Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome.

Forkhead box G1 (FOXG1) has important functions in neuronal differentiation and balances excitatory/inhibitory network activity. Thus far, molecular processes underlying FOXG1 function are largely unexplored. Here, we present a multiomics data set exploring how FOXG1 impacts neuronal maturation at the chromatin level in the mouse hippocampus. At a genome-wide level, FOXG1 i) both represses and activates transcription, ii) binds mainly to enhancer regions, iii) reconfigures the epigenetic landscape through bidirectional alteration of H3K27ac, H3K4me3, and chromatin accessibility, and iv) operates synergistically with NEUROD1. Interestingly, we could not detect a clear hierarchy of FOXG1 and NEUROD1, but instead, provide the evidence that they act in a highly cooperative manner to control neuronal maturation. Genes affected by the chromatin alterations impact synaptogenesis and axonogenesis. Inhibition of histone deacetylases partially rescues transcriptional alterations upon FOXG1 reduction. This integrated multiomics view of changes upon FOXG1 reduction reveals an unprecedented multimodality of FOXG1 functions converging on neuronal maturation. It fuels therapeutic options based on epigenetic drugs to alleviate, at least in part, neuronal dysfunction.

General Stereodivergent Enantioselective Total Synthetic Approach toward Macrosphelides A-G and M.

A straightforward enantioselective total synthesis algorithm for the preparation of 8 out of 13 macrosphelides within 9-11 steps starting from tert-butyl sorbate is presented. The use of a cyclic sulfate as both protecting and reactivity directing group is the key element within this algorithm. A high-pressure transesterification allows for the selective ring-enlargement of the 15-membered macrosphelides into the 16-membered counterparts. The absolute configurations of the natural products were unambiguously assigned both by the chemical synthesis and by X-ray structure analysis.

Histone methylation during neural development.

Post-translational modification of histone proteins, such as the methylation of lysine and arginine residues, influences the higher order of chromatin and leads to gene activation or silencing. Histone methyltransferases or demethylases actively add or remove various methylation marks in a cell-type-specific and context-dependent way. They are therefore important players in regulating the transcriptional program of a cell. Some control of the various cellular programs is necessary during the differentiation of stem cells along a specific lineage, when differentiation to alternative lineages needs to be suppressed. One example is the development of neurons from neural stem cells during neurogenesis. Neurogenesis is a highly organized process that requires the proper coordination of survival, proliferation, differentiation and migration signals. This holds true for both embryonic and neural stem cells that give rise to the various cell types of the central nervous system. The control of embryonic and neural stem cell self-renewal and differentiation is achieved by both extrinsic and intrinsic signals that regulate gene expression precisely. Recent advances in neuroscience support the importance of epigenetic modifications, such as the methylation and acetylation of histones, as an important intrinsic mechanism for the regulation of central nervous system development. This review summarizes our current knowledge of histone methylation processes during neural development and provides insights into the function of histone methylation enzymes and their role during central nervous system development.

Nuclear factor kappaB-dependent gene expression profiling of Hodgkin's disease tumor cells, pathogenetic significance, and link to constitutive signal transducer and activator of transcription 5a activity.

Constitutive nuclear nuclear factor (NF)-kappaB activity is observed in a variety of hematopoietic and solid tumors. Given the distinctive role of constitutive NF-kappaB for Hodgkin and Reed-Sternberg (HRS) cell viability, we performed molecular profiling in two Hodgkin's disease (HD) cell lines to identify NF-kappaB target genes. We recognized 45 genes whose expression in both cell lines was regulated by NF-kappaB. The NF-kappaB-dependent gene profile comprises chemokines, cytokines, receptors, apoptotic regulators, intracellular signaling molecules, and transcription factors, the majority of which maintain a marker-like expression in HRS cells. Remarkably, we found 17 novel NF-kappaB target genes. Using chromatin immunoprecipitation we demonstrate that NF-kappaB is recruited directly to the promoters of several target genes, including signal transducer and activator of transcription (STAT)5a, interleukin-13, and CC chemokine receptor 7. Intriguingly, NF-kappaB positively regulates STAT5a expression and signaling pathways in HRS cells, and promotes its persistent activation. In fact, STAT5a overexpression was found in most tumor cells of tested patients with classical HD, indicating a critical role for HD. The gene profile underscores a central role of NF-kappaB in the pathogenesis of HD and potentially of other tumors with constitutive NF-kappaB activation.

ZFP36L1 is regulated by growth factors and cytokines in keratinocytes and influences their VEGF production.

Keratinocyte-derived growth factors and cytokines play an important role in epidermal homeostasis and particularly in cutaneous wound repair. Thus, we analyzed a potential role of the ZFP36/tristetraprolin family of zinc finger proteins, which are targets of these factors, but also regulate their production, in keratinocytes. We show that expression of ZFP36, ZFP36L1, and ZFP36L2 is induced by a broad variety of growth factors and cytokines, and by scratch wounding. Since ZFP36L1 is a modulator of vascular endothelium growth factor (VEGF) mRNA stability, we subsequently used siRNA technology to inhibit ZFP36L1 gene expression. Notably, this treatment resulted in prolonged maintenance of elevated VEGF levels in HaCaT keratinocytes upon epidermal growth factor stimulation of these cells. Taken together, our results suggest an important role of ZFP36L1 in wound healing.

Pluripotency associated genes are reactivated by chromatin-modifying agents in neurosphere cells.

Chromatin architecture in stem cells determines the pattern of gene expression and thereby cell identity and fate. The chromatin-modifying agents trichostatin A (TSA) and 5-Aza-2'-deoxycytidine (AzaC) affect histone acetylation and DNA methylation, respectively, and thereby influence chromatin structure and gene expression. In our previous work, we demonstrated that TSA/AzaC treatment of neurosphere cells induces hematopoietic activity in vivo that is long-term, multilineage, and transplantable. Here, we have analyzed the TSA/AzaC-induced changes in gene expression by global gene expression profiling. TSA/AzaC caused both up- and downregulation of genes, without increasing the total number of expressed genes. Chromosome analysis showed no hot spot of TSA/AzaC impact on a particular chromosome or chromosomal region. Hierarchical cluster analysis revealed common gene expression patterns among neurosphere cells treated with TSA/AzaC, embryonic stem (ES) cells, and hematopoietic stem cells. Furthermore, our analysis identified several stem cell genes and pluripotency-associated genes that are induced by TSA/AzaC in neurosphere cells, including Cd34, Cd133, Oct4, Nanog, Klf4, Bex1, and the Dppa family members Dppa2, 3, 4, and 5. Sox2 and c-Myc are constitutively expressed in neurosphere cells. We propose a model in which TSA/AzaC, by removal of epigenetic inhibition, induces the reactivation of several stem cell and pluripotency-associated genes, and their coordinate expression enlarges the differentiation potential of somatic precursor cells.

Strong induction of the Tis11B gene in myogenic differentiation.

TIS11B is a zinc-finger protein of the tristetraprolin (TTP) family. Using cDNA microarray analysis, we could identify the Tis11B gene based on its differential expression in myogenesis. Here, we demonstrate that expression of the Tis11B gene is strongly induced during differentiation of the murine myoblast cell line C2C12. By contrast, expression of Ttp itself was not induced in myogenesis. Pretreatment of the cells with the translation inhibitor cycloheximide demonstrated that Tis11B was a primary response gene in this process. In addition, pretreatment with the transcription inhibitor actinomycin D demonstrated that gene expression was regulated at the transcriptional level. Since specific inhibitors of p38 MAP kinase completely blocked Tis11B induction, we conclude that expression of the Tis11B gene is regulated at least in part by this signaling pathway which plays a central role in myogenesis. Induction of Tis11B expression was also observed in primary myoblasts isolated from two different mouse strains, indicating physiological relevance of our results. In addition, TIS11B might also be an important player during myogenic differentiation and regeneration in vivo, as we detected a marked decrease in expression in several muscle tissues of the dystrophic mdx mouse, a model for continuous muscle degeneration and regeneration. These data suggest that TIS11B is an important regulator of myogenesis.

Parallel processing of objects in a naming task.

The authors investigated whether speakers who named several objects processed them sequentially or in parallel. Speakers named object triplets, arranged in a triangle, in the order left, right, and bottom object. The left object was easy or difficult to identify and name. During the saccade from the left to the right object, the right object shown at trial onset (the interloper) was replaced by a new object (the target), which the speakers named. Interloper and target were identical or unrelated objects, or they were conceptually unrelated objects with the same name (e.g., bat [animal] and [baseball] bat). The mean duration of the gazes to the target was shorter when interloper and target were identical or had the same name than when they were unrelated. The facilitatory effects of identical and homophonous interlopers were significantly larger when the left object was easy to process than when it was difficult to process. This interaction demonstrates that the speakers processed the left and right objects in parallel.

Towards determining the differentiation program of antigen-presenting dendritic cells by transcriptional profiling.

Dendritic cells (DC) represent professional antigen-presenting cells that develop from hematopoietic progenitors through successive steps of differentiation. Employing DNA microarray technology, we analysed the specific changes in gene expression that occur when human progenitor cells differentiate into DC. CD34 progenitor cells were first amplified in vitro with stem cell factor (SCF), Flt3 ligand (FL), thrombopoietin and IL-6/soluble IL-6 receptor fusion protein, and cells were then induced to differentiate into DC with IL-4 and GM-CSF. DC maturation was induced by TNFalpha. Progenitor cells and DC were subjected to transcriptional profiling by DNA microarrays that represent 13000 human genes. Our analysis revealed specific changes in the expression of a large number of cell surface antigens including molecules involved in antigen uptake and processing, cell migration and antigen presentation. Genes encoding such molecules were upregulated during DC differentiation as were genes encoding cytokines, cytokine receptors, chemokines and chemokine receptors. Stem cell genes and genes related to the multilineage differentiation potential and proliferative state of progenitor cells were downregulated. Our analysis also provides information on the expression profiles of transcriptional regulators such as the NF-kappaB/rel and STAT transcription factors. Interestingly, NF-kappaB/rel factors were found to be expressed in both progenitor cells and DC at similar levels and were induced by TNFalpha. In contrast, expression of STAT factors increased during DC differentiation and their expression was virtually unaffected by TNFalpha.

Immunoglobulin-like transcripts ILT2, ILT3 and ILT7 are expressed by human dendritic cells and down-regulated following activation.

Immunoglobulin-like transcripts (ILT) represent novel immunoglobulin superfamily receptors that are expressed in myeloid, lymphoid and dendritic cells (DC). Here, we studied by gene expression profiling with DNA microarrays ILT expression in different DC subsets, including plasmacytoid DC (PDC), monocyte-derived DC (Mo-DC) and DC obtained by in vitro differentiation from CD34(+) progenitor cells, and DC activated in the presence of different activating agents. ILT2 and ILT3 were expressed in PDC, Mo-DC and DC obtained from CD34(+) cells. ILT7 mRNA was present in PDC, but absent in Mo-DC and DC obtained from CD34(+) cells, indicating that ILT7 mRNA expression seems to be a marker for PDC. CpG-DNA and inflammatory stimuli, such as TNF alpha, prostaglandin E2 (PGE2) and soluble CD40 ligand (sCD40L), and different combinations thereof are frequently employed for DC activation. Here, we demonstrate that ILT2 and ILT3 expression is down-regulated following DC activation by CpG-DNA and inflammatory stimuli at both mRNA and protein levels. Thus, activation of human DC with such stimuli involves down-regulation of inhibitory ILT2 and ILT3 receptors, and this could represent a novel mechanism contributing to DC activation.

Enantioselective synthesis of anti-ß-hydroxy-α-amido esters via transfer hydrogenation.

The asymmetric transfer hydrogenation of α-amido-ß-keto esters to provide the corresponding anti-ß-hydroxy-α-amido esters in good to excellent yields, diastereoselectivity, and enantioselectivity is reported. The procedure is operationally simple, and delicate handling of the catalyst is not necessary.

GAR22: a novel target gene of thyroid hormone receptor causes growth inhibition in human erythroid cells.

OBJECTIVE: Thyroid hormone receptors (TRs) are ligand-dependent transcription factors with a major impact on erythroid cell development. Here we investigated TR activity on red cell gene expression and identified TR target genes. The impact of the TR target gene GAR22 (growth arrest-specific 2 [GAS2]-related gene on chromosome 22) on red cell differentiation was determined. MATERIALS AND METHODS: Stem cell factor/erythropoietin (SCF/EPO)-dependent red cell progenitors were differentiated in vitro in the presence or absence of thyroid hormone. Hormone-induced changes in gene expression were measured by a genome-wide approach with DNA microarrays. Ectopic expression of the TR target gene GAR22 was used to determine its impact on red cell differentiation. RESULTS: Ligand-activated TR effectively accelerated red cell progenitor differentiation in vitro concomitantly with inducing growth arrest. We demonstrate that activated TR-induced specific gene expression patterns of up- or downregulated genes, including distinct clusters associated with accelerated differentiation in response to treatment. Mining for T3-induced genes identified basic transcription element binding protein 1/Krüppel-like factor 9 (BTEB1/KLF9) and GAR22 as TR target genes. BTEB1/KLF9 is a known TR target gene while GAR22, initially identified as a putative tumor suppressor, represents a novel TR target gene. We demonstrate that ectopic GAR22 expression in red cell progenitors lengthens the cell cycle and causes growth inhibition, but leaves red cell gene expression unaffected. CONCLUSION: This study identifies GAR22 as a novel and direct TR target gene. Our results suggest that hormone-induced GAR22 might represent an important trigger of growth inhibition induced by thyroid hormone in red cell progenitors.

Infection of mature dendritic cells with herpes simplex virus type 1 dramatically reduces lymphoid chemokine-mediated migration.

Herpes simplex virus type 1 (HSV-1) is able to establish latency in infected individuals. In order to characterize potential new immune-escape mechanisms, mature dendritic cells (DCs) were infected with HSV-1 and total cellular RNA was isolated from infected and mock-infected populations at different time points. RNA profiling on Affymetrix Human Genome U133A arrays demonstrated a dramatic downregulation of the migration-mediating surface molecules CCR7 and CXCR4, an observation that was further confirmed by RT-PCR and fluorescence-activated cell sorting analyses. Furthermore, migration assays revealed that, upon infection of mature DCs, CCR7- and CXCR4-mediated migration towards the corresponding CCL19 and CXCL12 chemokine gradients was strongly reduced. It is noteworthy that the infection of immature DCs with HSV-1 prior to maturation led to a failure of CCR7 and CXCR4 upregulation during DC maturation and, as a consequence, also induced a block in their migratory capacity. Additional migration assays with a Deltavhs mutant virus lacking the virion host shutoff (vhs) gene, which is known to degrade cellular mRNAs, suggested a vhs-independent mechanism. These results indicate that HSV-1-infected mature DCs are limited in their capacity to migrate to secondary lymphoid organs, the areas of antigen presentation and T-cell stimulation, thus inhibiting an antiviral immune response. This represents a novel, previously unrecognized mechanism for HSV-1 to escape the human immune system.

Transcriptional profiling identifies Id2 function in dendritic cell development.

Dendritic cells (DCs) are potent antigen-presenting cells with a pivotal role in antigen-specific immune responses. Here, we found that the helix-loop-helix transcription factor Id2 is up-regulated during DC development in vitro and crucial for the development of distinct DC subsets in vivo. Id2-/- mice lack Langerhans cells (LCs), the cutaneous contingent of DCs, and the splenic CD8alpha+ DC subset is markedly reduced. Mice deficient for transforming growth factor (TGF)-beta also lack LCs, and we demonstrate here that, in DCs, TGF-beta induces Id2 expression. We also show that Id2 represses B cell genes in DCs. These findings reveal a TGF-beta-Id2 signaling pathway in DCs and suggest a mechanism by which Id2 affects the lineage choice of B cell and DC progenitors.