Lipid droplets regulate autophagosome biogenesis

The source of the autophagic membrane and the regulation of autophagosome biogenesis are still elusive open issues in the field of autophagy. In our recent study of the role of lipid droplets (LDs) and their constituents in autophagy, we provided evidence that both the biogenesis of LDs and its lipolysis by specific lipases are important for autophagosome biogenesis. Our study sheds new light on the source of the autophagic membrane and suggests that a flow of membranes from the endoplasmic reticulum (ER) to LDs, and from LDs to the ER, is essential for autophagosome biogenesis.     

Associating Genes and Protein Complexes with Disease via Network Propagation

A fundamental challenge in human health is the identification of disease-causing genes. Recently, several studies have tackled this challenge via a network-based approach, motivated by the observation that genes causing the same or similar diseases tend to lie close to one another in a network of protein-protein or functional interactions. However, most of these approaches use only local network information in the inference process and are restricted to inferring single gene associations. Here, we provide a global, network-based method for prioritizing disease genes and inferring protein complex associations, which we call PRINCE. The method is based on formulating constraints on the prioritization function that relate to its smoothness over the network and usage of prior information. We exploit this function to predict not only genes but also protein complex associations with a disease of interest. We test our method on gene-disease association data, evaluating both the prioritization achieved and the protein complexes inferred. We show that our method outperforms extant approaches in both tasks. Using data on 1,369 diseases from the OMIM knowledgebase, our method is able (in a cross validation setting) to rank the true causal gene first for 34% of the diseases, and infer 139 disease-related complexes that are highly coherent in terms of the function, expression and conservation of their member proteins. Importantly, we apply our method to study three multi-factorial diseases for which some causal genes have been found already: prostate cancer, alzheimer and type 2 diabetes mellitus. PRINCE''s predictions for these diseases highly match the known literature, suggesting several novel causal genes and protein complexes for further investigation.     

Selective inhibition of inducible NO synthase activity in vivo reverses inflammatory abnormalities in surfactant protein D-deficient mice

Surfactant protein D (SP-D)-deficient (SP-D-/-) mice exhibit early development of emphysema. Previously we have shown that SP-D deficiency results in increased production and activity of inducible NO synthase (iNOS). In this study, we examined whether treatment with the iNOS inhibitor 1400W could inhibit the inflammatory phenotype. Mice were treated with 1400W systemically for 7 wk from 3 wk of age. Treatment reduced total lung NO synthase activity to 14.7+/-6.1% of saline-treated 10-wk-old SP-D-/- littermates. Long-term administration of 1400W reduced lung inflammation and cellular infiltration; and significantly attenuated the increased levels of matrix metalloproteinases 2 and 9, chemokines (KC, TARC), and cytokines (IFN-gamma) seen in bronchoalveolar lavage (BAL) of SP-D-/- mice. Abrogation of these levels was associated with decreasing BAL chemotactic activity for RAW cells. Two weeks of treatment with 1400W reduced total lung NO synthase (NOS) activity to 12.7+/-6.3% of saline-treated SP-D-/- mice. Short-term iNOS inhibition resulted in attenuation of pulmonary inflammation within SP-D-/- mice as shown by decreases in total BAL cell count (63+/-6% of SP-D-/- control), macrophage size (>25 microm) within the BAL (62+/-10% of SP-D-/- control), and a percentage of BAL macrophages producing oxidants (76+/-9% of SP-D-/- control). These studies showed that s.c. delivery of 1400W can be achieved in vivo and can attenuate the inflammatory processes within SP-D deficiency. Our results represent the first report linking defects in the innate immune system in the lung with alterations in NO homeostasis.     

Arabidopsis phosphatidylinositol phosphate kinase 1 binds F-actin and recruits phosphatidylinositol 4-kinase beta1 to the actin cytoskeleton

The actin cytoskeleton can be influenced by phospholipids and lipid-modifying enzymes. In animals the phosphatidylinositol phosphate kinases (PIPKs) are associated with the cytoskeleton through a scaffold of proteins; however, in plants such an interaction was not clear. Our approach was to determine which of the plant PIPKs interact with actin and determine whether the PIPK-actin interaction is direct. Our results indicate that AtPIPK1 interacts directly with actin and that the binding is mediated through a predicted linker region in the lipid kinase. AtPIPK1 also recruits AtPI4Kbeta1 to the cytoskeleton. Recruitment of AtPI4Kbeta1 to F-actin was dependent on the C-terminal catalytic domain of phosphatidylinositol-4-phosphate 5-kinase but did not require the presence of the N-terminal 251 amino acids, which includes 7 putative membrane occupation and recognition nexus motifs. In vivo studies confirm the interaction of plant lipid kinases with the cytoskeleton and suggest a role for actin in targeting PIPKs to the membrane.     

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

The rate of conservation of a gene in evolution is believed to be correlated with its biological importance. Recent studies have devised various conservation measures for genes and have shown that they are correlated with several biological characteristics of functional importance. Specifically, the state-of-the-art propensity for gene loss (PGL) measure was shown to be strongly correlated with gene essentiality and its number of protein–protein interactions (PPIs). The observed correlation between conservation and functional importance varies however between conservation measures, underscoring the need for accurate and general measures for the rate of gene conservation. Here we develop a novel maximum-likelihood approach to computing the rate in which a gene is lost in evolution, motivated by the same principles as those underlying PGL. However, in difference to PGL which considers only the most parsimonious ancestral states of the internal nodes of the phylogenetic tree relating the species, our approach weighs in a probabilistic manner all possible ancestral states, and includes the branch length information as part of the probabilistic model. In application to data of 16 eukaryotic genomes, our approach shows higher correlations with experimental data than PGL, including data on gene lethality, level of connectivity in a PPI network and coherence within functionally related genes.     

LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis

Autophagy is a unique membrane trafficking pathway describing the formation and targeting of double membrane autophagosomes to the vacuole/lysosome. The biogenesis of autophagosomes and their delivery to the vacuole/lysosome depend on multiple membrane fusion events. Using a cell-free system, we have investigated the ability of LC3 and GATE-16, two mammalian Atg8 orthologs, to mediate membrane fusion. We found that both proteins promote tethering and membrane fusion, mediated by the proteins' N-terminal α helices. We further show that short, 10 amino acid long synthetic peptides derived from the N terminus of LC3 or GATE-16 are sufficient to promote membrane fusion. Our data indicate that the fusion activity of LC3 is mediated by positively charged amino acids, whereas the activity of GATE-16 is mediated by hydrophobic interactions. Finally, we demonstrate that LC3 and GATE-16 N termini in general and specific residues needed for the fusion activity are essential for the proteins role in autophagosome biogenesis.     

Shedding light on mammalian microautophagy

ESCRT complexes are implicated in mediating membrane protein degradation, whereas hsc70 mediates cytosolic protein degradation via chaperone-mediated autophagy. In this issue of Developmental Cell, Sahu et?al. (2011) describe in mammalian cells the involvement of ESCRT complexes and hsc70 in the degradation of cytosolic proteins in a process resembling microautophagy.     

Activation of cytotoxic and regulatory functions of NK cells by Sindbis viral vectors

Oncolytic viruses (OVs) represent a relatively novel anti-cancer modality. Like other new cancer treatments, effective OV therapy will likely require combination with conventional treatments. In order to design combinatorial treatments that work well together, a greater scrutiny of the mechanisms behind the individual treatments is needed. Sindbis virus (SV) based vectors have previously been shown to target and kill tumors in xenograft, syngeneic, and spontaneous mouse models. However, the effect of SV treatment on the immune system has not yet been studied. Here we used a variety of methods, including FACS analysis, cytotoxicity assays, cell depletion, imaging of tumor growth, cytokine blockade, and survival experiments, to study how SV therapy affects Natural Killer (NK) cell function in SCID mice bearing human ovarian carcinoma tumors. Surprisingly, we found that SV anti-cancer efficacy is largely NK cell-dependent. Furthermore, the enhanced therapeutic effect previously observed from Sin/IL12 vectors, which carry the gene for interleukin 12, is also NK cell dependent, but works through a separate IFNγ-dependent mechanism, which also induces the activation of peritoneal macrophages. These results demonstrate the multimodular nature of SV therapy, and open up new possibilities for potential synergistic or additive combinatorial therapies with other treatments.