While T-cell responses are directly modulated by Toll-like receptor (TLR) ligands, the mechanism and physiological function of nucleic acids (NAs)-mediated T cell costimulation remains unclear. Here we show that unlike in innate cells, T-cell costimulation is induced even by non-CpG DNA and by self-DNA, which is released from dead cells and complexes with antimicrobial peptides or histones. Such NA complexes are internalized by T cells and induce costimulatory responses independently of known NA sensors, including TLRs, RIG-I-like receptors (RLRs), inflammasomes and STING-dependent cytosolic DNA sensors. Such NA-mediated costimulation crucially induces Th2 differentiation by suppressing T-bet expression, followed by the induction of GATA-3 and Th2 cytokines. These findings unveil the function of NA sensing by T cells to trigger and amplify allergic inflammation.

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Site occupancy of interstitial deuterium atoms in face-centred cubic iron

Machida, Akihiko; Saitoh, Hiroyuki; Sugimoto, Hidehiko; Hattori, Takanori; Sano-Furukawa, Asami; Endo, Naruki; Katayama, Yoshinori; Iizuka, Riko; Sato, Toyoto; Matsuo, Motoaki; Orimo, Shin-ichi; Aoki, Katsutoshi

2014 Nature Communications

doi: 10.1038/ncomms6063pmid: 25256789

Hydrogen composition and occupation state provide basic information for understanding various properties of the metal–hydrogen system, ranging from microscopic properties such as hydrogen diffusion to macroscopic properties such as phase stability. Here the deuterization process of face-centred cubic Fe to form solid-solution face-centred cubic FeDx is investigated using in situ neutron diffraction at high temperature and pressure. In a completely deuterized specimen at 988 K and 6.3 GPa, deuterium atoms occupy octahedral and tetrahedral interstitial sites with an occupancy of 0.532(9) and 0.056(5), respectively, giving a deuterium composition x of 0.64(1). During deuterization, the metal lattice expands approximately linearly with deuterium composition at a rate of 2.21 Å3 per deuterium atom. The minor occupation of the tetrahedral site is thermally driven by the intersite movement of deuterium atoms along the ‹111› direction in the face-centred cubic metal lattice.

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A20 controls intestinal homeostasis through cell-specific activities

Vereecke, Lars; Vieira-Silva, Sara; Billiet, Thomas; van Es, Johan H.; Mc Guire, Conor; Slowicka, Karolina; Sze, Mozes; van den Born, Maaike; De Hertogh, Gert; Clevers, Hans; Raes, Jeroen; Rutgeerts, Paul; Vermeire, Severine; Beyaert, Rudi; van Loo, Geert

2014 Nature Communications

doi: 10.1038/ncomms6103pmid: 25267258

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RETRACTED ARTICLE: Senescence impairs direct conversion of human somatic cells to neurons

Sun, Chong-kui; Zhou, Di; Zhang, Zhen; He, Liming; Zhang, Fan; Wang, Xiaowei; Yuan, Jie; Chen, Qianming; Wu, Ling-Gang; Yang, Qin

2014 Nature Communications

doi: 10.1038/ncomms5112pmid: 24934763

Recent reports have shown that fibroblasts can be converted to neurons by forced expression of transcription factors. However, the mechanisms underlying this conversion remain unclear. Here, we show that the efficiency of neuronal conversion of embryonic human fibroblasts aged in culture is lower than that in cells in early culture stages. Moreover, depletion of p16Ink4aand p19Arf involved in the activation of cellular senescence is sufficient to convert human fibroblast and epithelial cells into neurons. The induced neurons express neuron-specific proteins, generate action potentials and neurotransmitter receptor-mediated currents. Genome-wide transcriptional analysis shows that the induced neurons have a profile different from fibroblasts and similar to that of control neurons induced by established methods. We further noted that expression of p53 blocks the neuronal conversion, whereas expression of human telomerase reverse transcriptase (hTERT) induces it. Our results indicate that overcoming senescence is a crucial step for neuronal conversion of somatic cells.

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Clonal culturing of human embryonic stem cells on laminin-521/E-cadherin matrix in defined and xeno-free environment

Rodin, Sergey; Antonsson, Liselotte; Niaudet, Colin; Simonson, Oscar E.; Salmela, Elina; Hansson, Emil M.; Domogatskaya, Anna; Xiao, Zhijie; Damdimopoulou, Pauliina; Sheikhi, Mona; Inzunza, José; Nilsson, Ann-Sofie; Baker, Duncan; Kuiper, Raoul; Sun, Yi; Blennow, Elisabeth; Nordenskjöld, Magnus; Grinnemo, Karl-Henrik; Kere, Juha;

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RETRACTED ARTICLE: O-GlcNAc-mediated interaction between VER2 and TaGRP2 elicits TaVRN1 mRNA accumulation during vernalization in winter wheat

Xiao, Jun; Xu, Shujuan; Li, Chunhua; Xu, Yunyuan; Xing, Lijing; Niu, Yuda; Huan, Qing; Tang, Yimiao; Zhao, Changping; Wagner, Doris; Gao, Caixia; Chong, Kang

2014 Nature Communications

doi: 10.1038/ncomms5572pmid: 25091017

Vernalization, sensing of prolonged cold, is important for seasonal flowering in eudicots and monocots. While vernalization silences a repressor (FLC, MADS-box transcription factor) in eudicots, it induces an activator (TaVRN1, an AP1 clade MADS-box transcription factor) in monocots. The mechanism for TaVRN1 induction during vernalization is not well understood. Here we reveal a novel mechanism for controlling TaVRN1 mRNA accumulation in response to prolonged cold sensing in wheat. The carbohydrate-binding protein VER2, a jacalin lectin, promotes TaVRN1 upregulation by physically interacting with the RNA-binding protein TaGRP2. TaGRP2 binds to TaVRN1 pre-mRNA and inhibits TaVRN1 mRNA accumulation. The physical interaction between VER2 and TaGRP2 is controlled by TaGRP2 O-GlcNAc modification, which gradually increases during vernalization. The interaction between VER2 and O-GlcNAc-TaGRP2 reduces TaGRP2 protein accumulation in the nucleus and/or promotes TaGRP2 dissociation from TaVRN1, leading to TaVRN1 mRNA accumulation. Our data reveal a new mechanism for sensing prolonged cold in temperate cereals.

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Dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans

Pelisch, Federico; Sonneville, Remi; Pourkarimi, Ehsan; Agostinho, Ana; Blow, J. Julian; Gartner, Anton; Hay, Ronald T.

2014 Nature Communications

doi: 10.1038/ncomms6485pmid: 25475837

The small ubiquitin-like modifier (SUMO), initially characterized as a suppressor of a mutation in the gene encoding the centromeric protein MIF2, is involved in many aspects of cell cycle regulation. The dynamics of conjugation and deconjugation and the role of SUMO during the cell cycle remain unexplored. Here we used Caenorhabditis elegans to establish the contribution of SUMO to a timely and accurate cell division. Chromatin-associated SUMO conjugates increase during metaphase but decrease rapidly during anaphase. Accumulation of SUMO conjugates on the metaphase plate and proper chromosome alignment depend on the SUMO E2 conjugating enzyme UBC-9 and SUMO E3 ligase PIASGEI-17. Deconjugation is achieved by the SUMO protease ULP-4 and is crucial for correct progression through the cell cycle. Moreover, ULP-4 is necessary for Aurora BAIR-2 extraction from chromatin and relocation to the spindle mid-zone. Our results show that dynamic SUMO conjugation plays a role in cell cycle progression.

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Hypothalamic S1P/S1PR1 axis controls energy homeostasis

Silva, Vagner R. R.; Micheletti, Thayana O.; Pimentel, Gustavo D.; Katashima, Carlos K.; Lenhare, Luciene; Morari, Joseane; Mendes, Maria Carolina S.; Razolli, Daniela S.; Rocha, Guilherme Z.; de Souza, Claudio T.; Ryu, Dongryeol; Prada, Patrícia O.; Velloso, Lício A.; Carvalheira, José B. C.; Rodrigo Pauli, José; Cintra, Dennys E.; Ropelle, Eduardo R.

2014

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Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

Corominas, Roser; Yang, Xinping; Lin, Guan Ning; Kang, Shuli; Shen, Yun; Ghamsari, Lila; Broly, Martin; Rodriguez, Maria; Tam, Stanley; Trigg, Shelly A.; Fan, Changyu; Yi, Song; Tasan, Murat; Lemmens, Irma; Kuang, Xingyan; Zhao, Nan; Malhotra, Dheeraj; Michaelson, Jacob J.; Vacic, Vladimir; Calderwood, Michael A.;

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Antigen capture and archiving by lymphatic endothelial cells following vaccination or viral infection

Tamburini, Beth A.; Burchill, Matthew A.; Kedl, Ross M.

2014 Nature Communications

doi: 10.1038/ncomms4989pmid: 24905362

Antigen derived from viral infections with influenza and vesicular stomatitis virus can persist after resolution of infection. Here we show that antigen can similarly persist for weeks following viral challenge and vaccination. Antigen is captured by lymphatic endothelial cells (LECs) under conditions that induce LEC proliferation. Consistent with published data showing that viral antigen persistence impacts the function of circulating memory T cells, we find that vaccine-elicited antigen persistence, found on LECs, positively influences the degree of protective immunity provided by circulating memory CD8+ T cells. The coupling of LEC proliferation and antigen capture identifies a mechanism by which the LECs store, or ‘archive’, antigens for extended periods of time after antigen challenge, thereby increasing IFNγ/IL-2 production and enhancing protection against infection. These findings therefore have the potential to have an impact on future vaccination strategies and our understanding of the role for persisting antigen in both vaccine and infectious settings.

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Cell BioEssays Journal of Applied Crystallography Zeitschrift fur Naturforschung - Section C Journal of Biosciences Cells Cell and Bioscience Biological Procedures Online FEBS Open Bio BioResearch Open Access Biopolymers and Cell

The transcription factor NF-κB is indispensable for intestinal immune homeostasis, but contributes to chronic inflammation and inflammatory bowel disease (IBD). A20, an inhibitor of both NF-κB and apoptotic signalling, was identified as a susceptibility gene for multiple inflammatory diseases, including IBD. Despite absence of spontaneous intestinal inflammation in intestinal epithelial cell (IEC) specific A20 knockout mice, we found additional myeloid-specific A20 deletion to synergistically drive intestinal pathology through cell-specific mechanisms. A20 ensures intestinal barrier stability by preventing cytokine-induced IEC apoptosis, while A20 prevents excessive cytokine production in myeloid cells. Combining IEC and myeloid A20 deletion induces ileitis and severe colitis, characterized by IEC apoptosis, Paneth and goblet cell loss, epithelial hyperproliferation and intestinal microbiota dysbiosis. Continuous epithelial cell death and regeneration in an inflammatory environment sensitizes cells for neoplastic transformation and the development of colorectal tumours in aged mice.

Betsholtz, Christer;

Hovatta, Outi;

Tryggvason, Karl

2014 Nature Communications

doi: 10.1038/ncomms4195pmid: 24463987

Lack of robust methods for establishment and expansion of pluripotent human embryonic stem (hES) cells still hampers development of cell therapy. Laminins (LN) are a family of highly cell-type specific basement membrane proteins important for cell adhesion, differentiation, migration and phenotype stability. Here we produce and isolate a human recombinant LN-521 isoform and develop a cell culture matrix containing LN-521 and E-cadherin, which both localize to stem cell niches in vivo. This matrix allows clonal derivation, clonal survival and long-term self-renewal of hES cells under completely chemically defined and xeno-free conditions without ROCK inhibitors. Neither LN-521 nor E-cadherin alone enable clonal survival of hES cells. The LN-521/E-cadherin matrix allows hES cell line derivation from blastocyst inner cell mass and single blastomere cells without a need to destroy the embryo. This method can facilitate the generation of hES cell lines for development of different cell types for regenerative medicine purposes.

Nature Communications

doi: 10.1038/ncomms5859pmid: 25255053

Sphingosine 1-phosphate receptor 1 (S1PR1) is a G-protein-coupled receptor for sphingosine-1-phosphate (S1P) that has a role in many physiological and pathophysiological processes. Here we show that the S1P/S1PR1 signalling pathway in hypothalamic neurons regulates energy homeostasis in rodents. We demonstrate that S1PR1 protein is highly enriched in hypothalamic POMC neurons of rats. Intracerebroventricular injections of the bioactive lipid, S1P, reduce food consumption and increase rat energy expenditure through persistent activation of STAT3 and the melanocortin system. Similarly, the selective disruption of hypothalamic S1PR1 increases food intake and reduces the respiratory exchange ratio. We further show that STAT3 controls S1PR1 expression in neurons via a positive feedback mechanism. Interestingly, several models of obesity and cancer anorexia display an imbalance of hypothalamic S1P/S1PR1/STAT3 axis, whereas pharmacological intervention ameliorates these phenotypes. Taken together, our data demonstrate that the neuronal S1P/S1PR1/STAT3 signalling axis plays a critical role in the control of energy homeostasis in rats.

Roth, Frederick P.;

Tavernier, Jan;

Horvath, Steve;

Salehi-Ashtiani, Kourosh;

2014 Nature Communications

doi: 10.1038/ncomms4650pmid: 24722188

Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases.