Oxygen gradients can determine epigenetic asymmetry and cellular differentiation via differential regulation of Tet activity in embryonic stem cells.

Graded levels of molecular oxygen (O2) exist within developing mammalian embryos and can differentially regulate cellular specification pathways. During differentiation, cells acquire distinct epigenetic landscapes, which determine their function, however the mechanisms which regulate this are poorly understood. The demethylation of 5-methylcytosine (5mC) is achieved via successive oxidation reactions catalysed by the Ten-Eleven-Translocation (Tet) enzymes, yielding the 5-hydroxymethylcytosine (5hmC) intermediate. These require O2 as a co-factor, and hence may link epigenetic processes directly to O2 gradients during development. We demonstrate that the activities of Tet enzymes display distinct patterns of [O2]-dependency, and that Tet1 activity, specifically, is subject to differential regulation within a range of O2 which is physiologically relevant in embryogenesis. Further, differentiating embryonic stem cells displayed a transient burst of 5hmC, which was both dependent upon Tet1 and inhibited by low (1%) [O2]. A GC-rich promoter region within the Tet3 locus was identified as a significant target of this 5mC-hydroxylation. Further, this region was shown to associate with Tet1, and display the histone epigenetic marks, H3K4me3 and H3K27me3, which are characteristic of a bivalent, developmentally 'poised' promoter. We conclude that Tet1 activity, determined by [O2] may play a critical role in regulating cellular differentiation and fate in embryogenesis.

Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126.

Chemical pollutant exposure is a risk factor contributing to the growing epidemic of non-alcoholic fatty liver disease (NAFLD) affecting human populations that consume a western diet. Although it is recognized that intoxication by chemical pollutants can lead to NAFLD, there is limited information available regarding the mechanism by which typical environmental levels of exposure can contribute to the onset of this disease. Here, we describe the alterations in gene expression profiles and metabolite levels in the human HepaRG liver cell line, a validated model for cellular steatosis, exposed to the polychlorinated biphenyl (PCB) 126, one of the most potent chemical pollutants that can induce NAFLD. Sparse partial least squares classification of the molecular profiles revealed that exposure to PCB 126 provoked a decrease in polyunsaturated fatty acids as well as an increase in sphingolipid levels, concomitant with a decrease in the activity of genes involved in lipid metabolism. This was associated with an increased oxidative stress reflected by marked disturbances in taurine metabolism. A gene ontology analysis showed hallmarks of an activation of the AhR receptor by dioxin-like compounds. These changes in metabolome and transcriptome profiles were observed even at the lowest concentration (100 pM) of PCB 126 tested. A decrease in docosatrienoate levels was the most sensitive biomarker. Overall, our integrated multi-omics analysis provides mechanistic insight into how this class of chemical pollutant can cause NAFLD. Our study lays the foundation for the development of molecular signatures of toxic effects of chemicals causing fatty liver diseases to move away from a chemical risk assessment based on in vivo animal experiments.

A novel human IgA monoclonal antibody protects against tuberculosis.

Abs have been shown to be protective in passive immunotherapy of tuberculous infection using mouse experimental models. In this study, we report on the properties of a novel human IgA1, constructed using a single-chain variable fragment clone (2E9), selected from an Ab phage library. The purified Ab monomer revealed high binding affinities for the mycobacterial α-crystallin Ag and for the human FcαRI (CD89) IgA receptor. Intranasal inoculations with 2E9IgA1 and recombinant mouse IFN-γ significantly inhibited pulmonary H37Rv infection in mice transgenic for human CD89 but not in CD89-negative littermate controls, suggesting that binding to CD89 was necessary for the IgA-imparted passive protection. 2E9IgA1 added to human whole-blood or monocyte cultures inhibited luciferase-tagged H37Rv infection although not for all tested blood donors. Inhibition by 2E9IgA1 was synergistic with human rIFN-γ in cultures of purified human monocytes but not in whole-blood cultures. The demonstration of the mandatory role of FcαRI (CD89) for human IgA-mediated protection is important for understanding of the mechanisms involved and also for translation of this approach toward development of passive immunotherapy of tuberculosis.

Cytokine interactions that determine the outcome of Mycobacterial infection of macrophages.

Macrophages are the target cells for mycobacterial infections. They are also largely responsible for intracellular killing of mycobacteria, which is dependent on the cytokine environment. Interferon-gamma (IFN-gamma) is chiefly responsible for macrophage activation and bactericidal capacity while Th2 cytokines have a contrasting effect. However, cytokines rarely act in isolation during an infection. Instead, multiple cytokines, both activating and inhibitory, are present and their concentration levels and mutual interactions are likely to determine the ultimate outcome of an infection. Here, we used an in vitro infection model of mouse macrophages to study the effect of cytokine interactions on the infection with Mycobacterium bovis strain BCG. We measured nitric oxide (NO) production and bacterial survival in cells following stimulation with various combinations of cytokines. The surprising finding was that high concentrations of IL-10 (i.e., above 16.5 ng/ml), which is generally considered to be a macrophage-suppressive cytokine, enhanced IFN-gamma-induced NO production. Furthermore, the simultaneous addition of either of the two Th2 cytokines IL-4 or IL-13, strongly inhibited IFN-gamma-mediated NO production and bacterial killing even at a low concentration of 0.62 ng/ml, but could not reverse the synergistic action of IFN-gamma and TNF-alpha, even when the Th2 cytokines were present at high concentrations (i.e., 50 ng/ml). Therefore, macrophage activity is heavily dependent on the cytokine micro-environment where the final outcome is determined in equal measures by the nature of cytokines present, the timing of their accumulation and their concentration levels.

Editor's Highlight: Transcriptome Profiling Reveals Bisphenol A Alternatives Activate Estrogen Receptor Alpha in Human Breast Cancer Cells.

Plasticizers with estrogenic activity, such as bisphenol A (BPA), have potential adverse health effects in humans. Due to mounting evidence of these health effects, BPA is being phased out and replaced by other bisphenol variants in "BPA-free" products. We have compared estrogenic activity of BPA with 6 bisphenol analogues [bisphenol S (BPS); bisphenol F (BPF); bisphenol AP (BPAP); bisphenol AF (BPAF); bisphenol Z (BPZ); bisphenol B (BPB)] in 3 human breast cancer cell lines. Estrogenicity was assessed (10-11-10-4 M) by cell growth in an estrogen receptor (ER)-mediated cell proliferation assay, and by the induction of estrogen response element-mediated transcription in a luciferase assay. BPAF was the most potent bisphenol, followed by BPB > BPZ ∼ BPA > BPF ∼ BPAP > BPS. The addition of ICI 182,780 antagonized the activation of ERs. Data mining of ToxCast high-throughput screening assays confirm our results but also show divergence in the sensitivities of the assays. Gene expression profiles were determined in MCF-7 cells by microarray analysis. The comparison of transcriptome profile alterations resulting from BPA alternatives with an ERα gene expression biomarker further indicates that all BPA alternatives act as ERα agonists in MCF-7 cells. These results were confirmed by Illumina-based RNA sequencing. In conclusion, BPA alternatives are not necessarily less estrogenic than BPA in human breast cancer cells. BPAF, BPB, and BPZ were more estrogenic than BPA. These findings point to the importance of better understanding the risk of adverse effects from exposure to BPA alternatives, including hormone-dependent breast cancer.

Evaluation of estrogen receptor alpha activation by glyphosate-based herbicide constituents.

The safety, including the endocrine disruptive capability, of glyphosate-based herbicides (GBHs) is a matter of intense debate. We evaluated the estrogenic potential of glyphosate, commercial GBHs and polyethoxylated tallowamine adjuvants present as co-formulants in GBHs. Glyphosate (≥10,000 µg/L or 59 µM) promoted proliferation of estrogen-dependent MCF-7 human breast cancer cells. Glyphosate also increased the expression of an estrogen response element-luciferase reporter gene (ERE-luc) in T47D-KBluc cells, which was blocked by the estrogen antagonist ICI 182,780. Commercial GBH formulations or their adjuvants alone did not exhibit estrogenic effects in either assay. Transcriptomics analysis of MCF-7 cells treated with glyphosate revealed changes in gene expression reflective of hormone-induced cell proliferation but did not overlap with an ERα gene expression biomarker. Calculation of glyphosate binding energy to ERα predicts a weak and unstable interaction (-4.10 kcal mol-1) compared to estradiol (-25.79 kcal mol-1), which suggests that activation of this receptor by glyphosate is via a ligand-independent mechanism. Induction of ERE-luc expression by the PKA signalling activator IBMX shows that ERE-luc is responsive to ligand-independent activation, suggesting a possible mechanism of glyphosate-mediated activation. Our study reveals that glyphosate, but not other components present in GBHs, can activate ERα in vitro, albeit at relatively high concentrations.

Infectious bursal disease virus: strains that differ in virulence differentially modulate the innate immune response to infection in the chicken bursa.

Little is understood about the immune responses involved in the pathogenesis of infectious bursal disease virus (IBDV). Strains of IBDV differ in their virulence: F52/70 is a classical virulent strain (vIBDV), whereas UK661 is a very virulent strain (vvIBDV) that causes greater pathology and earlier mortality. The exact causes of clinical disease and death are still unclear. Pro-inflammatory cytokines such as interleukin (IL)-1beta and IL-6, produced by activated macrophages, could play a role, as could cytokines produced by T and natural killer (NK) cells, such as interferon (IFN)-gamma, which stimulate macrophages. We quantified mRNA transcription in bursal tissue, by real-time quantitative reverse transcription- polymerase chain reaction (RT-PCR), for the type I IFN (IFN-alpha and IFN-beta), pro-inflammatory cytokines (IL-1beta, IL-6, and CXCLi2), the anti-inflammatory cytokine transforming growth factor (TGF)-beta4, and Th1 cytokines (IFN-gamma, IL-2 [and the closely related IL-15], IL-12, and IL-18) for the first 5 days after infection of 3-week-old chickens with F52/70 or UK661 and compared these with levels in bursal tissue from uninfected age-matched controls. Both strains induced a pro-inflammatory response, evidenced by increased mRNA transcription of IL-1beta, IL-6, and CXCLi2, and down-regulation of TGF-beta4, of similar magnitude and timing. IFN-gamma mRNA was induced by both strains, although to a greater degree by the vvIBDV strain, indicating that a cell-mediated response is induced. Neither virus initially induced high levels of type I IFN. F52/70 seems to use a "stealth" approach by not inducing the type I IFNs, whereas UK661 down-regulates their expression. This suggests that both viruses modulate the host immune response, although probably by using different mechanisms.

A genomic analysis of chicken cytokines and chemokines.

As most mechanisms of adaptive immunity evolved during the divergence of vertebrates, the immune systems of extant vertebrates represent different successful variations on the themes initiated in their earliest common ancestors. The genes involved in elaborating these mechanisms have been subject to exceptional selective pressures in an arms race with highly adaptable pathogens, resulting in highly divergent sequences of orthologous genes and the gain and loss of members of gene families as different species find different solutions to the challenge of infection. Consequently, it has been difficult to transfer to the chicken detailed knowledge of the molecular mechanisms of the mammalian immune system and, thus, to enhance the already significant contribution of chickens toward understanding the evolution of immunity. The availability of the chicken genome sequence provides the opportunity to resolve outstanding questions concerning which molecular components of the immune system are shared between mammals and birds and which represent their unique evolutionary solutions. We have integrated genome data with existing knowledge to make a new comparative census of members of cytokine and chemokine gene families, distinguishing the core set of molecules likely to be common to all higher vertebrates from those particular to these 300 million-year-old lineages. Some differences can be explained by the different architectures of the mammalian and avian immune systems. Chickens lack lymph nodes and also the genes for the lymphotoxins and lymphotoxin receptors. The lack of functional eosinophils correlates with the absence of the eotaxin genes and our previously reported observation that interleukin- 5 (IL-5) is a pseudogene. To summarize, in the chicken genome, we can identify the genes for 23 ILs, 8 type I interferons (IFNs), IFN-gamma, 1 colony-stimulating factor (GM-CSF), 2 of the 3 known transforming growth factors (TGFs), 24 chemokines (1 XCL, 14 CCL, 8 CXCL, and 1 CX3CL), and 10 tumor necrosis factor superfamily (TNFSF) members. Receptor genes present in the genome suggest the likely presence of 2 other ILs, 1 other CSF, and 2 other TNFSF members.

Avian interleukin-12beta (p40): cloning and characterization of the cDNA and gene.

We isolated the chicken interleukin-12 (ChIL-12) p40 cDNA from a concanavalin A (ConA)-stimulated spleen cDNA library using the PCR with primers based on a partial 3' EST sequence in a chicken EST library. The cDNA encodes a polypeptide of 315 amino acids (aa), with a predicted mature peptide of 300 aa. ChIL-12 p40 has 46% and 41% amino acid identity with human (HuIL-12) and murine IL-12 (MuIL-12) p40, respectively. We also isolated a partial turkey IL-12 (TuIL-12) p40 cDNA sequence with 95% predicted aa identity with ChIL-12 p40. The structures of the ChIL-12 p40 gene and its promoter were determined by direct sequencing of a chicken BAC identified by hybridization with the cDNA. The gene structures of HuIL-12, MuIL-12, and ChIL-12 p40 all differ. The promoter of the ChIL-12 p40 gene shares some (an ETS consensus sequence, a C/EBP binding site, and a TATA box) but not all (an NF-kappaB binding site and a GA12 site are absent) of the transcription factor binding sites identified in the human and murine promoters. IL-12 p40 mRNA expression was identified in a wide variety of tissues and in B, T, and macrophage cell lines by RT-PCR.

Evolution of the interleukins.

As the adaptive immune system arose in jawed vertebrates, a reasonable working hypothesis is that cytokines involved exclusively in controlling the adaptive immune system, e.g. T1 and T2 cytokines, will only be found in jawed vertebrates whilst those with a role in innate responses, e.g. type I IFNs or pro-inflammatory cytokines, will be universal, or have functional equivalents in 'lower' animals. Progress to date in cloning cytokines, including interleukins, in vertebrates outside of mammals is limited and non-existent in invertebrates. T1 and T2 interleukins have only been cloned in birds. Receptors for T1 and T2 interleukins have been cloned in fish, however, suggesting the presence of the corresponding interleukins. Pro-inflammatory interleukins have been cloned in birds, fish and amphibia, but not reptiles. Cross-reactive bioassays, polyclonal antisera and mAbs suggest that an IL-6-like factor exists in starfish, as yet the only evidence for innate immune response cytokines in 'lower' animals.