Massive analysis of cDNA Ends (MACE) and miRNA expression profiling identifies proatherogenic pathways in chronic kidney disease

Epigenetic dysregulation contributes to the high cardiovascular disease burden in chronic kidney disease (CKD) patients. Although microRNAs (miRNAs) are central epigenetic regulators, which substantially affect the development and progression of cardiovascular disease (CVD), no data on miRNA dysregulation in CKD-associated CVD are available until now. We now performed high-throughput miRNA sequencing of peripheral blood mononuclear cells from ten clinically stable hemodialysis (HD) patients and ten healthy controls, which allowed us to identify 182 differentially expressed miRNAs (e.g., miR-21, miR-26b, miR-146b, miR-155). To test biological relevance, we aimed to connect miRNA dysregulation to differential gene expression. Genome-wide gene expression profiling by MACE (Massive Analysis of cDNA Ends) identified 80 genes to be differentially expressed between HD patients and controls, which could be linked to cardiovascular disease (e.g., KLF6, DUSP6, KLF4), to infection / immune disease (e.g., ZFP36, SOCS3, JUND), and to distinct proatherogenic pathways such as the Toll-like receptor signaling pathway (e.g., IL1B, MYD88, TICAM2), the MAPK signaling pathway (e.g., DUSP1, FOS, HSPA1A), and the chemokine signaling pathway (e.g., RHOA, PAK1, CXCL5). Formal interaction network analysis proved biological relevance of miRNA dysregulation, as 68 differentially expressed miRNAs could be connected to 47 reciprocally expressed target genes. Our study is the first comprehensive miRNA analysis in CKD that links dysregulated miRNA expression with differential expression of genes connected to inflammation and CVD. After recent animal data suggested that targeting miRNAs is beneficial in experimental CVD, our data may now spur further research in the field of CKD-associated human CVD.     

METAMORPHOSIS IN THE ARACEAE

In the Araceae, as in many other monocotyledons, the stem undergoes gradual thickening as successive internodes are produced. Along with this primary thickening of the stem, successive foliage leaves will be larger and often more complex. In many species, in addition to these and other gradual changes, there are abrupt changes, metamorphoses, that occur under certain conditions. Some metamorphoses are the result of endogenous cycling (e.g., Syngonium, Rhektophyllum, Philodendron linnaei), some are a response to changes in conditions in the environment, usually the gain or loss of contact with a substrate (e.g., Syngonium, Monstera, Rhodospatha, Philodendron section Pteromischum), and some occur when the plant reaches a certain level of maturity (e.g., Monstera). Some of these latter changes are associated with a transition from monopodial to sympodial growth (e.g., Philodendron, Anthurium). Metamorphosis enhances the developmental plasticity of the Araceae in two distinct ways: it allows for a more complex relationship between size and shape in the development to maturity, and it allows shoots to engage in dispersal activities and developmental holding patterns when conditions are not suitable for development to the adult form and reproduction.     

A systems‐based approach to investigate dose‐ and time‐dependent methylmercury‐induced gene expression response in C57BL/6 mouse embryos undergoing neurulation

BACKGROUND: Aberrations during neurulation due to genetic and/or environmental factors underlie a variety of adverse developmental outcomes, including neural tube defects (NTDs). Methylmercury (MeHg) is a developmental neurotoxicant and teratogen that perturbs a wide range of biological processes/pathways in animal models, including those involved in early gestation (e.g., cell cycle, cell differentiation). Yet, the relationship between these MeHg‐linked effects and changes in gestational development remains unresolved. Specifically, current information lacks mechanistic comparisons across dose or time for MeHg exposure during neurulation. These detailed investigations are crucial for identifying sensitive indicators of toxicity and for risk assessment applications. METHODS: Using a systems‐based toxicogenomic approach, we examined dose‐ and time‐dependent effects of MeHg on gene expression in C57BL/6 mouse embryos during cranial neural tube closure, assessing for significantly altered genes and associated Gene Ontology (GO) biological processes. Using the GO‐based application GO‐Quant, we quantitatively assessed dose‐ and time‐dependent effects on gene expression within enriched GO biological processes impacted by MeHg. RESULTS: We observed MeHg to significantly alter expression of 883 genes, including several genes (e.g., Vangl2, Celsr1, Ptk7, Twist, Tcf7) previously characterized to be crucial for neural tube development. Significantly altered genes were associated with development cell adhesion, cell cycle, and cell differentiation–related GO biological processes. CONCLUSIONS: Our results suggest that MeHg‐induced impacts within these biological processes during gestational development may underlie MeHg‐induced teratogenic and neurodevelopmental toxicity outcomes. Birth Defects Res (Part B) 89:188–200, 2010. © 2010 Wiley‐Liss, Inc.     

Cellular interactions determine neuronal phenotypes in rodent retinal cultures

Progenitor cells isolated from early rat embryo retinas differentiate into phenotypes normally generated early in retinal development (e.g., ganglion cells), whereas progenitors isolated from postnatal retinas differentiate into later-generated retinal cell types (e.g., rod photoreceptors; Reh and Kljavin, J. Neurosci. 9:4179–4189; 1989; Adler and Hatlee, 1989; Science 243:391–393; Sparrow, Hicks, and Barnstable, 1990, Dev. Brain Res. 51:69–84). To determine whether this change in committment is intrinsic to the progenitor cells, or alternatively can be modified by interactions with their developing environment, I co-cultured mouse and rat retinal cells, from different developmental stages, and identified the resulting phenotypes with species-specific and cell class-specific antibodies. I found that the phenotypes into which mouse neuroepithelial cells differentiate depends on the phenotypes of the rat cells that surround them. Retinal precursor cells from embryonic day (E) 10–12 will adopt the rod photoreceptor phenotype only when close to cells expressing this phenotype. By contrast, when the E10–12 retinal progenitor cells are cultured with cells from the cerebral cortex, they differentiate primarily into large multipolar neurons, similar in their morphology and antigen expression to retinal ganglion cells. These results indicate that interactions among the cells of the developing retina are important in the determination of cell fate. © 1992 John Wiley & Sons, Inc.     

Resistance and susceptibility of some wheat lines to bird cherry-oat aphid <Emphasis Type="Italic">Rhopalosiphum padi</Emphasis> (Hemiptera: Aphididae)

Bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most serious pests of cereals, with an almost worldwide distribution. A primary screening test was carried out to gauge the resistance or susceptibility of 40 wheat lines to R. padi, and follow-up experiments were conducted to determine the development and fecundity rates of R. padi on eight lines. The forty wheat lines examined were classified into two major classes and four subclasses: A (e.g., ERWYT 87-1) and B (e.g., ERWYT 87-20, ERWYT 87-11), with the highest average number of aphids 14 days after infestation, subclass C (e.g., ERWYT 88-8, ERWYT 87-6, ERWYT 87-4), with the lowest average number of aphids, and subclass D (e.g., ERWYT 88-12, ERWYT 88-13), with intermediate status. Aphid nymph developmental time and survival both differed among the wheat lines. Differences were also observed in the fecundity of R. padi, the intrinsic rate of increase (r _m), and other parameters among the wheat lines tested. The highest and lowest values of r _m were obtained for ERWYT 87-1 and ERWYT 88-8 (0.36 and 0.26 nymphs/female/day, respectively). Three lines (ERWYT 87-4, ERWYT 87-6, ERWYT 88-8) were relatively resistant to R. padi, which could prove useful in the development of IPM programs for this aphid in wheat fields.     

The DNA methylation profile of activated human natural killer cells

Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., TNFA, LTA, IL13, CSF2). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. BHLHE40 was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.     

Cumulative lifetime maternal stress and epigenome-wide placental DNA methylation in the PRISM cohort

Evolving evidence links maternal stress exposure to changes in placental DNA methylation of specific genes regulating placental function that may have implications for the programming of a host of chronic disorders. Few studies have implemented an epigenome-wide approach. Using the Infinium HumanMethylation450 BeadChip (450K), we investigated epigenome-wide placental DNA methylation in relation to maternal experiences of traumatic and non-traumatic stressors over her lifetime assessed using the Life Stressor Checklist-Revised (LSC-R) survey (n = 207). We found differential DNA methylation at epigenome-wide statistical significance (FDR = 0.05) for 112 CpGs. Additionally, we observed three clusters that exhibited differential methylation in response to high maternal lifetime stress. Enrichment analyses, conducted at an FDR = 0.20, revealed lysine degradation to be the most significant pathway associated with maternal lifetimes stress exposure. Targeted enrichment analyses of the three largest clusters of probes, identified using the gap statistic, were enriched for genes associated with endocytosis (i.e., SMAP1, ANKFY1), tight junctions (i.e., EPB41L4B), and metabolic pathways (i.e., INPP5E, EEF1B2). These pathways, also identified in the top 10 KEGG pathways associated with maternal lifetime stress exposure, play important roles in multiple physiological functions necessary for proper fetal development. Further, two genes were identified to exhibit multiple probes associated with maternal lifetime stress (i.e., ANKFY1, TM6SF1). The methylation status of the probes belonging to each cluster and/or genes exhibiting multiple hits, may play a role in the pathogenesis of adverse health outcomes in children born to mothers with increased lifetime stress exposure.     

Mitochondrial quality control mediated by PINK1 and PRKN: links to iron metabolism and tumor immunity

Mitochondrial quality control is an essential process required to maintain cellular homeostasis and functions. Mutations of PINK1 and PRKN/PARK2 contribute to the risk of Parkinson disease. Our recent findings indicate that depletion of Pink1 and Prkn promotes pancreatic tumorigenesis in KRAS-driven engineered mouse models. Mechanistically, PINK1- and PRKN-mediated autophagic degradation of mitochondrial iron importers (e.g., SLC25A37 and SLC25A28) suppresses pancreatic tumor growth by attenuating mitochondrial iron accumulation, inflammasome activation, HMGB1 release, and subsequent immune checkpoint expression. Consequently, pharmacological or genetic inhibition of mitochondrial iron-dependent signals prolongs animal survival and reverses pancreatic tumor phenotype in vivo. Thus, PINK1- and PRKN-mediated immunometabolism provides new insights into the tumor microenvironment and could be a suitable target for new pancreatic cancer treatments.     

Vying for the control of inflammasomes: The cytosolic frontier of enteric bacterial pathogen–host interactions

Enteric pathogen–host interactions occur at multiple interfaces, including the intestinal epithelium and deeper organs of the immune system. Microbial ligands and activities are detected by host sensors that elicit a range of immune responses. Membrane‐bound toll‐like receptors and cytosolic inflammasome pathways are key signal transducers that trigger the production of pro‐inflammatory molecules, such as cytokines and chemokines, and regulate cell death in response to infection. In recent years, the inflammasomes have emerged as a key frontier in the tussle between bacterial pathogens and the host. Inflammasomes are complexes that activate caspase‐1 and are regulated by related caspases, such as caspase‐11, ‐4, ‐5 and ‐8. Importantly, enteric bacterial pathogens can actively engage or evade inflammasome signalling systems. Extracellular, vacuolar and cytosolic bacteria have developed divergent strategies to subvert inflammasomes. While some pathogens take advantage of inflammasome activation (e.g. Listeria monocytogenes, Helicobacter pylori), others (e.g. E. coli, Salmonella, Shigella, Yersinia sp.) deploy a range of virulence factors, mainly type 3 secretion system effectors, that subvert or inhibit inflammasomes. In this review we focus on inflammasome pathways and their immune functions, and discuss how enteric bacterial pathogens interact with them. These studies have not only shed light on inflammasome‐mediated immunity, but also the exciting area of mammalian cytosolic immune surveillance.     

A hassle a day may keep the doctor away: stress and the augmentation of immune function

Stress may be defined as a sequence of events, that begins witha stimulus (stressor), that is recognized by the brain (stressperception), and which results in the activation of physiologicfight/flight/fright systems within the body (stress response).Many evolutionary selection pressures are stressors, and oneof the primary functions of the brain is to perceive stress,warn the body of danger, and enable an organism to respond.We hypothesized that under acute conditions, just as the stressresponse prepares the cardiovascular and musculoskeletal systemsfor fight or flight, it may also prepare the immune system forchallenges (e.g., wounding) which may be imposed by a stressor(e.g., an aggressor). Initial studies showed that acute (2h)stress induced a significant trafficking of immune cells tothe skin. Since the skin is an organism's major protective barrier,we hypothesized that this leukocyte redistribution may serveto enhance skin immunity during acute stress. We tested thishypothesis using the delayed type hypersensitivity (DTH) reaction,which mediates resistance to various infectious agents, as amodel for skin immune function. Acute stress administered immediatelybefore antigen exposure significantly enhanced skin DTH. Adrenalectomy(ADX) eliminated the stress-induced enhancement of DTH whileadministration of physiological doses of corticosterone and/orepinephrine to ADX animals enhanced skin DTH in the absenceof stress. These studies showed that changes in leukocyte distributionand circulating stress hormones are systemic mediators of theimmunoenhancing effects of acute stress. We recently identifiedgamma interferon as a local cytokine mediator of a stress-inducedimmunoenhancement. Our results suggest that during acute stressthe brain sends preparatory warning signals to the immune systemjust as it does to other fight/flight systems of the body.     

昆虫水平基因转移及其研究进展

水平基因转移(horizontal gene transfer, HGT)是生物体获得遗传信息的方式之一,对生物体进化起重要作用。近年来,越来越多昆虫中的水平基因转移现象被报道,如在鳞翅目(如家蚕、甜菜夜蛾、小菜蛾、斜纹夜蛾)、半翅目(如柑橘粉蚧、烟粉虱)、鞘翅目(如咖啡果小蠹、米象、光肩星天牛)、膜翅目(如金小蜂)、双翅目(如果蝇、白纹伊蚊)等昆虫中广泛存在水平转移基因,且不同的水平转移基因对昆虫的营养合成与共生、吸收与消化、毒素产生与解毒、生长和发育、体色改变等方面有着重要作用。本文结合国内外专家学者的相关报道,就HGT的研究步骤与技术方法、评判HGT发生的方法、昆虫HGT的供体与功能几个方面进行了总结和讨论,以期更加深入地了解水平基因转移现象,为探究水平基因转移的作用机制、理解昆虫的进化、遗传和行为、并将水平基因转移应用到农业生产中为农业害虫的绿色防治提供更多思路。     

VEGFR1 Activity Modulates Myeloid Cell Infiltration in Growing Lung Metastases but Is Not Required for Spontaneous Metastasis Formation

The role of vascular endothelial growth factor receptor 1 (VEGFR1/Flt1) in tumor metastasis remains incompletely characterized. Recent reports suggested that blocking VEGFR1 activity or the interaction with its ligands (VEGF and PlGF) has anti-tumor effects. Moreover, several studies showed that VEGFR1 mediates tumor progression to distant metastasis. All these effects may be exerted indirectly by recruitment of bone marrow-derived cells (BMDCs), such as myeloid cells. We investigated the role of VEGFR1 activity in BMDCs during the pre-metastatic phase, i.e., prior to metastatic nodule formation in mice after surgical removal of the primary tumor. Using pharmacologic blockade or genetic deletion of the tyrosine kinase domain of VEGFR1, we demonstrate that VEGFR1 activity is not required for the infiltration of de novo myeloid BMDCs in the pre-metastatic lungs in two tumor models and in two mouse models. Moreover, in line with emerging clinical observations, we show that blockade of VEGFR1 activity neither prevents nor changes the rate of spontaneous metastasis formation after primary tumor removal. Prevention of metastasis will require further identification and exploration of cellular and molecular pathways that mediate the priming of the metastatic soil.     

Legionella pneumophila-induced suppression of early blastogenic responsiveness of murine spleen cells to specific and nonspecific stimulation in vitro

Legionella pneumophila whole cells, including viable organisms or a killed vaccine, early after injection into mice suppressed the blastogenic responses of mouse spleen cells to both specific (i.e.,Legionella) and nonspecific (i.e., plant mitogen andEschericia coli lipopolysaccharide) stimulators. Mice given injections of sublethal numbers of viableLegionella or of a killed vaccine evidenced 3–4 weeks thereafter a marked increase in blastogenic sensitivity of their spleen cells to theLegionella antigen, either whole cells or soluble antigen, but no increase in responsiveness to nonspecific mitogens (i.e., concanavalin A, phytohemagglutinin, andE. coli lipopolysaccharide) was evident. In contrast, during the first week or so after injection of mice with either viable or killedLegionella, marked suppression of blastogenic responsiveness of spleen cells toLegionella antigens was evident. Concomitant suppression also occurred to concanavalin A and phytohemagglutinin, as well as toE. coli lipopolysaccharide. However, by the second week after injection of the animals with live or killedLegionella, such suppression disappeared. The importance of such early specific suppression of a cellular immune response early after exposure toLegionella antigen, in contrast with the early and sustained rise in specific antibody formation is being further investigated.     

Isolation of EpH4 mammary epithelial cell subpopulations which differ in their morphogenetic properties

Summary EpH4 is a nontumorigenic cell line derived from spontaneously immortalized mouse mammary gland epithelial cells (Fialka et al., 1996). When grown in collagen gels, EpH4 cells give rise to different types of structures, e.g., solid cords or branching tubes. By removing and subsequently dissociating single three-dimensional colonies of defined morphology, we have isolated six clonal subpopulations of EpH4 cells which display distinct morphogenetic properties in collagen gel cultures. Thus, cells from the H₁B clone form branching cords devoid of a central lumen, K₃A₃ cells from cords enclosing small multifocal lumina, and J₃B₁ cells form large cavitary structures containing a wide lumen. I₃G₂ cells form either cords or tubes, depending on the type of serum added to the culture medium. Finally, when grown in serum-free medium, Be1a cells form spherical cysts, whereas Be4a cells form long, extensively branched tubes. In additional assays of morphogenesis, i.e., cell sandwiching between two collagen gels or culture on a thick layer of Matrigel (a laminin-rich extracellular matrix), all clones form epithelial-cell-lined cavitary structures, except H₁B cells which are unable to generate lumina under these conditions. The EpH4 sublines we have isolated provide an in vitro system for studying the mechanisms responsible for lumen formation and branching morphogenesis, as well as for identifying the factors which subvert these developmental processes during mammary carcinogenesis.     

Spirochete round bodies Syphilis, Lyme disease & AIDS: Resurgence of “the great imitator”?

We advocate investigation of spirochete cyclical symbioses (e.g.,Borrelia sp.,Leptospira sp., Treponema sp.) given the newly established verification of a developmental history in these gram-negative motile helical eubacteria, both in pure culture and in mammals. Symbiotic spirochetes can be compared to free-living relatives for their levels of integration (behavioral, metabolic, gene product or genetic levels), Detailed research that correlates life histories of symbiotic spirochetes to changes in the immune system of associated vertebrates is sorely needed. Genome analyses show that in necrotrophic symbioses (Borrelia andTreponema sp.) of humans and other primates, integration of the bionts occurs at the gene product and genetic level. Spirochete round bodies (also called cysts, L-forms and sphaeroplasts) can be induced by many types of unfavorable conditions (e.g., threats of starvation, desiccation, oxidation, penicillin and other antibiotics). Reversion to familiar helical, motile active swimmers by placement of pure cultures into favorable environments in some cases can be controlled. These observations are supported by a European literature, especially Russian, apparently unknown to American medicine and medical research.