Cell Type-specific Differences Research Articles

An agonist of Toll-like receptor 5 sustains hepatic natural killer and dendritic cell recruitment to the liver while eliciting anti-cancer effects against liver metastases (P2110)

Abstract Toll-like receptors (TLRs) are key components of innate immunity that act as sensors of conserved microbial patterns. To elucidate the mechanisms behind differences in physiological responses mediated by different TLRs, we compared tissue specificity of NF-κB activation in mice by agonists of three cell-surface TLRs: TLR5 agonist CBLB502, a pharmacologically optimized Salmonella flagellin derivative; TLR4 agonist, LPS; and TLR2/6 agonist CBLB612, a mycoplasma lipopeptide mimic. While the liver was defined as a major primary target organ of all three TLR agonists, the cellular response to each agonist was distinct. Thus, liver hepatocytes directly respond to TLR5 and TLR2/6 but not to TLR4, while Kupffer macrophages respond to TLR2/6 and TLR4 but not to TLR5 agonists. Mobilization of NK and DCs to the liver was transient (<24 h) in response to CBLB612 and LPS and sustained (>120 h) following CBLB502 administration. Differences in the liver innate immune response to these three TLR agonists are likely a reflection of cell type-specific expression and differences in molecular mechanisms triggered by different TLRs. Durable hepatic NK cell response by CBLB502 elicits strong TLR5 agonist-dependent effects against colon and breast cancer liver metastases. These long-lasting, TLR5-mediated changes within the liver provide important groundwork for further clinical development of CBLB502, which is currently in clinical trials as a potential radioprotector and immunotherapeutic agent.

Differential dendritic targeting of AMPA receptor subunit mRNAs in adult rat hippocampal principal neurons and interneurons

In hippocampal neurons, AMPA receptors (AMPARs) mediate fast excitatory postsynaptic responses at glutamatergic synapses, and are involved in various forms of synaptic plasticity. Dendritic local protein synthesis of selected AMPAR subunit mRNAs is considered an additional mechanism to independently and rapidly control the strength of individual synapses. We have used fluorescent in situ hybridization and immunocytochemistry to analyze the localization of AMPAR subunit (GluA1-4) mRNAs and their relationship with the translation machinery in principal cells and interneurons of the adult rat hippocampus. The mRNAs encoding all four AMPAR subunits were detected in the somata and dendrites of CA3 and CA1 pyramidal cells and those of six classes of CA1 γ-aminobutyric acid (GABA)ergic interneurons. GluA1-4 subunit mRNAs were highly localized to the apical dendrites of pyramidal cells, whereas in interneurons they were present in multiple dendrites. In contrast, in the dentate gyrus, GluA1-4 subunit mRNAs were virtually restricted to the somata and were absent from the dendrites of granule cells. These different regional and cell type-specific labeling patterns also correlated with the localization of markers for components of the protein synthesis machinery. Our results support the local translation of GluA1-4 mRNAs in dendrites of hippocampal pyramidal cells and CA1 interneurons but not in granule cells of the dentate gyrus. Furthermore, the regional and cell type-specific differences we observed suggest that each cell type uses distinct ways of regulating the local translation of AMPAR subunits.

Abstract 3524: Functional characterization of KIT and FcεR1 receptor mutations in Mast Cell Leukemia using Single Cell Network Profiling (SCNP).

Abstract Background: A recent report described an imatinib/dasatinib (Imat/Dasat) resistant MCL patient (pt) with mutations in KIT (V654A) and FcεR1 (L188F) receptors [Spector et al, Leukemia 2011]. The pt did not respond to cytarabine-based induction therapy combined with Dasat or to post-induction Imat. The functional consequence of the receptor mutations on downstream signaling networks, and sensitivity to alternative therapeutics, was unknown. SCNP is a flow cytometry-based assay that quantitatively and simultaneously measures, in single cells, extracellular surface markers and activation of intracellular signaling proteins in response to modulation. SCNP was applied to interrogate downstream signaling networks and network sensitivity to targeted therapeutics by examining: 1) Basal and modulated signaling using stem cell factor (SCF) or α-IgE 2) Effect on basal and modulated signaling of: a) KIT inhibitors Imat, Dasat, and Nilotinib b) PI3K inhibitor GDC-0941 c) SYK inhibitor fostamatinib R406 Methods: Cryopreserved MCL BMMCs and healthy donor BMMCs were processed alongside fresh healthy donor basophils (FHDB) as controls. BMMCs were modulated with SCF for 5 and 15 min +/-KIT or PI3K inhib. MCL BMMCs and FHDB were modulated with α-IgE for 5min +/- fostamatinib. Signaling in the KIT and FcεR1 pathways was quantified through measurement of p-AKT/ p-ERK/ p-S6 and p-ERK/ p-PLCγ2 / p-SYK levels, respectively, in the MCL population: CD45+, CD34+, CD33+, and CD117+. Results: As previous reported, the V654A KIT mutation did not result in constitutive activation of the PI3K or MAPK pathways in MCL blasts, but was associated with dysfunctional SCF modulated signaling. Specifically, SCNP identified SCF induced p-AKT levels at 5min, higher (2X) compared to CD34+/CD117+ FHDB, and sustained to 15min with no simultaneous induction of p-ERK or p-S6. Consistent with the clinically observed Imat/Dasat resistance of the MCL case, in vitro AKT induction was unaffected by the presence of KIT inhibitors but sensitive to the PI3K inhib GDC-0941. KIT inhibitors and GDC-0941 blocked SCF induced signaling in the healthy BMMC control. Despite robust p-ERK induction in the FHDB control after α-IgE modulation of the FcεR1 receptor and inhibition by fostamatinib treatment, no basal or α-IgE modulated FcεR1 receptor signaling was detected in MCL BMMC cells. Conclusions: SCNP functionally characterizes signaling and drug resistance profiles in MCL BMMCs and can potentially inform on therapeutic selection. Despite robust p-ERK induction in the FHDB control after α-IgE modulation of the FcεR1 receptor and inhibition by fostamatinib treatment, no basal or α-IgE modulated FcεR1 receptor signaling was detected in the cryopreserved MCL BMMCs. Further studies will elucidate whether the lack of detected signal could be related to the freeze/thaw process and/or to cell-type specific differences. Citation Format: Matt Westfall, Mona S. Spector, Michael Gulrajani, Carol Marimpietri, Athena Kritharis, Scott Z. Fields, Steven L. Allen, Rachael Hawtin. Functional characterization of KIT and FcεR1 receptor mutations in Mast Cell Leukemia using Single Cell Network Profiling (SCNP). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3524. doi:10.1158/1538-7445.AM2013-3524

Directing nuclear deformation on micropillared surfaces by substrate geometry and cytoskeleton organization

We have recently demonstrated strong nuclear deformation of SaOs-2 osteosarcoma cells on poly-l-lactic acid (PLLA) micropillar substrates. In the present study, we first demonstrated that chemical and mechanical properties of the micropillar substrates have no dominant effect on deformation. However, SaOs-2 nucleus deformation could be strongly modulated by varying the pillar size and spacing, highlighting the importance of geometric constraints for shaping the nucleus. Furthermore, comparing the capacity for nuclear deformation in three different osteosarcoma cell lines (SaOs-2, MG-63 and OHS-4) revealed strong cell-type specific differences. Surprisingly, the highly-deformable SaOs-2 cell line displayed the highest cell stiffness as assessed by AFM-based colloidal force spectroscopy and featured a more prominent array of actin fibres above the nucleus, suggesting a link between actin-mediated cell stiffness and cell nucleus deformation. In contrast, in MG-63 and OHS-4 cells dense microtubule and vimentin networks seem to facilitate some nuclear deformation even in the absence of a prominent actin cytoskeleton. Together these results suggest that an interaction of all three cytoskeletal elements is needed for efficient nuclear deformation. In conclusion, the dominant parameters influencing nuclear deformation on micropillar substrates are not their material properties but the substrate geometry together with cell phenotype and cytoskeleton organization.

Comparative lipidomics analysis of HIV-1 particles and their producer cell membrane in different cell lines

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus that obtains its lipid envelope by budding through the plasma membrane of infected host cells. Various studies indicated that the HIV-1 membrane differs from the producer cell plasma membrane suggesting virus budding from pre-existing subdomains or virus-mediated induction of a specialized budding membrane. To perform a comparative lipidomics analysis by quantitative mass spectrometry, we first evaluated two independent methods to isolate the cellular plasma membrane. Subsequent lipid analysis of plasma membranes and HIV-1 purified from two different cell lines revealed a significantly different lipid composition of the viral membrane compared with the host cell plasma membrane, independent of the cell type investigated. Virus particles were significantly enriched in phosphatidylserine, sphingomyelin, hexosylceramide and saturated phosphatidylcholine species when compared with the host cell plasma membrane of the producer cells; they showed reduced levels of unsaturated phosphatidylcholine species, phosphatidylethanolamine and phosphatidylinositol. Cell type-specific differences in the lipid composition of HIV-1 and donor plasmamembranes were observed for plasmalogen-phosphatidylethanolamine and phosphatidylglycerol, which were strongly enriched only in HIV-1 derived from MT-4 cells. MT-4 cell-derived HIV-1 also contained dihydrosphingomyelin as reported previously, but this lipid class was also enriched in the host cell membrane. Taken together, these data strongly support the hypothesis that HIV-1 selects a specific lipid environment for its morphogenesis.

Infection of macrophages withMycobacterium tuberculosisinduces global modifications to phagosomal function

The phagosome is a central mediator of both the homeostatic and microbicidal functions of a macrophage. Following phagocytosis, Mycobacterium tuberculosis (Mtb) is able to establish infection through arresting phagosome maturation and avoiding the consequences of delivery to the lysosome. The infection of a macrophage by Mtb leads to marked changes in the behaviour of both the macrophage and the surrounding tissue as the bacterium modulates its environment to promote its survival. In this study, we use functional physiological assays to probe the biology of the phagosomal network in Mtb-infected macrophages. The resulting data demonstrate that Mtb modifies phagosomal function in a TLR2/TLR4-dependent manner, and that most of these modifications are consistent with an increase in the activation status of the cell. Specifically, superoxide burst is enhanced and lipolytic activity is decreased upon infection. There are some species- or cell type-specific differences between human and murine macrophages in the rates of acidification and the degree of proteolysis. However, the most significant modification is the marked reduction in intra-phagosomal lipolysis because this correlates with the marked increase in the retention of host lipids in the infected macrophage, which provides a potential source of nutrients that can be accessed by Mtb.

Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling

Innate immunity is the first line of defense against invasion of pathogens. Toll-like receptor (TLR) signaling is involved in a variety of human diseases extending far beyond immune system–related diseases, affecting a number of different tissues and cell-types. Computational models often do not account for cell-type specific differences in signaling networks. Investigation of these differences and its phenotypic implications could increase understanding of cell signaling and processes such as inflammation. The wealth of knowledge for TLR signaling has been recently summarized in a stoichiometric signaling network applicable for constraint-based modeling and analysis (COBRA). COBRA methods have been applied to investigate tissue-specific metabolism using omics data integration. Comparable approaches have not been conducted using signaling networks. In this study, we present ihsTLRv2, an updated TLR signaling network accounting for the association of 314 genes with 558 network reactions. We present a mapping procedure for transcriptomic data onto signaling networks and demonstrate the generation of a monocyte-specific TLR network. The generated monocyte network is characterized through expression of a specific set of isozymes rather than reduction of pathway contents. While further tailoring the network to a specific stimulation condition, we observed that the quantitative changes in gene expression due to LPS stimulation affected the tightly connected set of genes. Differential expression influenced about one third of the entire TLR signaling network, in particular, NF-B activation. Thus, a cell-type and condition-specific signaling network can provide functional insight into signaling cascades. Furthermore, we demonstrate the energy dependence of TLR signaling pathways in monocytes.

What Drosophila spermatocytes tell us about the mechanisms underlying cytokinesis

Cytokinesis separates the genomic material and organelles of a dividing cell equitably into two physically distinct daughter cells at the end of cell division. This highly choreographed process involves coordinated reorganization and regulated action of the actin and microtubule cytoskeletal systems, an assortment of motor proteins, and membrane trafficking components. Due to their large size, the ease with which exquisite cytological analysis may be performed on them, and the availability of numerous mutants and other genetic tools, Drosophila spermatocytes have provided an excellent system for exploring the mechanistic basis for the temporally programmed and precise spatially localized events of cytokinesis. Mutants defective in male meiotic cytokinesis can be easily identified in forward genetic screens by the production of multinucleate spermatids. In addition, the weak spindle assembly checkpoint in spermatocytes, which causes only a small delay of anaphase onset in the presence of unattached chromosomes, allows investigation of whether gene products required for spindle assembly and chromosome segregation are also involved in cytokinesis. Perhaps due to the large size of spermatocytes and the requirement for two rapid-fire rounds of division without intervening S or growth phases during meiosis, male meiotic mutants have also revealed much about molecular mechanisms underlying new membrane addition during cytokinesis. Finally, cell type-specific differences in the events that set up and complete cytokinesis are emerging from comparison of spermatocytes with cells undergoing mitosis either elsewhere in the organism or in tissue culture.

Gene Expression and Functional Annotation of the Human Ciliary Body Epithelia

PurposeThe ciliary body (CB) of the human eye consists of the non-pigmented (NPE) and pigmented (PE) neuro-epithelia. We investigated the gene expression of NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. We also developed molecular signatures for the NPE and PE and studied possible new clues for glaucoma.MethodsWe isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44×k Agilent microarrays. For microarray conformations, we used a literature study, RT-PCRs, and immunohistochemical stainings. We analyzed the gene expression data with R and with the knowledge database Ingenuity.ResultsThe gene expression profiles and functional annotations of the NPE and PE were highly similar. We found that the most important functionalities of the NPE and PE were related to developmental processes, neural nature of the tissue, endocrine and metabolic signaling, and immunological functions. In total 1576 genes differed statistically significantly between NPE and PE. From these genes, at least 3 were cell-specific for the NPE and 143 for the PE. Finally, we observed high expression in the (N)PE of 35 genes previously implicated in molecular mechanisms related to glaucoma.ConclusionOur gene expression analysis suggested that the NPE and PE of the CB were quite similar. Nonetheless, cell-type specific differences were found. The molecular machineries of the human NPE and PE are involved in a range of neuro-endocrinological, developmental and immunological functions, and perhaps glaucoma.

Irinotecan induces senescence and apoptosis in colonic cells in vitro

Irinotecan (CPT-11) is topoisomerase I inhibitor used in the treatment of disseminated colorectal cancer. In colon cancer cells it induces DNA damage which leads to cytotoxicity with ensuing apoptosis or premature senescence. Despite its clinical use and efficiency in malignant colonocytes, its effects in normal colonic cells are relatively underexplored. In this work we report that CPT-11 induces dose-dependent cytotoxicity which results in apoptosis and premature senescence whose occurrence nevertheless varies in relation to the type of exposed cells. In normal colonic epithelial cells (NCM) the prevailing type of response is apoptosis whereas in normal colonic fibroblasts (NCF) it is premature senescence. Further analyses showed that CPT-11 induced in both types of cells DNA damage and activated stress response pathways including p53 and p16 but with varying activity of stress kinase p38 and selected stress-associated microRNAs. Epithelial cells upregulated the expression of p53, which was subsequently specifically phosphorylated, massively activated p38 and initiated mitochondrial, caspase-dependent apoptosis. These events occurred in the presence of moderately increased expression of miR-34a only. Conversely, in colonic fibroblasts p38 was only moderately activated, p53 as well as p16 expressions were upregulated in the presence of increased expression of miR-34a, miR-128a and miR-449a. Caspase-dependent apoptosis was found only in a minority of treated cells and the premature senescence phenotype was prevailing. Specific inhibition further proved that p53-dependent as well as independent mechanisms might be responsible for these cell type-specific differences.

The Transmembrane Domains of TNF-Related Apoptosis-Inducing Ligand (TRAIL) Receptors 1 and 2 Co-Regulate Apoptotic Signaling Capacity

TNF-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor (TNF) ligand family that exerts its apoptotic activity in human cells by binding to two transmembrane receptors, TRAILR1 and TRAILR2. In cells co-expressing both receptors the particular contribution of either protein to the overall cellular response is not well defined. Here we have investigated whether differences in the signaling capacities of TRAILR1 and TRAILR2 can be attributed to certain functional molecular subdomains. We generated and characterized various chimeric receptors comprising TRAIL receptor domains fused with parts from other members of the TNF death receptor family. This allowed us to compare the contribution of particular domains of the two TRAIL receptors to the overall apoptotic response and to identify elements that regulate apoptotic signaling. Our results show that the TRAIL receptor death domains are weak apoptosis inducers compared to those of CD95/Fas, because TRAILR-derived constructs containing the CD95/Fas death domain possessed strongly enhanced apoptotic capabilities. Importantly, major differences in the signaling strengths of the two TRAIL receptors were linked to their transmembrane domains in combination with the adjacent extracellular stalk regions. This was evident from receptor chimeras comprising the extracellular part of TNFR1 and the intracellular signaling part of CD95/Fas. Both receptor chimeras showed comparable ligand binding affinities and internalization kinetics. However, the respective TRAILR2-derived molecule more efficiently induced apoptosis. It also activated caspase-8 and caspase-3 more strongly and more quickly, albeit being expressed at lower levels. These results suggest that the transmembrane domains together with their adjacent stalk regions can play a major role in control of death receptor activation thereby contributing to cell type specific differences in TRAILR1 and TRAILR2 signaling.

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.

Random Mutagenesis of β-Tubulin Defines a Set of Dispersed Mutations That Confer Paclitaxel Resistance

Previous research showed that mutations in β1-tubulin are frequently involved in paclitaxel resistance but the question of whether the mutations are restricted by cell-type specific differences remains obscure. To circumvent cellular constraints, we randomly mutagenized β-tubulin cDNA, transfected it into CHO cells, and selected for paclitaxel resistance. A total of 26 β1-tubulin mutations scattered throughout the sequence were identified and a randomly chosen subset were confirmed to confer paclitaxel resistance using site-directed mutagenesis of β-tubulin cDNA and transfection into wild-type cells. Immunofluorescence microscopy and biochemical fractionation studies indicated that cells expressing mutant tubulin had decreased microtubule polymer and frequently suffered mitotic defects that led to the formation of large multinucleated cells, suggesting a resistance mechanism that involves destabilization of the microtubule network. Consistent with this conclusion, the mutations were predominantly located in regions that are likely to be involved in lateral or longitudinal subunit interactions. Notably, fourteen of the new mutations overlapped previously reported mutations in drug resistant cells or in patients with developmental brain abnormalities. A random mutagenesis approach allowed isolation of a wider array of drug resistance mutations and demonstrated that similar mutations can cause paclitaxel resistance and human neuronal abnormalities.

2′-O Methylation of the Viral mRNA Cap by West Nile Virus Evades Ifit1-Dependent and -Independent Mechanisms of Host Restriction In Vivo

Prior studies have shown that 2′-O methyltransferase activity of flaviviruses, coronaviruses, and poxviruses promotes viral evasion of Ifit1, an interferon-stimulated innate immune effector protein. Viruses lacking 2′-O methyltransferase activity exhibited attenuation in primary macrophages that was rescued in cells lacking Ifit1 gene expression. Here, we examined the role of Ifit1 in restricting pathogenesis in vivo of wild type WNV (WNV-WT) and a mutant in the NS5 gene (WNV-E218A) lacking 2′-O methylation of the 5′ viral RNA cap. While deletion of Ifit1 had marginal effects on WNV-WT pathogenesis, WNV-E218A showed increased replication in peripheral tissues of Ifit1 −/− mice after subcutaneous infection, yet this failed to correlate with enhanced infection in the brain or lethality. In comparison, WNV-E218A was virulent after intracranial infection as judged by increased infection in different regions of the central nervous system (CNS) and a greater than 16,000-fold decrease in LD50 values in Ifit1 −/− compared to wild type mice. Ex vivo infection experiments revealed cell-type specific differences in the ability of an Ifit1 deficiency to complement the replication defect of WNV-E218A. In particular, WNV-E218A infection was impaired in both wild type and Ifit1 −/− brain microvascular endothelial cells, which are believed to participate in blood-brain barrier (BBB) regulation of virus entry into the CNS. A deficiency of Ifit1 also was associated with increased neuronal death in vivo, which was both cell-intrinsic and mediated by immunopathogenic CD8+ T cells. Our results suggest that virulent strains of WNV have largely evaded the antiviral effects of Ifit1, and viral mutants lacking 2′-O methylation are controlled in vivo by Ifit1-dependent and -independent mechanisms in different cell types.

Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons

Proper functioning of working memory involves the expression of stimulus-selective persistent activity in pyramidal neurons of the prefrontal cortex (PFC), which refers to neural activity that persists for seconds beyond the end of the stimulus. The mechanisms which PFC pyramidal neurons use to discriminate between preferred vs. neutral inputs at the cellular level are largely unknown. Moreover, the presence of pyramidal cell subtypes with different firing patterns, such as regular spiking and intrinsic bursting, raises the question as to what their distinct role might be in persistent firing in the PFC. Here, we use a compartmental modeling approach to search for discriminatory features in the properties of incoming stimuli to a PFC pyramidal neuron and/or its response that signal which of these stimuli will result in persistent activity emergence. Furthermore, we use our modeling approach to study cell-type specific differences in persistent activity properties, via implementing a regular spiking (RS) and an intrinsic bursting (IB) model neuron. We identify synaptic location within the basal dendrites as a feature of stimulus selectivity. Specifically, persistent activity-inducing stimuli consist of activated synapses that are located more distally from the soma compared to non-inducing stimuli, in both model cells. In addition, the action potential (AP) latency and the first few inter-spike-intervals of the neuronal response can be used to reliably detect inducing vs. non-inducing inputs, suggesting a potential mechanism by which downstream neurons can rapidly decode the upcoming emergence of persistent activity. While the two model neurons did not differ in the coding features of persistent activity emergence, the properties of persistent activity, such as the firing pattern and the duration of temporally-restricted persistent activity were distinct. Collectively, our results pinpoint to specific features of the neuronal response to a given stimulus that code for its ability to induce persistent activity and predict differential roles of RS and IB neurons in persistent activity expression.

A Resource for the Conditional Ablation of microRNAs in the Mouse

The importance of miRNAs during development and disease processes is well established. However, most studies have been done in cells or with patient tissues, and therefore the physiological roles of miRNAs are not well understood. To unravel in vivo functions of miRNAs, we have generated conditional, reporter-tagged knockout-first mice for numerous evolutionarily conserved miRNAs. Here, we report the generation of 162 miRNA targeting vectors, 64 targeted ES cell lines, and 46 germline-transmitted miRNA knockout mice. In vivo lacZ reporter analysis in 18 lines revealed highly tissue-specific expression patterns and their miRNA expression profiling matched closely with published expression data. Most miRNA knockout mice tested were viable, supporting a mechanism by which miRNAs act redundantly with other miRNAs or other pathways. These data and collection of resources will be of value for the in vivo dissection of miRNA functions in mouse models.

Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response

Effective antiviral immunity depends on the ability of infected cells or cells triggered with virus-derived nucleic acids to produce type I interferon (IFN), which activates transcription of numerous antiviral genes. However, disproportionately strong or chronic IFN expression is a common cause of inflammatory and autoimmune diseases. We describe an epigenetic mechanism that determines cell type-specific differences in IFN and IFN-stimulated gene (ISG) expression in response to exogenous signals. We identify di-methylation of histone H3 at lysine 9 (H3K9me2) as a suppressor of IFN and IFN-inducible antiviral gene expression. We show that levels of H3K9me2 at IFN and ISG correlate inversely with the scope and amplitude of IFN and ISG expression in fibroblasts and dendritic cells. Accordingly, genetic ablation or pharmacological inactivation of lysine methyltransferase G9a, which is essential for the generation of H3K9me2, resulted in phenotypic conversion of fibroblasts into highly potent IFN-producing cells and rendered these cells resistant to pathogenic RNA viruses. In summary, our studies implicate H3K9me2 and enzymes controlling its abundance as key regulators of innate antiviral immunity.

HIV Compartmentalization: A Review on a Clinically Important Phenomenon

Viral diversity plays an important role in the pathogenesis of HIV disease. However, within an individual, HIV can vary substantially from one tissue or cell type to another, thereby creating viral compartments. HIV compartmentalization has been well documented in the brain, cerebrospinal fluid, and genital tract, although there are also data for viral compartmentalization within the gut, lung, liver, kidney, and breast milk. The precise mechanisms that lead to the development of HIV compartmentalization have not been adequately examined but likely include differential immune selection pressures, cell type-specific differences in replication or gene expression, local concentrations of antiviral drugs and/or drug resistance, and co-infections that alter the cellular microenvironment. Identifying and characterizing distinct viral sub-populations enhances our overall understanding of HIV pathogenesis and could ultimately result in the development of novel strategies to impair the ability of these viruses to adapt to and/or infect a given cell/tissue type.

Human cytomegalovirus transcriptome activity differs during replication in human fibroblast, epithelial and astrocyte cell lines

Broad cell tropism contributes to the pathogenesis of human cytomegalovirus (HCMV), but the extent to which cell type influences HCMV gene expression is unclear. A bespoke HCMV DNA microarray was used to monitor the transcriptome activity of the low passage Merlin strain of HCMV at 12, 24, 48 and 72 h post-infection, during a single round of replication in human fetal foreskin fibroblast cells (HFFF-2s), human retinal pigmented epithelial cells (RPE-1s) and human astrocytoma cells (U373MGs). In order to correlate transcriptome activity with concurrent biological responses, viral cytopathic effect, growth kinetics and genomic loads were examined in the three cell types. The temporal expression pattern of viral genes was broadly similar in HFFF-2s and RPE-1s, but dramatically different in U373MGs. Of the 165 known HCMV protein-coding genes, 41 and 48 were differentially regulated in RPE-1s and U373MGs, respectively, compared with HFFF-2s, and 22 of these were differentially regulated in both RPE-1s and U373MGs. In RPE-1s, all differentially regulated genes were downregulated, but, in U373MGs, some were down- and others upregulated. Differentially regulated genes were identified among the immediate-early, early, early late and true-late viral gene classes. Grouping of downregulated genes according to function at landmark stages of the replication cycle led to the identification of potential bottleneck stages (genome replication, virion assembly, and virion maturation and release) that may account for cell type-dependent viral growth kinetics. The possibility that cell type-specific differences in expressed cellular factors are responsible for modulation of viral gene expression is discussed.

A Role for SMN Exon 7 Splicing in the Selective Vulnerability of Motor Neurons in Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is an inherited motor neuron disease caused by homozygous loss of the Survival Motor Neuron 1 (SMN1) gene. In the absence of SMN1, inefficient inclusion of exon 7 in transcripts from the nearly identical SMN2 gene results in ubiquitous SMN decrease but selective motor neuron degeneration. Here we investigated whether cell type-specific differences in the efficiency of exon 7 splicing contribute to the vulnerability of SMA motor neurons. We show that normal motor neurons express markedly lower levels of full-length SMN mRNA from SMN2 than do other cells in the spinal cord. This is due to inefficient exon 7 splicing that is intrinsic to motor neurons under normal conditions. We also find that SMN depletion in mammalian cells decreases exon 7 inclusion through a negative feedback loop affecting the splicing of its own mRNA. This mechanism is active in vivo and further decreases the efficiency of exon 7 inclusion specifically in motor neurons of severe-SMA mice. Consistent with expression of lower levels of full-length SMN, we find that SMN-dependent downstream molecular defects are exacerbated in SMA motor neurons. These findings suggest a mechanism to explain the selective vulnerability of motor neurons to loss of SMN1.