregulation of vacuolar Zn²⁺ transporters. Low Zn²⁺ levels cause the degradation of the influx transporter Cot1, whereas high Zn²⁺ levels trigger the degradation of the efflux channel Zrt3. The degradation process depends on the vacuole membrane recycling and degradation pathway. Unexpectedly, we identified a RING domain–containing E3 ligase Tul1 and its interacting proteins in the Dsc complex that are important for the ubiquitination of Cot1 and partial ubiquitination of Zrt3. Our study demonstrated that the Dsc complex can function at the vacuole to regulate the composition and lifetime of vacuolar membrane proteins.     

An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma

BackgroundFew driver genes have been well established in esophageal squamous cell carcinoma (ESCC). Identification of the genomic aberrations that contribute to changes in gene expression profiles can be used to predict driver genes.MethodsWe searched for driver genes in ESCC by integrative analysis of gene expression microarray profiles and copy number data. To narrow down candidate genes, we performed survival analysis on expression data and tested the genetic vulnerability of each genes using public RNAi screening data. We confirmed the results by performing RNAi experiments and evaluating the clinical relevance of candidate genes in an independent ESCC cohort.ResultsWe found 10 significantly recurrent copy number alterations accompanying gene expression changes, including loci 11q13.2, 7p11.2, 3q26.33, and 17q12, which harbored CCND1, EGFR, SOX2, and ERBB2, respectively. Analysis of survival data and RNAi screening data suggested that GRB7, located on 17q12, was a driver gene in ESCC. In ESCC cell lines harboring 17q12 amplification, knockdown of GRB7 reduced the proliferation, migration, and invasion capacities of cells. Moreover, siRNA targeting GRB7 had a synergistic inhibitory effect when combined with trastuzumab, an anti-ERBB2 antibody. Survival analysis of the independent cohort also showed that high GRB7 expression was associated with poor prognosis in ESCC.ConclusionOur integrative analysis provided important insights into ESCC pathogenesis. We identified GRB7 as a novel ESCC driver gene and potential new therapeutic target.     

Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis

Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation-mimicking SEPT9 mutant rescued these effects. Collectively, this study provides the first global analysis of phosphorylation-mediated processes during infection with an extracellular, diarrheagenic bacterial pathogen.Diarrheagenic E. coli are a major global health burden and cause much morbidity and mortality worldwide. Enteropathogenic E. coli (EPEC)¹ is the causative agent of potentially fatal infantile diarrhea and remains an endemic health threat for children in developing countries. EPEC and the closely related enterohemorrhagic E. coli (EHEC) belong to the group of attaching and effacing (A/E) pathogens that form distinct A/E lesions on the surface of intestinal epithelial cells causing the loss of the characteristic intestinal brush border architecture (1).Upon attachment to intestinal cells, EPEC uses a syringe-like molecular apparatus, the type III secretion system (T3SS), to inject at least 25 unique bacterial effector proteins into the host cell (2–4). Once translocated into mammalian cells, these effectors manipulate a wide range of host signaling pathways, thereby subverting host cell function and promoting virulence (5). The bacterial translocated intimin receptor (Tir) is one of the first and most abundant effectors injected into the host cell: it mediates intimate attachment of EPEC to the enterocyte apical surface via its interaction with the bacterial surface adhesin intimin (6, 7). In concert with other effectors, Tir also provokes an expansive cytoskeletal rearrangement leading to the formation of actin-rich protrusions, termed pedestals, beneath the site of bacterial attachment (8). Besides altering the host cell cytoskeleton, EPEC effectors also manipulate cellular trafficking, host immune response and ion and water homeostasis to cause disease (5). Although significant effort in recent years has led to the identification of multiple key players in both the host and the pathogen, the complex interactions between EPEC and the epithelial host cell, and the underlying molecular mechanisms, are still collectively not well understood.There is increasing evidence that hijacking host post-translational mechanisms such as protein phosphorylation is a key strategy for bacterial pathogens to efficiently subvert host cell function (9) and there are several indications that this may be the case for EPEC. For example, Tir is phosphorylated upon insertion into the host cell membrane and this event plays a role in the rearrangement of the actin cytoskeleton (10). Another EPEC-encoded effector, NleH, contains a functional kinase domain suggesting the potential of directly phosphorylating host cell targets (11). Moreover, the phosphorylation profiles of a few specific host proteins such as cortactin, CT10 regulator of kinase (CRK) adaptors, focal adhesion kinase (FAK) and mitogen-activated protein kinase 1 (MAPK1), as well as alterations in tyrosine phosphorylation of host proteins, are impacted in an EPEC effector-dependent manner (12–18). These are selective observations though. Thus, a more comprehensive, system-level analysis is needed to better understand how and to what extent EPEC hijacks host cell phosphorylation to cause disease.Recent advances in quantitative phosphoproteomics have made it possible to successfully profile the changes in host protein phosphorylation following infection by the invasive, diarrheagenic bacterial pathogens Shigella and Salmonella (19–21). To our knowledge, no such analysis has been reported for a noninvasive, diarrheagenic bacterial pathogen such as EPEC. In this study, we applied a stable isotope labeling by amino acids in cell culture (SILAC)-based (22) quantitative phosphoproteomics approach to assess the impact of EPEC infection on the host cell phosphoproteome. The integration of time course experiments and the use of an EPEC mutant deficient in type III secretion (T3S) provided further insights into the dynamics as well as the effector dependence of these processes. This experimental approach enabled identification of both stable and transient interactions between EPEC bacterial effectors and host proteins. Additional infection studies focusing on a newly identified host target, septin-9, further emphasizes the biological significance of the manipulation of host protein phosphorylation in EPEC pathogenesis.     

Impact of Preexisting Interstitial Lung Disease on Acute,Extensive Radiation Pneumonitis: Retrospective Analysis of Patients with Lung Cancer

IntroductionThis study investigated the clinical characteristics and predictive factors for developing acute extended radiation pneumonitis with a focus on the presence and radiological characteristics of preexisting interstitial lung disease.MethodsOf 1429 irradiations for lung cancer from May 2006 to August 2013, we reviewed 651 irradiations involving the lung field. The presence, compatibility with usual interstitial pneumonia, and occupying area of preexisting interstitial lung disease were retrospectively evaluated by pretreatment computed tomography. Cases of non-infectious, non-cardiogenic, acute respiratory failure with an extended bilateral shadow developing within 30 days after the last irradiation were defined as acute extended radiation pneumonitis.ResultsNine (1.4%) patients developed acute extended radiation pneumonitis a mean of 6.7 days after the last irradiation. Although preexisting interstitial lung disease was found in 13% of patients (84 patients), 78% of patients (7 patients) with acute extended radiation pneumonitis cases had preexisting interstitial lung disease, which resulted in incidences of acute extended radiation pneumonitis of 0.35 and 8.3% in patients without and with preexisting interstitial lung disease, respectively. Multivariate logistic analysis indicated that the presence of preexisting interstitial lung disease (odds ratio = 22.6; 95% confidence interval = 5.29–155; p < 0.001) and performance status (≥2; odds ratio = 4.22; 95% confidence interval = 1.06–20.8; p = 0.049) were significant predictive factors. Further analysis of the 84 patients with preexisting interstitial lung disease revealed that involvement of more than 10% of the lung field was the only independent predictive factor associated with the risk of acute extended radiation pneumonitis (odds ratio = 6.14; 95% confidence interval = 1.0–37.4); p = 0.038).ConclusionsPretreatment computed tomography evaluations of the presence of and area size occupied by preexisting interstitial lung disease should be assessed for safer irradiation of areas involving the lung field.