Structural mechanism of ligand activation in human GABAB receptor

Yong Geng,     Martin Bush,     Lidia Mosyak,     Feng Wang     & Qing R. Fan

                                                                            

Abstract:

Human GABAB (γ-aminobutyric acid class B) receptor is a G-protein-coupled receptor central to inhibitory neurotransmission in the brain. It functions as an obligatory heterodimer of the subunits GBR1 and GBR2. Here we present the crystal structures of a heterodimeric complex between the extracellular domains of GBR1 and GBR2 in the apo, agonist-bound and antagonist-bound forms. The apo and antagonist-bound structures represent the resting state of the receptor; the agonist-bound complex corresponds to the active state. Both subunits adopt an open conformation at rest, and only GBR1 closes on agonist-induced receptor activation. The agonists and antagonists are anchored in the interdomain crevice of GBR1 by an overlapping set of residues. An antagonist confines GBR1 to the open conformation of the inactive state, whereas an agonist induces its domain closure for activation. Our data reveal a unique activation mechanism for GABAB receptor that involves the formation of a novel heterodimer interface between subunits.

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Keywords:ligand,human,GABAB reeptor,heterodimer

Targeting Plasmodium PI(4)K to eliminate malaria

Case W. McNamara,     Marcus C. S. Lee,     Chek Shik Lim,     Siau Hoi Lim,     Jason Roland,     Advait Nagle,     Oliver Simon,     Bryan K. S. Yeung,     Arnab K. Chatterjee,     Susan L. McCormack,     Micah J. Manary,     Anne-Marie Zeeman,     Koen J. Dechering,     T. R. Santha Kumar,     Philipp P. Henrich, Kerstin Gagaring,     Maureen Ibanez,     Nobutaka Kato,     Kelli L. Kuhen,     Christoph Fischli, Matthias Rottmann,     David M. Plouffe,     Badry Bursulaya,     Stephan Meister,     Lucia Rameh

                                                                                        

Abstract:

Achieving the goal of malaria elimination will depend on targeting Plasmodium pathways essential across all life stages. Here we identify a lipid kinase, phosphatidylinositol-4-OH kinase (PI(4)K), as the target of imidazopyrazines, a new antimalarial compound class that inhibits the intracellular development of multiple Plasmodium species at each stage of infection in the vertebrate host. Imidazopyrazines demonstrate potent preventive, therapeutic, and transmission-blocking activity in rodent malaria models, are active against blood-stage field isolates of the major human pathogens P. falciparum and P. vivax, and inhibit liver-stage hypnozoites in the simian parasite P. cynomolgi. We show that imidazopyrazines exert their effect through inhibitory interaction with the ATP-binding pocket of PI(4)K, altering the intracellular distribution of phosphatidylinositol-4-phosphate. Collectively, our data define PI(4)K as a key Plasmodium vulnerability, opening up new avenues of target-based discovery to identify drugs with an ideal activity profile for the prevention, treatment and elimination of malaria.

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Keywords:plasmodium,malaria,imidazopyrazine,hypnozoites,phosphotidylinositol-4-OH,kinase

Ultrafast endocytosis at mouse hippocampal synapses

Shigeki Watanabe,     Benjamin R. Rost,     Marcial Camacho-Pérez,     M. Wayne Davis,     Berit Söhl-Kielczynski,     Christian Rosenmund     & Erik M. Jorgensen

                                                                                             

Abstract:

To sustain neurotransmission, synaptic vesicles and their associated proteins must be recycled locally at synapses. Synaptic vesicles are thought to be regenerated approximately 20 s after fusion by the assembly of clathrin scaffolds or in approximately 1 s by the reversal of fusion pores via ‘kiss-and-run’ endocytosis. Here we use optogenetics to stimulate cultured hippocampal neurons with a single stimulus, rapidly freeze them after fixed intervals and examine the ultrastructure using electron microscopy—‘flash-and-freeze’ electron microscopy. Docked vesicles fuse and collapse into the membrane within 30 ms of the stimulus. Compensatory endocytosis occurs within 50 to 100 ms at sites flanking the active zone. Invagination is blocked by inhibition of actin polymerization, and scission is blocked by inhibiting dynamin. Because intact synaptic vesicles are not recovered, this form of recycling is not compatible with kiss-and-run endocytosis; moreover, it is 200-fold faster than clathrin-mediated endocytosis. It is likely that ‘ultrafast endocytosis’ is specialized to restore the surface area of the membrane rapidly.

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Keywords:endocytosis,mouse,hippocampal,optogenetics,dynamin

Ferromagnetism in suspensions of magnetic platelets in liquid crystal

Alenka Mertelj,     Darja Lisjak,     Miha Drofenik     & Martin Čopič

                                                                                 

Abstract:

More than four decades ago, Brochard and de Gennes proposed that colloidal suspensions of ferromagnetic particles in nematic (directionally ordered) liquid crystals could form macroscopic ferromagnetic phases at room temperature. The experimental realization of these predicted phases has hitherto proved elusive, with such systems showing enhanced paramagnetism but no spontaneous magnetization in the absence of an external magnetic field. Here we show that nanometre-sized ferromagnetic platelets suspended in a nematic liquid crystal can order ferromagnetically on quenching from the isotropic phase. Cooling in the absence of a magnetic field produces a polydomain sample exhibiting the two opposing states of magnetization, oriented parallel to the direction of nematic ordering. Cooling in the presence of a magnetic field yields a monodomain sample; magnetization can be switched by domain wall movement on reversal of the applied magnetic field. The ferromagnetic properties of this dipolar fluid are due to the interplay of the nematic elastic interaction (which depends critically on the shape of the particles) and the magnetic dipolar interaction. This ferromagnetic phase responds to very small magnetic fields and may find use in magneto-optic devices.

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Keywords:ferromagnetism,magnetic platelets,liquid crystal,hitherto,paramagnetism

D14–SCFD3-dependent degradation of D53 regulates strigolactone signalling

Feng Zhou,     Qibing Lin,     Lihong Zhu,     Yulong Ren,     Kunneng Zhou,     Nitzan Shabek,     Fuqing Wu,     Haibin Mao,     Wei Dong,     Lu Gan,     Weiwei Ma,     He Gao,     Jun Chen,     Chao Yang,     Dan Wang, Junjie Tan,     Xin Zhang,     Xiuping Guo,     Jiulin Wang,     Ling Jiang,     Xi Liu,     Weiqi Chen,     Jinfang Chu,     Cunyu Yan,     Kotomi Ueno     et al.

                                                                                           

Abstract:

Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the α/β hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses.

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Keywords:D53,strigolactone,arbuscular mycorrhizal,Clp ATPase

DWARF 53 acts as a repressor of strigolactone signalling in rice

Liang Jiang,     Xue Liu,     Guosheng Xiong,     Huihui Liu,     Fulu Chen,     Lei Wang,     Xiangbing Meng, Guifu Liu,     Hong Yu,     Yundong Yuan,     Wei Yi,     Lihua Zhao,     Honglei Ma,     Yuanzheng He, Zhongshan Wu,     Karsten Melcher,     Qian Qian,     H. Eric Xu,     Yonghong Wang     & Jiayang Li

                                                                                   

Abstract:

Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp–Cullin–F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCFD3 ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCFD3 ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14–D3 complex.

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Keywords:DWARF 53,strigolactone,rice,ubiquitination,SKP-cullin-F-box

Astrocytes mediate synapse elimination through MEGF10 and MERTK pathways

Won-Suk Chung,     Laura E. Clarke,     Gordon X. Wang,     Benjamin K. Stafford,     Alexander Sher, Chandrani Chakraborty,     Julia Joung,     Lynette C. Foo,     Andrew Thompson,     Chinfei Chen, Stephen J. Smith     & Ben A. Barres

                                                                                            

Abstract:

To achieve its precise neural connectivity, the developing mammalian nervous system undergoes extensive activity-dependent synapse remodelling. Recently, microglial cells have been shown to be responsible for a portion of synaptic pruning, but the remaining mechanisms remain unknown. Here we report a new role for astrocytes in actively engulfing central nervous system synapses. This process helps to mediate synapse elimination, requires the MEGF10 and MERTK phagocytic pathways, and is strongly dependent on neuronal activity. Developing mice deficient in both astrocyte pathways fail to refine their retinogeniculate connections normally and retain excess functional synapses. Finally, we show that in the adult mouse brain, astrocytes continuously engulf both excitatory and inhibitory synapses. These studies reveal a novel role for astrocytes in mediating synapse elimination in the developing and adult brain, identify MEGF10 and MERTK as critical proteins in the synapse remodelling underlying neural circuit refinement, and have important implications for understanding learning and memory as well as neurological disease processes

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Keywords:astrocytes,MEGF10,MERTK,retinogeniculate,phagocytic,

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

Frédéric Ariey,     Benoit Witkowski,     Chanaki Amaratunga,     Johann Beghain,     Anne-Claire Langlois,     Nimol Khim,     Saorin Kim,     Valentine Duru,     Christiane Bouchier,     Laurence Ma, Pharath Lim,     Rithea Leang,     Socheat Duong,     Sokunthea Sreng,     Seila Suon,     Char Meng Chuor,     Denis Mey Bout,     Sandie Ménard,     William O. Rogers,     Blaise Genton,     Thierry Fandeur,     Olivo Miotto,     Pascal Ringwald,     Jacques Le Bras,     Antoine Berry     et al.

                                                                                    

Abstract:

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (‘K13-propeller’) with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.

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Keywords:artemisinin,plasmodium falciparium,malaria,cambodian

The complete genome sequence of a Neanderthal from the Altai Mountains

Kay Prüfer,     Fernando Racimo,     Nick Patterson,     Flora Jay,     Sriram Sankararaman,     Susanna Sawyer,     Anja Heinze,     Gabriel Renaud,     Peter H. Sudmant,     Cesare de Filippo,     Heng Li, Swapan Mallick,     Michael Dannemann,     Qiaomei Fu,     Martin Kircher,     Martin Kuhlwilm, Michael Lachmann,     Matthias Meyer,     Matthias Ongyerth,     Michael Siebauer,     Christoph Theunert,     Arti Tandon,     Priya Moorjani,     Joseph Pickrell,     James C. Mullikin     et al.

                                                                                  

Abstract:

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

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Keywords:genome sequence,altai mountains,denisovans,interbreeding

Structural basis for Ca2+ selectivity of a voltage-gated calcium channel

Lin Tang,     Tamer M. Gamal El-Din,     Jian Payandeh,     Gilbert Q. Martinez,     Teresa M. Heard, Todd Scheuer,     Ning Zheng     & William A. Catterall

                                                                                      

Abstract:

Voltage-gated calcium (CaV) channels catalyse rapid, highly selective influx of Ca2+ into cells despite a 70-fold higher extracellular concentration of Na+. How CaV channels solve this fundamental biophysical problem remains unclear. Here we report physiological and crystallographic analyses of a calcium selectivity filter constructed in the homotetrameric bacterial NaV channel NaVAb. Our results reveal interactions of hydrated Ca2+ with two high-affinity Ca2+-binding sites followed by a third lower-affinity site that would coordinate Ca2+ as it moves inward. At the selectivity filter entry, Site 1 is formed by four carboxyl side chains, which have a critical role in determining Ca2+ selectivity. Four carboxyls plus four backbone carbonyls form Site 2, which is targeted by the blocking cations Cd2+ and Mn2+, with single occupancy. The lower-affinity Site 3 is formed by four backbone carbonyls alone, which mediate exit into the central cavity. This pore architecture suggests a conduction pathway involving transitions between two main states with one or two hydrated Ca2+ ions bound in the selectivity filter and supports a ‘knock-off’ mechanism of ion permeation through a stepwise-binding process. The multi-ion selectivity filter of our CaVAb model establishes a structural framework for understanding the mechanisms of ion selectivity and conductance by vertebrate CaV channels.

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Keywords:ca2+,voltage,gated,calcium channel,carboxyls,cations

Spread in model climate sensitivity traced to atmospheric convective mixing

Steven C. Sherwood,     Sandrine Bony     & Jean-Louis Dufresne

                                                                                       

Abstract:

Equilibrium climate sensitivity refers to the ultimate change in global mean temperature in response to a change in external forcing. Despite decades of research attempting to narrow uncertainties, equilibrium climate sensitivity estimates from climate models still span roughly 1.5 to 5 degrees Celsius for a doubling of atmospheric carbon dioxide concentration, precluding accurate projections of future climate. The spread arises largely from differences in the feedback from low clouds, for reasons not yet understood. Here we show that differences in the simulated strength of convective mixing between the lower and middle tropical troposphere explain about half of the variance in climate sensitivity estimated by 43 climate models. The apparent mechanism is that such mixing dehydrates the low-cloud layer at a rate that increases as the climate warms, and this rate of increase depends on the initial mixing strength, linking the mixing to cloud feedback. The mixing inferred from observations appears to be sufficiently strong to imply a climate sensitivity of more than 3 degrees for a doubling of carbon dioxide. This is significantly higher than the currently accepted lower bound of 1.5 degrees, thereby constraining model projections towards relatively severe future warming.

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Keywords:equilibrium,carbondioxide,warming

Patterning and growth control by membrane-tethered Wingless

Cyrille Alexandre,     Alberto Baena-Lopez     & Jean-Paul Vincent

                                                          

Abstract:

Wnts are evolutionarily conserved secreted signalling proteins that, in various developmental contexts, spread from their site of synthesis to form a gradient and activate target-gene expression at a distance. However, the requirement for Wnts to spread has never been directly tested. Here we used genome engineering to replace the endogenous wingless gene, which encodes the main Drosophila Wnt, with one that expresses a membrane-tethered form of the protein. Surprisingly, the resulting flies were viable and produced normally patterned appendages of nearly the right size, albeit with a delay. We show that, in the prospective wing, prolonged wingless transcription followed by memory of earlier signalling allows persistent expression of relevant target genes. We suggest therefore that the spread of Wingless is dispensable for patterning and growth even though it probably contributes to increasing cell proliferation.

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Keywords:patterning,membrane,wingless,drosophila

Elephant shark genome provides unique insights into gnathostome evolution

Byrappa Venkatesh,     Alison P. Lee,     Vydianathan Ravi,     Ashish K. Maurya,     Michelle M. Lian, Jeremy B. Swann,     Yuko Ohta,     Martin F. Flajnik,     Yoichi Sutoh,     Masanori Kasahara,     Shawn Hoon,     Vamshidhar Gangu,     Scott W. Roy,     Manuel Irimia,     Vladimir Korzh,     Igor Kondrychyn, Zhi Wei Lim,     Boon-Hui Tay,     Sumanty Tohari,     Kiat Whye Kong,     Shufen Ho,     Belen Lorente-Galdos,     Javier Quilez,     Tomas Marques-Bonet,     Brian J. Raney     et al.

                                                                    

Abstract:

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

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keywords:genome,gnathostome,evolution,living fossil

Diversity of ageing across the tree of life

Owen R. Jones,     Alexander Scheuerlein,     Roberto Salguero-Gómez,     Carlo Giovanni Camarda,     Ralf Schaible,     Brenda B. Casper,     Johan P. Dahlgren,     Johan Ehrlén,     María B. García,     Eric S. Menges,     Pedro F. Quintana-Ascencio,     Hal Caswell,     Annette Baudisch     & James W. Vaupel

                                                                          

Abstract:

Evolution drives, and is driven by, demography. A genotype moulds its phenotype’s age patterns of mortality and fertility in an environment; these two patterns in turn determine the genotype’s fitness in that environment. Hence, to understand the evolution of ageing, age patterns of mortality and reproduction need to be compared for species across the tree of life. However, few studies have done so and only for a limited range of taxa. Here we contrast standardized patterns over age for 11 mammals, 12 other vertebrates, 10 invertebrates, 12 vascular plants and a green alga. Although it has been predicted that evolution should inevitably lead to increasing mortality and declining fertility with age after maturity, there is great variation among these species, including increasing, constant, decreasing, humped and bowed trajectories for both long- and short-lived species. This diversity challenges theoreticians to develop broader perspectives on the evolution of ageing and empiricists to study the demography of more species.

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Keywords:ageing,vertebrates,taxa

UvrD facilitates DNA repair by pulling RNA polymerase backwards

Vitaly Epshtein,     Venu Kamarthapu,     Katelyn McGary,     Vladimir Svetlov,     Beatrix Ueberheide, Sergey Proshkin,     Alexander Mironov     & Evgeny Nudle

                                                                          

Abstract:

UvrD helicase is required for nucleotide excision repair, although its role in this process is not well defined. Here we show that Escherichia coli UvrD binds RNA polymerase during transcription elongation and, using its helicase/translocase activity, forces RNA polymerase to slide backward along DNA. By inducing backtracking, UvrD exposes DNA lesions shielded by blocked RNA polymerase, allowing nucleotide excision repair enzymes to gain access to sites of damage. Our results establish UvrD as a bona fide transcription elongation factor that contributes to genomic integrity by resolving conflicts between transcription and DNA repair complexes. Furthermore, we show that the elongation factor NusA cooperates with UvrD in coupling transcription to DNA repair by promoting backtracking and recruiting nucleotide excision repair enzymes to exposed lesions. Because backtracking is a shared feature of all cellular RNA polymerases, we propose that this mechanism enables RNA polymerases to function as global DNA damage scanners in bacteria and eukaryotes.

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Keywords:UvrD,dna repair,RNA polymerase,helicase

Biochemical reconstitution of topological DNA binding by the cohesin ring

Yasuto Murayama     & Frank Uhlmann

                                                               

Abstract;

Cohesion between sister chromatids, mediated by the chromosomal cohesin complex, is a prerequisite for faithful chromosome segregation in mitosis. Cohesin also has vital roles in DNA repair and transcriptional regulation. The ring-shaped cohesin complex is thought to encircle sister DNA strands, but its molecular mechanism of action is poorly understood and the biochemical reconstitution of cohesin activity in vitro has remained an unattained goal. Here we reconstitute cohesin loading onto DNA using purified fission yeast cohesin and its loader complex, Mis4Scc2–Ssl3Scc4 (Schizosaccharomyces pombe gene names appear throughout with their more commonly known Saccharomyces cerevisiae counterparts added in superscript). Incubation of cohesin with DNA leads to spontaneous topological loading, but this remains inefficient. The loader contacts cohesin at multiple sites around the ring circumference, including the hitherto enigmatic Psc3Scc3 subunit, and stimulates cohesin’s ATPase, resulting in efficient topological loading. The in vitro reconstitution of cohesin loading onto DNA provides mechanistic insight into the initial steps of the establishment of sister chromatid cohesion and other chromosomal processes mediated by cohesin.

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Keywords:DNA binding,cohesin ring,saccharomyces cervisiae

CNVs conferring risk of autism or schizophrenia affect cognition in controls

Hreinn Stefansson,     Andreas Meyer-Lindenberg,     Stacy Steinberg,     Brynja Magnusdottir, Katrin Morgen,     Sunna Arnarsdottir,     Gyda Bjornsdottir,     G. Bragi Walters,     Gudrun A. Jonsdottir,     Orla M. Doyle,     Heike Tost,     Oliver Grimm,     Solveig Kristjansdottir,     Heimir Snorrason,     Solveig R. Davidsdottir,     Larus J. Gudmundsson,     Gudbjorn F. Jonsson, Berglind Stefansdottir,     Isafold Helgadottir,     Magnus Haraldsson,     Birna Jonsdottir,     Johan H. Thygesen,     Adam J. Schwarz,     Michael Didriksen,     Tine B. Stensbøl     et al.

                                                                              

Abstract:

In a small fraction of patients with schizophrenia or autism, alleles of copy-number variants (CNVs) in their genomes are probably the strongest factors contributing to the pathogenesis of the disease. These CNVs may provide an entry point for investigations into the mechanisms of brain function and dysfunction alike. They are not fully penetrant and offer an opportunity to study their effects separate from that of manifest disease. Here we show in an Icelandic sample that a few of the CNVs clearly alter fecundity (measured as the number of children by age 45). Furthermore, we use various tests of cognitive function to demonstrate that control subjects carrying the CNVs perform at a level that is between that of schizophrenia patients and population controls. The CNVs do not all affect the same cognitive domains, hence the cognitive deficits that drive or accompany the pathogenesis vary from one CNV to another. Controls carrying the chromosome 15q11.2 deletion between breakpoints 1 and 2 (15q11.2(BP1-BP2) deletion) have a history of dyslexia and dyscalculia, even after adjusting for IQ in the analysis, and the CNV only confers modest effects on other cognitive traits. The 15q11.2(BP1-BP2) deletion affects brain structure in a pattern consistent with both that observed during first-episode psychosis in schizophrenia and that of structural correlates in dyslexia.

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Keywords:autism,schizophrenia,cognition,brain function

Architecture of the large subunit of the mammalian mitochondrial ribosome

Basil J. Greber,     Daniel Boehringer,     Alexander Leitner,     Philipp Bieri,     Felix Voigts-Hoffmann,     Jan P. Erzberger,     Marc Leibundgut,     Ruedi Aebersold     & Nenad Ban

                                                                 

Abstact:

Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain

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Keywords:mammalian,mitochondrial,ribosome,phosphorylation,remodelled

Cell death by pyroptosis drives CD4 T-cell depletion in HIV-1 infection

Gilad Doitsh,     Nicole L. K. Galloway,     Xin Geng,     Zhiyuan Yang,     Kathryn M. Monroe,     Orlando Zepeda,     Peter W. Hunt,     Hiroyu Hatano,     Stefanie Sowinski,     Isa Muñoz-Arias     & Warner C. Greene

                                                                        

Abstract:

The pathway causing CD4 T-cell death in HIV-infected hosts remains poorly understood although apoptosis has been proposed as a key mechanism. We now show that caspase-3-mediated apoptosis accounts for the death of only a small fraction of CD4 T cells corresponding to those that are both activated and productively infected. The remaining over 95% of quiescent lymphoid CD4 T cells die by caspase-1-mediated pyroptosis triggered by abortive viral infection. Pyroptosis corresponds to an intensely inflammatory form of programmed cell death in which cytoplasmic contents and pro-inflammatory cytokines, including IL-1β, are released. This death pathway thus links the two signature events in HIV infection—CD4 T-cell depletion and chronic inflammation—and creates a pathogenic vicious cycle in which dying CD4 T cells release inflammatory signals that attract more cells to die. This cycle can be broken by caspase 1 inhibitors shown to be safe in humans, raising the possibility of a new class of ‘anti-AIDS’ therapeutics targeting the host rather than the virus.

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Keywords:pyroptosis,CD4,T-cells,HIV-1 \,caspase-1

Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV

Mario Roederer,     Brandon F. Keele,     Stephen D. Schmidt,     Rosemarie D. Mason,     Hugh C. Welles,     Will Fischer,     Celia Labranche,     Kathryn E. Foulds,     Mark K. Louder,     Zhi-Yong Yang, John-Paul M. Todd,     Adam P. Buzby,     Linh V. Mach,     Ling Shen,     Kelly E. Seaton,     Brandy M. Ward,     Robert T. Bailer,     Raphael Gottardo,     Wenjuan Gu,     Guido Ferrari,     S. Munir Alam, Thomas N. Denny,     David C. Montefiori,     Georgia D. Tomaras,     Bette T. Korber     et al.

                                                                           

Abstact:

A major challenge for the development of a highly effective AIDS vaccine is the identification of mechanisms of protective immunity. To address this question, we used a nonhuman primate challenge model with simian immunodeficiency virus (SIV). We show that antibodies to the SIV envelope are necessary and sufficient to prevent infection. Moreover, sequencing of viruses from breakthrough infections revealed selective pressure against neutralization-sensitive viruses; we identified a two-amino-acid signature that alters antigenicity and confers neutralization resistance. A similar signature confers resistance of human immunodeficiency virus (HIV)-1 to neutralization by monoclonal antibodies against variable regions 1 and 2 (V1V2), suggesting that SIV and HIV share a fundamental mechanism of immune escape from vaccine-elicited or naturally elicited antibodies. These analyses provide insight into the limited efficacy seen in HIV vaccine trials.

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Keywords:virological,immunological,siv,vaccine,hiv,antigenicity

Discovery and saturation analysis of cancer genes across 21 tumour types

Michael S. Lawrence,     Petar Stojanov,     Craig H. Mermel,     James T. Robinson,     Levi A. Garraway,     Todd R. Golub,     Matthew Meyerson,     Stacey B. Gabriel,     Eric S. Lander     & Gad Getz

                                                                      

Abstract:

Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600–5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.

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Keywords:cancer genes,tumours,exome sequence,homeostatis

ANP32E is a histone chaperone that removes H2A.Z from chromatin

Arnaud Obri,     Khalid Ouararhni,     Christophe Papin,     Marie-Laure Diebold,     Kiran Padmanabhan,     Martin Marek,     Isabelle Stoll,     Ludovic Roy,     Patrick T. Reilly,     Tak W. Mak, Stefan Dimitrov,     Christophe Romier     & Ali Hamiche

                                                                                

Abstract:

H2A.Z is an essential histone variant implicated in the regulation of key nuclear events. However, the metazoan chaperones responsible for H2A.Z deposition and its removal from chromatin remain unknown. Here we report the identification and characterization of the human protein ANP32E as a specific H2A.Z chaperone. We show that ANP32E is a member of the presumed H2A.Z histone-exchange complex p400/TIP60. ANP32E interacts with a short region of the docking domain of H2A.Z through a new motif termed H2A.Z interacting domain (ZID). The 1.48 Å resolution crystal structure of the complex formed between the ANP32E-ZID and the H2A.Z/H2B dimer and biochemical data support an underlying molecular mechanism for H2A.Z/H2B eviction from the nucleosome and its stabilization by ANP32E through a specific extension of the H2A.Z carboxy-terminal α-helix. Finally, analysis of H2A.Z localization in ANP32E−/− cells by chromatin immunoprecipitation followed by sequencing shows genome-wide enrichment, redistribution and accumulation of H2A.Z at specific chromatin control regions, in particular at enhancers and insulators.

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Keywords:ANP32E,histone,chaperone,chromatin

Stimulus-triggered fate conversion of somatic cells into pluripotency

Haruko Obokata,     Teruhiko Wakayama,     Yoshiki Sasai,     Koji Kojima,     Martin P. Vacanti,     Hitoshi Niwa,     Masayuki Yamato     & Charles A. Vacanti

                                                                              

Abstract:

Here we report a unique cellular reprogramming phenomenon, called stimulus-triggered acquisition of pluripotency (STAP), which requires neither nuclear transfer nor the introduction of transcription factors. In STAP, strong external stimuli such as a transient low-pH stressor reprogrammed mammalian somatic cells, resulting in the generation of pluripotent cells. Through real-time imaging of STAP cells derived from purified lymphocytes, as well as gene rearrangement analysis, we found that committed somatic cells give rise to STAP cells by reprogramming rather than selection. STAP cells showed a substantial decrease in DNA methylation in the regulatory regions of pluripotency marker genes. Blastocyst injection showed that STAP cells efficiently contribute to chimaeric embryos and to offspring via germline transmission. We also demonstrate the derivation of robustly expandable pluripotent cell lines from STAP cells. Thus, our findings indicate that epigenetic fate determination of mammalian cells can be markedly converted in a context-dependent manner by strong environmental cues.

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Keywords:somatic cells,pluripotency,methylation,blastocyst

The evolution of lncRNA repertoires and expression patterns in tetrapods

Anamaria Necsulea,     Magali Soumillon,     Maria Warnefors,     Angélica Liechti,     Tasman Daish, Ulrich Zeller,     Julie C. Baker,     Frank Grützner     & Henrik Kaessmann

                                                                         

Abstract:

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

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Keywords:IncRNA,tetrapods,microRNA

An environmental bacterial taxon with a large and distinct metabolic repertoire

Micheal C. Wilson,     Tetsushi Mori,     Christian Rückert,     Agustinus R. Uria,     Maximilian J. Helf, Kentaro Takada,     Christine Gernert,     Ursula A. E. Steffens,     Nina Heycke,     Susanne Schmitt, Christian Rinke,     Eric J. N. Helfrich,     Alexander O. Brachmann,     Cristian Gurgui,     Toshiyuki Wakimoto,     Matthias Kracht,     Max Crüsemann,     Ute Hentschel,     Ikuro Abe,     Shigeki Matsunaga,     Jörn Kalinowski,     Haruko Takeyama     & Jörn Piel

                                                  

Abstract:

Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. ‘Entotheonella’ spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum ‘Tectomicrobia’. The pronounced bioactivities and chemical uniqueness of ‘Entotheonella’ compounds provide significant opportunities for ecological studies and drug discovery.

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Keywords:taxon,acitomycetes,phylotypes,entotheonella

In vivo discovery of immunotherapy targets in the tumour microenvironment

Penghui Zhou,     Donald R. Shaffer,     Diana A. Alvarez Arias,     Yukoh Nakazaki,     Wouter Pos, Alexis J. Torres,     Viviana Cremasco,     Stephanie K. Dougan,     Glenn S. Cowley,     Kutlu Elpek, Jennifer Brogdon,     John Lamb,     Shannon J. Turley,     Hidde L. Ploegh,     David E. Root,     J. Christopher Love,     Glenn Dranoff,     Nir Hacohen,     Harvey Cantor     & Kai W. Wucherpfennig

                                                     

Abstract:

Recent clinical trials showed that targeting of inhibitory receptors on T cells induces durable responses in a subset of cancer patients, despite advanced disease. However, the regulatory switches controlling T-cell function in immunosuppressive tumours are not well understood. Here we show that such inhibitory mechanisms can be systematically discovered in the tumour microenvironment. We devised an in vivo pooled short hairpin RNA (shRNA) screen in which shRNAs targeting negative regulators became highly enriched in murine tumours by releasing a block on T-cell proliferation upon tumour antigen recognition. Such shRNAs were identified by deep sequencing of the shRNA cassette from T cells infiltrating tumour or control tissues. One of the target genes was Ppp2r2d, a regulatory subunit of the PP2A phosphatase family. In tumours, Ppp2r2d knockdown inhibited T-cell apoptosis and enhanced T-cell proliferation as well as cytokine production. Key regulators of immune function can therefore be discovered in relevant tissue microenvironments

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Keywords:immunotherapy,tumour,RNA[shRNA],phosphate

Fifty thousand years of Arctic vegetation and megafaunal diet

Eske Willerslev,     John Davison,     Mari Moora,     Martin Zobel,     Eric Coissac,     Mary E. Edwards, Eline D. Lorenzen,     Mette Vestergård,     Galina Gussarova,     James Haile,     Joseph Craine, Ludovic Gielly,     Sanne Boessenkool,     Laura S. Epp,     Peter B. Pearman,     Rachid Cheddadi, David Murray,     Kari Anne Bråthen,     Nigel Yoccoz,     Heather Binney,     Corinne Cruaud,     Patrick Wincker,     Tomasz Goslar,     Inger Greve Alsos,     Eva Bellemain     et al.

                                                                                        

Abstract:

Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr BP (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr BP), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr BP, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.

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Keywords:megafaunal diet,meta barcoding,graminoids

Molecular control of δ-opioid receptor signalling

Gustavo Fenalti,     Patrick M. Giguere,     Vsevolod Katritch,     Xi-Ping Huang,     Aaron A. Thompson,     Vadim Cherezov,     Bryan L. Roth     & Raymond C. Stevens

                                                                                  

Abstract:

Opioids represent widely prescribed and abused medications, although their signal transduction mechanisms are not well understood. Here we present the 1.8 Å high-resolution crystal structure of the human δ-opioid receptor (δ-OR), revealing the presence and fundamental role of a sodium ion in mediating allosteric control of receptor functional selectivity and constitutive activity. The distinctive δ-OR sodium ion site architecture is centrally located in a polar interaction network in the seven-transmembrane bundle core, with the sodium ion stabilizing a reduced agonist affinity state, and thereby modulating signal transduction. Site-directed mutagenesis and functional studies reveal that changing the allosteric sodium site residue Asn 131 to an alanine or a valine augments constitutive β-arrestin-mediated signalling. Asp95Ala, Asn310Ala and Asn314Ala mutations transform classical δ-opioid antagonists such as naltrindole into potent β-arrestin-biased agonists. The data establish the molecular basis for allosteric sodium ion control in opioid signalling, revealing that sodium-coordinating residues act as ‘efficacy switches’ at a prototypic G-protein-coupled receptor.

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Keywords:opioids,allosteric control,beta arrestin mediated signalling,Asn 131

A polygenic burden of rare disruptive mutations in schizophrenia

Shaun M. Purcell,     Jennifer L. Moran,     Menachem Fromer,     Douglas Ruderfer,     Nadia Solovieff,     Panos Roussos,     Colm O’Dushlaine,     Kimberly Chambert,     Sarah E. Bergen,     Anna Kähler,     Laramie Duncan,     Eli Stahl,     Giulio Genovese,     Esperanza Fernández,     Mark O. Collins,     Noboru H. Komiyama,     Jyoti S. Choudhary,     Patrik K. E. Magnusson,     Eric Banks, Khalid Shakir,     Kiran Garimella,     Tim Fennell,     Mark DePristo,     Seth G. N. Grant,     Stephen J. Haggarty     et al.

                                                                           

Abstract:

Schizophrenia is a common disease with a complex aetiology, probably involving multiple and heterogeneous genetic factors. Here, by analysing the exome sequences of 2,536 schizophrenia cases and 2,543 controls, we demonstrate a polygenic burden primarily arising from rare (less than 1 in 10,000), disruptive mutations distributed across many genes. Particularly enriched gene sets include the voltage-gated calcium ion channel and the signalling complex formed by the activity-regulated cytoskeleton-associated scaffold protein (ARC) of the postsynaptic density, sets previously implicated by genome-wide association and copy-number variation studies. Similar to reports in autism, targets of the fragile X mental retardation protein (FMRP, product of FMR1) are enriched for case mutations. No individual gene-based test achieves significance after correction for multiple testing and we do not detect any alleles of moderately low frequency (approximately 0.5 to 1 per cent) and moderately large effect. Taken together, these data suggest that population-based exome sequencing can discover risk alleles and complements established gene-mapping paradigms in neuropsychiatric disease.

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Keywords:aetiology,schizophrenia,scaffold protein

De novo mutations in schizophrenia implicate synaptic networks

Menachem Fromer,     Andrew J. Pocklington,     David H. Kavanagh,     Hywel J. Williams,     Sarah Dwyer,     Padhraig Gormley,     Lyudmila Georgieva,     Elliott Rees,     Priit Palta,     Douglas M. Ruderfer,     Noa Carrera,     Isla Humphreys,     Jessica S. Johnson,     Panos Roussos,     Douglas D. Barker,     Eric Banks,     Vihra Milanova,     Seth G. Grant,     Eilis Hannon,     Samuel A. Rose,     Kimberly Chambert,     Milind Mahajan,     Edward M. Scolnick,     Jennifer L. Moran,     George Kirov     et al.

                                                                                  

Abstract:

Inherited alleles account for most of the genetic risk for schizophrenia. However, new (de novo) mutations, in the form of large chromosomal copy number changes, occur in a small fraction of cases and disproportionally disrupt genes encoding postsynaptic proteins. Here we show that small de novo mutations, affecting one or a few nucleotides, are overrepresented among glutamatergic postsynaptic proteins comprising activity-regulated cytoskeleton-associated protein (ARC) and N-methyl-D-aspartate receptor (NMDAR) complexes. Mutations are additionally enriched in proteins that interact with these complexes to modulate synaptic strength, namely proteins regulating actin filament dynamics and those whose messenger RNAs are targets of fragile X mental retardation protein (FMRP). Genes affected by mutations in schizophrenia overlap those mutated in autism and intellectual disability, as do mutation-enriched synaptic pathways. Aligning our findings with a parallel case–control study, we demonstrate reproducible insights into aetiological mechanisms for schizophrenia and reveal pathophysiology shared with other neurodevelopmental disorders.

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Keywords:schizophrenia,synaptic networks,glutamatergic

Protein-guided RNA dynamics during early ribosome assembly

Hajin Kim,     Sanjaya C. Abeysirigunawarden,     Ke Chen,     Megan Mayerle,     Kaushik Ragunathan,     Zaida Luthey-Schulten,     Taekjip Ha     & Sarah A. Woodson

                                                                               

Abstract:

The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the ribosomal RNA structure so that later proteins may join the complex is poorly understood. Here we use single-molecule fluorescence resonance energy transfer (FRET) to observe real-time encounters between Escherichia coli ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4–RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free-energy path to protein–RNA recognition. Three-colour FRET and molecular dynamics simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. These protein-guided dynamics offer an alternative explanation for induced fit in RNA–protein complexes.

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Keywords:ribosome,RNA helix motion,RNA-protein complexes

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia

Liran I. Shlush,     Sasan Zandi,     Amanda Mitchell,     Weihsu Claire Chen,     Joseph M. Brandwein, Vikas Gupta,     James A. Kennedy,     Aaron D. Schimmer,     Andre C. Schuh,     Karen W. Yee, Jessica L. McLeod,     Monica Doedens,     Jessie J. F. Medeiros,     Rene Marke,     Hyeoung Joon Kim,     Kwon Lee,     John D. McPherson,     Thomas J. Hudson,     The HALT Pan-Leukemia Gene Panel Consortium,     Andrew M. K. Brown,     Quang M. Trinh,     Lincoln D. Stein,     Mark D. Minden, Jean C. Y. Wang     & John E. Dick

                                                                                              

Abstract:

In acute myeloid leukaemia (AML), the cell of origin, nature and biological consequences of initiating lesions, and order of subsequent mutations remain poorly understood, as AML is typically diagnosed without observation of a pre-leukaemic phase. Here, highly purified haematopoietic stem cells (HSCs), progenitor and mature cell fractions from the blood of AML patients were found to contain recurrent DNMT3A mutations (DNMT3Amut) at high allele frequency, but without coincident NPM1 mutations (NPM1c) present in AML blasts. DNMT3Amut-bearing HSCs showed a multilineage repopulation advantage over non-mutated HSCs in xenografts, establishing their identity as pre-leukaemic HSCs. Pre-leukaemic HSCs were found in remission samples, indicating that they survive chemotherapy. Therefore DNMT3Amut arises early in AML evolution, probably in HSCs, leading to a clonally expanded pool of pre-leukaemic HSCs from which AML evolves. Our findings provide a paradigm for the detection and treatment of pre-leukaemic clones before the acquisition of additional genetic lesions engenders greater therapeutic resistance.

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Keywords:pre-leukaemic,haematopoietic,stem cells

In situ identification of bipotent stem cells in the mammary gland

Anne C. Rios,     Nai Yang Fu,     Geoffrey J. Lindeman     & Jane E. Visvader

                                                                      

Abstract:

The mammary epithelium undergoes profound morphogenetic changes during development. Architecturally, it comprises two primary lineages, the inner luminal and outer myoepithelial cell layers. Two opposing concepts on the nature of mammary stem cells (MaSCs) in the postnatal gland have emerged. One model, based on classical transplantation assays, postulates that bipotent MaSCs have a key role in coordinating ductal epithelial expansion and maintenance in the adult gland, whereas the second model proposes that only unipotent MaSCs identified by lineage tracing contribute to these processes. Through clonal cell-fate mapping studies using a stochastic multicolour cre reporter combined with a new three-dimensional imaging strategy, we provide evidence for the existence of bipotent MaSCs as well as distinct long-lived progenitor cells. The cellular dynamics at different developmental stages support a model in which both stem and progenitor cells drive morphogenesis during puberty, whereas bipotent MaSCs coordinate ductal homeostasis and remodelling of the mouse adult gland.

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Keywords:bip[otent,stem cells,mammary glands

Geriatric muscle stem cells switch reversible quiescence into senescence

Pedro Sousa-Victor,     Susana Gutarra,     Laura García-Prat,     Javier Rodriguez-Ubreva,     Laura Ortet,     Vanessa Ruiz-Bonilla,     Mercè Jardí,     Esteban Ballestar,     Susana González,     Antonio L. Serrano,     Eusebio Perdiguero     & Pura Muñoz-Cánoves

                                                                                      

Abstract:

Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with ageing. Here we report that geriatric satellite cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and that this irreversibly affects their intrinsic regenerative and self-renewal capacities. In geriatric mice, resting satellite cells lose reversible quiescence by switching to an irreversible pre-senescence state, caused by derepression of p16INK4a (also called Cdkn2a). On injury, these cells fail to activate and expand, undergoing accelerated entry into a full senescence state (geroconversion), even in a youthful environment. p16INK4a silencing in geriatric satellite cells restores quiescence and muscle regenerative functions. Our results demonstrate that maintenance of quiescence in adult life depends on the active repression of senescence pathways. As p16INK4a is dysregulated in human geriatric satellite cells, these findings provide the basis for stem-cell rejuvenation in sarcopenic muscles.

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Keywords:geriatric,stem cells,quiescence,senescence

A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3

Aditya Murthy,     Yun Li,     Ivan Peng,     Mike Reichelt,     Anand Kumar Katakam,     Rajkumar Noubade,     Merone Roose-Girma,     Jason DeVoss,     Lauri Diehl,     Robert R. Graham     & Menno van Lookeren Campagne

                                                                                                                                                                                                               

Abstract:

Crohn’s disease is a debilitating inflammatory bowel disease (IBD) that can involve the entire digestive tract. A single-nucleotide polymorphism (SNP) encoding a missense variant in the autophagy gene ATG16L1 (rs2241880, Thr300Ala) is strongly associated with the incidence of Crohn’s disease. Numerous studies have demonstrated the effect of ATG16L1 deletion or deficiency; however, the molecular consequences of the Thr300Ala (T300A) variant remains unknown. Here we show that amino acids 296–299 constitute a caspase cleavage motif in ATG16L1 and that the T300A variant (T316A in mice) significantly increases ATG16L1 sensitization to caspase-3-mediated processing. We observed that death-receptor activation or starvation-induced metabolic stress in human and murine macrophages increased degradation of the T300A or T316A variants of ATG16L1, respectively, resulting in diminished autophagy. Knock-in mice harbouring the T316A variant showed defective clearance of the ileal pathogen Yersinia enterocolitica and an elevated inflammatory cytokine response. In turn, deletion of the caspase-3-encoding gene, Casp3, or elimination of the caspase cleavage site by site-directed mutagenesis rescued starvation-induced autophagy and pathogen clearance, respectively. These findings demonstrate that caspase 3 activation in the presence of a common risk allele leads to accelerated degradation of ATG16L1, placing cellular stress, apoptotic stimuli and impaired autophagy in a unified pathway that predisposes to Crohn’s disease.

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Keywords:Atg1611,autophagy,caspase 3,yersinia enterocolitica

C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma

Matthew Parker,     Kumarasamypet M. Mohankumar,     Chandanamali Punchihewa,     Ricardo Weinlich,     James D. Dalton,     Yongjin Li,     Ryan Lee,     Ruth G. Tatevossian,     Timothy N. Phoenix, Radhika Thiruvenkatam,     Elsie White,     Bo Tang,     Wilda Orisme,     Kirti Gupta,     Michael Rusch, Xiang Chen,     Yuxin Li,     Panduka Nagahawhatte,     Erin Hedlund,     David Finkelstein,     Gang Wu, Sheila Shurtleff,     John Easton,     Kristy Boggs,     Donald Yergeau     et al.

                                                                                     

Abstract:

Members of the nuclear factor-κB (NF-κB) family of transcriptional regulators are central mediators of the cellular inflammatory response. Although constitutive NF-κB signalling is present in most human tumours, mutations in pathway members are rare, complicating efforts to understand and block aberrant NF-κB activity in cancer. Here we show that more than two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of canonical NF-κB signalling, and an uncharacterized gene, C11orf95. In each case, C11orf95–RELA fusions resulted from chromothripsis involving chromosome 11q13.1. C11orf95–RELA fusion proteins translocated spontaneously to the nucleus to activate NF-κB target genes, and rapidly transformed neural stem cells—the cell of origin of ependymoma—to form these tumours in mice. Our data identify a highly recurrent genetic alteration of RELA in human cancer, and the C11orf95–RELA fusion protein as a potential therapeutic target in supratentorial ependymoma.

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Keywords:C11,f95,fusion drive,ependymoma

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

S. C. Mack,     H. Witt,     R. M. Piro,     L. Gu,     S. Zuyderduyn,     A. M. Stütz,     X. Wang,     M. Gallo,     L. Garzia,     K. Zayne,     X. Zhang,     V. Ramaswamy,     N. Jäger,     D. T. W. Jones,     M. Sill,     T. J. Pugh,     M. Ryzhova,     K. M. Wani,     D. J. H. Shih,     R. Head,     M. Remke,     S. D. Bailey,     T. Zichner,     C. C. Faria, M. Barszczyk     et al.

                                                                                      

Abstract:

Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.

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Keywords:epigenomic,tumours,methylator,ependymomas

Crystal structure of the plant dual-affinity nitrate transporter NRT1.1

Ji Sun,     John R. Bankston,     Jian Payandeh,     Thomas R. Hinds,     William N. Zagotta     & Ning Zheng

                                                                         

Abstract:

Nitrate is a primary nutrient for plant growth, but its levels in soil can fluctuate by several orders of magnitude. Previous studies have identified Arabidopsis NRT1.1 as a dual-affinity nitrate transporter that can take up nitrate over a wide range of concentrations. The mode of action of NRT1.1 is controlled by phosphorylation of a key residue, Thr 101; however, how this post-translational modification switches the transporter between two affinity states remains unclear. Here we report the crystal structure of unphosphorylated NRT1.1, which reveals an unexpected homodimer in the inward-facing conformation. In this low-affinity state, the Thr 101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, we show that functional NRT1.1 dimerizes in the cell membrane and that the phosphomimetic mutation of Thr 101 converts the protein into a monophasic high-affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, our results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes.

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Keywords:arabidopsis,phosphorylation,oligomeric,homodimer