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Cell Biology
CASP4 gene silencing in epithelial cancer cells leads to impairment of cell migration, cell-matrix adhesion and tissue invasion.
Dec 11, 2018   Scientific Reports
Papoff G, Presutti D, Lalli C, Bolasco G, Santini S, Manelfi C, Fustaino V, Alemà S, Ruberti G
CASP4 gene silencing in epithelial cancer cells leads to impairment of cell migration, cell-matrix adhesion and tissue invasion.
Dec 11, 2018
Scientific Reports
Inflammatory caspases, including human caspase-4 (CASP4), play key roles in innate immune responses to promote fusion of phagosomes harboring pathogenic bacteria with lysosomes, halt intracellular replication of pathogens, maturation and secretion of pro-inflammatory cytokines. The role of inflammatory caspases in cancer cells remains poorly investigated. Here, we explored the consequences of modulating CASP4 expression levels on the migratory behavior of epithelial cancer cell lines. By a gene silencing approach and in vitro and in vivo studies we show that down-regulation of CASP4 leads to impaired cell migration and cell-matrix adhesion. This phenotype is accompanied by an increased actin cytoskeleton polymerization, changes in the overall organization of adherens junctions (AJs) and number and size of focal adhesions. Interestingly, the cell migration deficit could be reversed by epithelial growth factor treatment, and depletion of calcium ions unveiled a role of CASP4 in the novo assembly of AJs, suggesting that the role of CASP4 is not cell-autonomous. Finally, CASP4-silenced A431 cells exhibited a severe reduction in their ability to invade lung tissue, when injected into nude mice. Overall, our data support the emerging evidence that inflammatory caspases can regulate cell migration through actin remodeling and uncover a novel role of CASP4 in cancer cell behavior.
Hassall's corpuscles with cellular-senescence features maintain IFNα production through neutrophils and pDC activation in the thymus.
Dec 11, 2018   International Immunology
Wang J, Sekai M, Matsui T, Fujii Y, Matsumoto M, Takeuchi O, Minato N, Hamazaki Y
Hassall's corpuscles with cellular-senescence features maintain IFNα production through neutrophils and pDC activation in the thymus.
Dec 11, 2018
International Immunology
Hassall's corpuscles (HCs) are composed of cornifying, terminally differentiated medullary thymic epithelial cells (mTECs) that are developed under the control of Aire. Here, we demonstrated that HC-mTECs show features of cellular senescence and produce inflammatory cytokines and chemokines including CXCL5, thereby recruiting and activating neutrophils to produce IL-23 in the thymic medulla. We further indicated that thymic plasmacytoid dendritic cells (pDCs) expressing IL-23 receptors constitutively produced Ifna, which plays a role in single positive (SP) cell maturation, in an Il23a-dependent manner. Neutrophil depletion with anti-Ly6G antibody injection resulted in a significant decrease of Ifna expression in the thymic pDCs, suggesting that thymic neutrophil activation underlies the Ifna expression in thymic pDCs in steady state conditions. A New Zealand White mouse strain showing HC hyperplasia exhibited greater numbers and activation of thymic neutrophils and pDCs than B6 mice, whereas Aire-deficient B6 mice with defective HC development and SP thymocyte maturation showed significantly compromised numbers and activation of these cells. These results collectively suggested that HC-mTECs with cell-senescence features initiate a unique cell activation cascade including neutrophils and pDCs leading to the constitutive IFNα expression required for SP T-cell maturation in the thymic medulla.
Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation.
Dec 11, 2018   Aging Cell
Tsakiri EN, Gumeni S, Iliaki KK, Benaki D, Vougas K, Sykiotis GP, Gorgoulis VG, Mikros E, Scorrano L, Trougakos IP
Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation.
Dec 11, 2018
Aging Cell
Metazoans viability depends on their ability to regulate metabolic processes and also to respond to harmful challenges by mounting anti-stress responses; these adaptations were fundamental forces during evolution. Central to anti-stress responses are a number of short-lived transcription factors that by functioning as stress sensors mobilize genomic responses aiming to eliminate stressors. We show here that increased expression of nuclear factor erythroid 2-related factor (Nrf2) in Drosophila activated cytoprotective modules and enhanced stress tolerance. However, while mild Nrf2 activation extended lifespan, high Nrf2 expression levels resulted in developmental lethality or, after inducible activation in adult flies, in altered mitochondrial bioenergetics, the appearance of Diabetes Type 1 hallmarks and aging acceleration. Genetic or dietary suppression of Insulin/IGF-like signaling (IIS) titrated Nrf2 activity to lower levels, largely normalized metabolic pathways signaling, and extended flies' lifespan. Thus, prolonged stress signaling by otherwise cytoprotective short-lived stress sensors perturbs IIS resulting in re-allocation of resources from growth and longevity to somatic preservation and stress tolerance. These findings provide a reasonable explanation of why most (if not all) cytoprotective stress sensors are short-lived proteins, and it also explains the build-in negative feedback loops (shown here for Nrf2); the low basal levels of these proteins, and why their suppressors were favored by evolution.
The impact of integrin β2 on granulocyte/macrophage progenitor proliferation.
Dec 11, 2018   Stem Cells (Dayton, Ohio)
Zhang LJ, Yan C, Schouteden S, Ma XJ, Zhao D, Peters T, Verfaillie CM, Feng YM
The impact of integrin β2 on granulocyte/macrophage progenitor proliferation.
Dec 11, 2018
Stem Cells (Dayton, Ohio)
RATIONALE: Previously we reported that although the HSPC frequency in bone marrow cells (BMC) was comparable between β2-/- and β2+/+ mice, transplantation of β2-/- BMC into lethally irradiated CD45.1 recipient resulted in more myeloid cell production than β2+/+ BMC. OBJECTIVE: To address if integrin β2 deficiency skews granulocyte/macrophage progenitor (GMP) proliferation. METHODS AND RESULTS: FACS analysis demonstrated that GMP frequency and cell number were higher and megakaryocyte/erythrocyte progenitor (MEP) frequency and cell number were lower in β2-/- mice than β2+/+ mice. However, the common myeloid progenitors (CMP) frequency and cell number were similar between the two groups. The increased GMP number was due to GMP proliferation as evidenced by the percentage of BrdU-incorporating GMP. Whole genome transcriptome analysis identified increased FcεRIα expression in β2-/- CMP compared to β2+/+ CMP. FcεRIα expression on β2-/- GMP was detected increased in β2-/- mice by qRT-PCR and FACS. Although transplantation of FcεRIαhi GMP or FcεRIαlo GMP into lethally irradiated CD45.1 recipient resulted in comparable myeloid cell production, transplantation of β2 deficient FcεRIαhi GMP generated more myeloid cells than β2+/+ FcεRIαhi GMP. GATA2 expression was increased in β2-/- GMP. Using a luciferase reporter assay, we demonstrated that mutation of the GATA2 binding site in the FcεRIα promoter region diminished FcεRIα transcription. In vitro, the addition of IgE, the ligand of FcεRIα, promoted GMP expansion, which was abrogated by inhibition of JNK phosphorylation. CONCLUSION: Integrin β2 deficiency promoted GMP proliferation and myeloid cell production, which was mediated via FcεRIα/IgE-induced JNK phosphorylation in GMP. © AlphaMed Press 2018.
Toll-like receptor 2 regulates metabolic reprogramming in gastric cancer via superoxide dismutase 2.
Dec 11, 2018   International Journal Of Cancer
Liu YD, Yu L, Ying L, Balic J, Gao H, Deng NT, West A, Yan F, Ji CB, Gough D, Tan P, Jenkins BJ, Li JK
Toll-like receptor 2 regulates metabolic reprogramming in gastric cancer via superoxide dismutase 2.
Dec 11, 2018
International Journal Of Cancer
Toll-like receptors (TLRs) play critical roles in host defence following recognition of conserved microbial- and host-derived components, and their dysregulation is a common feature of various inflammation-associated cancers, including gastric cancer (GC). Despite the recent recognition that metabolic reprogramming is a hallmark of cancer, the molecular effectors of altered metabolism during tumorigenesis remain unclear. Here, using bioenergetics function assays on human GC cells, we reveal that ligand-induced activation of TLR2, predominantly through TLR1/2 heterodimer, augments both oxidative phosphorylation (OXPHOS) and glycolysis, with a bias towards glycolytic activity. Notably, DNA microarray-based expression profiling of human cancer cells stimulated with TLR2 ligands demonstrated significant enrichment of gene-sets for oncogenic pathways previously implicated in metabolic regulation, including reactive oxygen species (ROS), p53 and Myc. Moreover, the redox gene encoding the manganese-dependent mitochondrial enzyme, superoxide dismutase (SOD)2, was strongly induced at the mRNA and protein levels by multiple signalling pathways downstream of TLR2, namely JAK-STAT3, JNK MAPK and NF-κB. Furthermore, siRNA-mediated suppression of SOD2 ameliorated the TLR2-induced metabolic shift in human GC cancer cells. Importantly, patient-derived tissue microarrays and bioinformatics interrogation of clinical datasets indicated that upregulated expression of TLR2 and SOD2 were significantly correlated in human GC, and the TLR2-SOD2 axis was associated with multiple clinical parameters of advanced stage disease, including distant metastasis, microvascular invasion and stage, as well as poor survival. Collectively, our findings reveal a novel TLR2-SOD2 axis as a potential biomarker for therapy and prognosis in cancer. This article is protected by copyright. All rights reserved.
Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.
Dec 11, 2018   International Journal Of Cancer
Sa JK, Choi SW, Zhao J, Lee Y, Zhang J, Kong DS, Choi JW, Seol HJ, Lee JI, Iavarone A, Rabadan R, Nam DH
Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.
Dec 11, 2018
International Journal Of Cancer
Hypermutagenesis refers to marked increase in the number of mutations due to continuous mutagenic process. Hypermutated tumors, have being found in several tumor types, are associated with inherited or acquired alterations in DNA repair pathways. Hypermutation has been observed in a subset of adult glioma patients as a direct result of temozolomide(TMZ)-induced mutagenesis. In present study, we have identified a rare subset of treatment-naïve adult gliomas with de novo hypermutator phenotype and explored the evolution of spontaneous and treatment-induced hypermutagenesis. We conducted Whole-Exome Sequencing (WES), Whole-Transcriptome Sequencing (WTS), and Single-Cell Sequencing (SCS) of TMZ-naïve and post-TMZ treated hypermutated tumors to identify distinct clinical or genomic manifestations that contribute to the development of hypermutation in untreated adult gliomas. TMZ-naïve hypermutated tumors were marked by absence of IDH1 somatic mutation and MGMT promoter (pMGMT) methylation, two genomic traits that were significantly associated with TMZ-induced hypermutagenic event in glioblastoma, and harbored inherited alterations in the mismatch repair (MMR) machinery. The immediate family members of the TMZ-naive hypermutated glioma patients were also previous diagnosed with cancer development history, suggesting that germline dysfunction of the MMR pathway could potentially pose hereditary risk to genetic predisposition of carcinogenesis in gliomas. Lastly, both TMZ-naïve and post-TMZ treated hypermutated tumors exhibited a significant increase in neoantigen load suggesting immunotherapeutic alternatives. Our results present new and unique understanding of hypermutagenic process in adult gliomas and an important step towards clinical implication of immunotherapy in glioma treatment. This article is protected by copyright. All rights reserved.
Identification, Characterization and Field Testing of Brassica napus Mutants Producing High-Oleic Oils.
Dec 11, 2018   The Plant Journal : For Cell And Molecular Biology
Bai S, Engelen S, Denolf P, Wallis JG, Lynch K, Bengtsson JD, Van Thournout M, Haesendonckx B, Browse J
Identification, Characterization and Field Testing of Brassica napus Mutants Producing High-Oleic Oils.
Dec 11, 2018
The Plant Journal : For Cell And Molecular Biology
Producing healthy, high-oleic oils and eliminating trans fatty acids from foods are two goals that can be addressed by reducing activity of the oleate desaturase, FAD2, in oilseeds. However, it is essential to understand the consequences of reducing FAD2 activity on the metabolism, cell biology and physiology of oilseed crop plants. Here, we translate knowledge from studies of fad2 mutants in Arabidopsis (Arabidopsis thaliana) to investigate the limits of non-GMO approaches to maximize oleic acid in the seed oil of canola (Brassica napus), a species that expresses three active FAD2 isozymes. A series of hypomorphic and null mutations in the FAD2.A5 isoform were characterized in yeast (Saccharomyes cerevisiae). Then, four of these were combined with null mutations in the other two isozymes, FAD2.C5 and FAD2.C1. The resulting mutant lines contained 71-87% oleic acid in their seed oil, compared with 62% in wild-type controls. All the mutant lines grew well in a greenhouse, but in field experiments we observed a clear demarcation in plant performance. Mutant lines containing less than 80% oleate in the seed oil were indistinguishable from wild-type controls in growth parameters and seed oil content. By contrast, lines with more than 80% oleate in the seed oil had significantly lower seedling establishment and vigor, delayed flowering and reduced plant height at maturity. These lines also had 7-11% reductions in seed oil content. Our results extend understanding of the B. napus FAD2 isozymes and define the practical limit to increasing oil oleate content in this crop species. This article is protected by copyright. All rights reserved.
Conversion of Fibroblasts to Hepatocytes In Vitro.
Dec 11, 2018   Methods In Molecular Biology (Clifton, N.J.)
Huang P, Sun L, Zhang L, Hui L
Conversion of Fibroblasts to Hepatocytes In Vitro.
Dec 11, 2018
Methods In Molecular Biology (Clifton, N.J.)
Primary hepatocytes are widely used in regenerative medicine, drug metabolism analysis, and in vitro drug screens. To overcome the shortage of liver donors, several strategies, such as differentiation of pluripotent stem cells and transdifferentiation from somatic cells, were developed to generate hepatocytes from alternative sources. Here, we describe in detail lenti-virus-based procedure for direct conversion of human fibroblasts to hepatocytes (hiHep cells) in vitro. A detailed protocol for preparation of human fibroblasts from scar tissues is also provided. Based on this protocol, FOXA3, HNF1A, and HNF4A are introduced into SV40-large-T-antigen-expressing human scar fibroblasts by lenti-virus. It usually takes about 5-7 days to get epithelial hiHep colonies. SV40-large-T-antigen-expressing hiHep (hiHepLT) cells are proliferative and can be expanded to a large number for potential uses.
Relationship between Volatile Anesthetics and Tumor Progression: Unveiling the Mystery.
Dec 11, 2018   Current Medical Science
Jiao B, Yang C, Huang NN, Yang N, Wei J, Xu H
Relationship between Volatile Anesthetics and Tumor Progression: Unveiling the Mystery.
Dec 11, 2018
Current Medical Science
A series of factors can be involved in the perioperative period to cause an increase in cancer-related mortality. Unfortunately, volatile anesthesia might aggravate the deleterious effects. In this article, we review the association of diverse volatile anesthetic agents with immune system and cancer cell biology, and examine the effects on angeogenesis and postoperative metastasis or recurrence. Isoflurane, haloflurane and enflurane enhance immunosuppression and upregulate hypoxia-inducible-factor 1 and matrix metalloproteinases, leading to the cancer malignant progression, whereas roles of desflurane and sevoflurane are still unclear. As the effects of volatile anesthetics on tumor immunity have been known, it will be beneficial for using selective drugs into anesthesia and operation in cancer patients.
Neuregulin 1 type III improves peripheral nerve myelination in a mouse model of congenital hypomyelinating neuropathy.
Dec 11, 2018   Human Molecular Genetics
Belin S, Ornaghi F, Shackleford G, Wang J, Scapin C,   . . . . . .   , Fratta P, D'Antonio M, Poitelon Y, Laura Feltri M, Wrabetz L
Neuregulin 1 type III improves peripheral nerve myelination in a mouse model of congenital hypomyelinating neuropathy.
Dec 11, 2018
Human Molecular Genetics
Myelin sheath thickness is precisely regulated and essential for rapid propagation of action potentials along myelinated axons. In the peripheral nervous system, extrinsic signals from the axonal protein neuregulin 1 type III regulate Schwann cell fate and myelination. Here we ask if modulating neuregulin 1 type III levels in neurons would restore myelination in a model of congenital hypomyelinating neuropathy (CHN). Using a mouse model of CHN, we improved the myelination defects by early overexpression of neuregulin 1 type III. Surprisingly, the improvement was independent from the upregulation of Egr2 or essential myelin genes. Rather, we observed the activation of MAPK/ERK and other myelin genes such as peripheral myelin protein 2 (Pmp2) and oligodendrocyte myelin glycoprotein (Omg). We also confirmed that the permanent activation of MAPK/ERK in Schwann cells has detrimental effects on myelination. Our findings demonstrate that the modulation of axon-to-glial neuregulin 1 type III signaling has beneficial effects and improves myelination defects during development in a model of CHN.
Microtubule-bundling protein Spef1 enables mammalian ciliary central apparatus formation.
Dec 11, 2018   Journal Of Molecular Cell Biology
Zheng J, Liu H, Zhu L, Chen Y, Zhao H, Zhang W, Li F, Xie L, Yan X, Zhu X
Microtubule-bundling protein Spef1 enables mammalian ciliary central apparatus formation.
Dec 11, 2018
Journal Of Molecular Cell Biology
Cilia are cellular protrusions containing nine microtubule (MT) doublets and function to propel cell movement or extracellular liquid flow through beating or sense environmental stimuli through signal transductions. Cilia require the central pair (CP) apparatus, consisting of two CP MTs covered with projections of CP proteins, for planar strokes. How the CP MTs of such '9 + 2' cilia are constructed, however, remains unknown. Here we identify Spef1, an evolutionarily conserved microtubule-bundling protein, as a core CP MT regulator in mammalian cilia. Spef1 was selectively expressed in mammalian cells with 9 + 2 cilia and specifically localized along the CP. Its depletion in multiciliated mouse ependymal cells by RNAi completely abolished the CP MTs and markedly attenuated ciliary localizations of CP proteins such as Hydin and Spag6, resulting in rotational beat of the ependymal cilia. Spef1, which binds to MTs through its N-terminal calponin-homologous domain, formed homodimers through its C-terminal coiled coil region to bundle and stabilize MTs. Disruption of either the MT-binding or the dimerization activity abolished the ability of exogenous Spef1 to restore the structure and functions of the CP apparatus. We propose that Spef1 bundles and stabilizes central MTs to enable the assembly and functions of the CP apparatus.
DNA replication initiation in Bacillus subtilis: structural and functional characterization of the essential DnaA-DnaD interaction.
Dec 11, 2018   Nucleic Acids Research
Martin E, Williams HEL, Pitoulias M, Stevens D, Winterhalter C, Craggs TD, Murray H, Searle MS, Soultanas P
DNA replication initiation in Bacillus subtilis: structural and functional characterization of the essential DnaA-DnaD interaction.
Dec 11, 2018
Nucleic Acids Research
The homotetrameric DnaD protein is essential in low G+C content gram positive bacteria and is involved in replication initiation at oriC and re-start of collapsed replication forks. It interacts with the ubiquitously conserved bacterial master replication initiation protein DnaA at the oriC but structural and functional details of this interaction are lacking, thus contributing to our incomplete understanding of the molecular details that underpin replication initiation in bacteria. DnaD comprises N-terminal (DDBH1) and C-terminal (DDBH2) domains, with contradicting bacterial two-hybrid and yeast two-hybrid studies suggesting that either the former or the latter interact with DnaA, respectively. Using Nuclear Magnetic Resonance (NMR) we showed that both DDBH1 and DDBH2 interact with the N-terminal domain I of DnaA and studied the DDBH2 interaction in structural detail. We revealed two families of conformations for the DDBH2-DnaA domain I complex and showed that the DnaA-interaction patch of DnaD is distinct from the DNA-interaction patch, suggesting that DnaD can bind simultaneously DNA and DnaA. Using sensitive single-molecule FRET techniques we revealed that DnaD remodels DnaA-DNA filaments consistent with stretching and/or untwisting. Furthermore, the DNA binding activity of DnaD is redundant for this filament remodelling. This in turn suggests that DnaA and DnaD are working collaboratively in the oriC to locally melt the DNA duplex during replication initiation.
Human stem cells home to and repair laser-damaged trabecular meshwork in a mouse model.
Dec 11, 2018   Communications Biology
Yun H, Wang Y, Zhou Y, Wang K, Sun M, Stolz DB, Xia X, Ethier CR, Du Y
Human stem cells home to and repair laser-damaged trabecular meshwork in a mouse model.
Dec 11, 2018
Communications Biology
Glaucoma is the leading cause of irreversible vision loss, and reducing elevated intraocular pressure is currently the only effective clinical treatment. The trabecular meshwork is the main resistance site for aqueous outflow that maintains intraocular pressure. In this study, we transplanted human trabecular meshwork stem cells (TMSCs) intracamerally into mice that received laser photocoagulation over a 180° arc of the trabecular meshwork. TMSCs preferentially homed and integrated to the laser-damaged trabecular meshwork region and expressed differentiated cell markers at 2 and 4 weeks. Laser-induced inflammatory and fibrotic responses were prevented by TMSC transplantation with simultaneous ultrastructure and function restoration. Cell affinity and migration assays and elevated expression of CXCR4 and SDF1 in laser-treated mouse trabecular meshwork suggest that the CXCR4/SDF1 chemokine axis plays an important role in TMSC homing. Our results suggest that TMSCs may be a viable candidate for trabecular meshwork refunctionalization as a novel treatment for glaucoma.
The molecular landscape of glioma in patients with Neurofibromatosis 1.
Dec 13, 2018   Nature Medicine Add nature.com free-link Cancel
D'Angelo F, Ceccarelli M, Tala , Garofano L, Zhang J,   . . . . . .   , Bhat KP, Eoli M, Sanson M, Lasorella A, Iavarone A
The molecular landscape of glioma in patients with Neurofibromatosis 1.
Dec 13, 2018
Nature Medicine
Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome in which glioma is one of the prevalent tumors. Gliomagenesis in NF1 results in a heterogeneous spectrum of low- to high-grade neoplasms occurring during the entire lifespan of patients. The pattern of genetic and epigenetic alterations of glioma that develops in NF1 patients and the similarities with sporadic glioma remain unknown. Here, we present the molecular landscape of low- and high-grade gliomas in patients affected by NF1 (NF1-glioma). We found that the predisposing germline mutation of the NF1 gene was frequently converted to homozygosity and the somatic mutational load of NF1-glioma was influenced by age and grade. High-grade tumors harbored genetic alterations of TP53 and CDKN2A, frequent mutations of ATRX associated with Alternative Lengthening of Telomere, and were enriched in genetic alterations of transcription/chromatin regulation and PI3 kinase pathways. Low-grade tumors exhibited fewer mutations that were over-represented in genes of the MAP kinase pathway. Approximately 50% of low-grade NF1-gliomas displayed an immune signature, T lymphocyte infiltrates, and increased neo-antigen load. DNA methylation assigned NF1-glioma to LGm6, a poorly defined Isocitrate Dehydrogenase 1 wild-type subgroup enriched with ATRX mutations. Thus, the profiling of NF1-glioma defined a distinct landscape that recapitulates a subset of sporadic tumors.
High-performance gene expression and knockout tools using sleeping beauty transposon system.
Dec 11, 2018   Mobile DNA
Hu K, Li Y, Wu W, Chen H, Chen Z, Zhang Y, Guo Y, Dong Y
High-performance gene expression and knockout tools using sleeping beauty transposon system.
Dec 11, 2018
Mobile DNA
Background: Similar to retro-/lenti- virus system, DNA transposons are useful tools for stable expression of exogenous genes in mammalian cells. Sleeping Beauty (SB) transposon has adopted for integrating genes into host genomes in recent studies. However, SB-derived vector system for proteins purifying/tracking and gene knockout are still not available. Results: In this study, we generated a series of vectors (termed as pSB vectors) containing Sleeping Beauty IRDR-L/R that can be transposed by SB transposase. Gateway cassette was combined to the pSB vectors to facilitate the cloning. Vectors with various tags, Flag, Myc, HA, V5 and SFB, were generated for multiple options. Moreover, we incorporated the CRISPR-Cas9 cassette into the pSB plasmids for gene knockout. Indeed, using one of these vectors (pSB-SFB-GFP), we performed Tandem Affinity Purification and identified that NFATc1 is a novel binding partner of FBW7. We also knocked out RCC2 and BRD7 using pSB-CRISPR vector respectively, and revealed the novel roles of these two proteins in mitosis. Conclusion: Our study demonstrated that the pSB series vectors are convenient and powerful tools for gene overexpression and knockout in mammalian cells, providing a new alternative approach for molecular cell biology research.
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants.
Dec 11, 2018   Microbiology Resource Announcements
Kopac S, Beatty H, Gialopsos P, Huntemann M, Clum A,   . . . . . .   , Ng V, Ivanova N, Kyrpides N, Woyke T, Klassen JL
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants.
Dec 11, 2018
Microbiology Resource Announcements
For their food source, Trachymyrmex septentrionalis ants raise symbiotic fungus gardens that contain bacteria whose functions are poorly understood. Here, we report the genome sequences of eight bacteria isolated from these fungus gardens to better describe the ecology of these strains and their potential to produce secondary metabolites in this niche.
Inducing rapid telomere irreparable damage in telomerase-expressing cancers.
Dec 11, 2018   Oncotarget
Zhang G, Shay JW
FoxG1 Directly Represses Dentate Granule Cell Fate During Forebrain Development.
Dec 11, 2018   Frontiers In Cellular Neuroscience
Han X, Gu X, Zhang Q, Wang Q, Cheng Y, Pleasure SJ, Zhao C
FoxG1 Directly Represses Dentate Granule Cell Fate During Forebrain Development.
Dec 11, 2018
Frontiers In Cellular Neuroscience
The cortex consists of 100s of neuronal subtypes that are organized into distinct functional regions; however, the mechanisms underlying cell fate determination remain unclear. Foxg1 is involved in several developmental processes, including telencephalic patterning, cell proliferation and cell fate determination. Constitutive disruption of Foxg1 leads to the transformation of cortical neurons into Cajal-Retzius (CR) cells, accompanied by a substantial expansion of the cortical hem through the consumption of the cortex. However, rather than the induction of a cell fate switch, another group has reported a large lateral to medial repatterning of the developing telencephalon as the explanation for this change in cell type output. Here, we conditionally disrupted Foxg1 in telencephalic progenitor cells by crossing Foxg1fl/fl mice with Nestin-CreERTM mice combined with tamoxifen (TM) induction at distinct developmental stages beginning at E10.5 to further elucidate the role of FoxG1 in cell fate determination after telencephalon pattern formation. The number of dentate gyrus (DG) granule-like cells was significantly increased in the cortex. The increase was even detected after deletion at E14.5. In vivo mosaic deletion and in vitro cell culture further revealed a cell-autonomous role for FoxG1 in repressing granule cell fate. However, the cortical hem, which is required for the patterning and the development of the hippocampus, was only slightly enlarged and thus may not contribute to the cell fate switch. Lef1 expression was significantly upregulated in the lateral, cortical VZ and FoxG1 may function upstream of Wnt signaling. Our results provide new insights into the functions of FoxG1 and the mechanisms of cell fate determination during telencephalic development.
Effects of caloric restriction on neuropathic pain, peripheral nerve degeneration and inflammation in normometabolic and autophagy defective prediabetic Ambra1 mice.
Dec 11, 2018   PloS One
Coccurello R, Nazio F, Rossi C, De Angelis F, Vacca V, Giacovazzo G, Procacci P, Magnaghi V, Ciavardelli D, Marinelli S
Effects of caloric restriction on neuropathic pain, peripheral nerve degeneration and inflammation in normometabolic and autophagy defective prediabetic Ambra1 mice.
Dec 11, 2018
PloS One
There is a growing interest on the role of autophagy in diabetes pathophysiology, where development of neuropathy is one of the most frequent comorbidities. We have previously demonstrated that neuropathic pain after nerve damage is exacerbated in autophagy-defective heterozygous Ambra1 mice. Here, we show the existence of a prediabetic state in Ambra1 mice, characterized by hyperglycemia, intolerance to glucose and insulin resistance. Thus, we further investigate the hypothesis that prediabetes may account for the exacerbation of allodynia and chronic pain and that counteracting the autophagy deficit may relieve the neuropathic condition. We took advantage from caloric restriction (CR) able to exert a double action: a powerful increase of autophagy and a control on the metabolic status. We found that CR ameliorates neuropathy throughout anti-inflammatory and metabolic mechanisms both in Ambra1 and in WT animals subjected to nerve injury. Moreover, we discovered that nerve lesion represents, per se, a metabolic stressor and CR reinstates glucose homeostasis, insulin resistance, incomplete fatty acid oxidation and energy metabolism. As autophagy inducer, CR promotes and anticipates Schwann cell autophagy via AMP-activated protein kinase (AMPK) that facilitates remyelination in peripheral nerve. In summary, we provide new evidence for the role of autophagy in glucose metabolism and identify in energy depletion by dietary restriction a therapeutic approach in the fight against neuropathic pain.
A transcriptomics analysis of the Tbx5 paralogues in zebrafish.
Dec 11, 2018   PloS One
Boyle Anderson EAT, Ho RK
A transcriptomics analysis of the Tbx5 paralogues in zebrafish.
Dec 11, 2018
PloS One
TBX5 is essential for limb and heart development. Mutations in TBX5 are associated with Holt-Oram syndrome in humans. Due to the teleost specific genome duplication, zebrafish have two copies of TBX5: tbx5a and tbx5b. Both of these genes are expressed in regions of the lateral plate mesoderm and retina. In this study, we perform comparative RNA sequencing analysis on zebrafish embryos during the stages of lateral plate mesoderm migration. This work shows that knockdown of the Tbx5 paralogues results in altered gene expression in many tissues outside of the lateral plate mesoderm, especially in the somitic mesoderm and the intermediate mesoderm. Specifically, knockdown of tbx5b results in changes in somite size, in the differentiation of vasculature progenitors and in later patterning of trunk blood vessels.
STAT6 degradation and ubiquitylated TRIML2 are essential for activation of human oncogenic herpesvirus.
Dec 11, 2018   PLoS Pathogens
Gu F, Wang C, Wei F, Wang Y, Zhu Q, Ding L, Xu W, Zhu C, Cai C, Qian Z, Yuan Z, Robertson E, Cai Q
STAT6 degradation and ubiquitylated TRIML2 are essential for activation of human oncogenic herpesvirus.
Dec 11, 2018
PLoS Pathogens
Aberrations in STAT6-mediated signaling are linked to the development of multiple cancer types. Increasing evidence has shown that activation of human oncogenic herpesvirus lytic replication is crucial for viral tumorigenesis. However, the role of STAT6 in herpesvirus lytic replication remains elusive. Here, by using Kaposi's sarcoma-associated herpesvirus (KSHV) as a model, we revealed that RTA, the master regulator of lytic replication, interacts with STAT6 and promotes lysine 48 (K48) and K63-linked ubiquitylation of STAT6 for degradation via the proteasome and lysosome systems. Moreover, degradation of STAT6 is dramatically associated with the increased ubiquitylated form of tripartite motif family like 2 (TRIML2, a tumor suppressor) for prolonged cell survival and virion production, which is also commonly observed in lytic activation of Epstein-Barr virus, herpes simplex virus 1 and cytomegalovirus. These results suggest that degradation of STAT6 is important for the lytic activation of KSHV and as such, may be an attractive therapeutic target.
A chromatin integration labelling method enables epigenomic profiling with lower input.
Dec 11, 2018   Nature Cell Biology Add nature.com free-link Cancel
Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y
A chromatin integration labelling method enables epigenomic profiling with lower input.
Dec 11, 2018
Nature Cell Biology
Chromatin plays a crucial role in gene regulation, and chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been the standard technique for examining protein-DNA interactions across the whole genome. However, it is difficult to obtain epigenomic information from limited numbers of cells by ChIP-seq because of sample loss during chromatin preparation and inefficient immunoprecipitation. In this study, we established an immunoprecipitation-free epigenomic profiling method named chromatin integration labelling (ChIL), which enables the amplification of genomic sequences closely associated with the target molecules before cell lysis. Using ChIL followed by sequencing (ChIL-seq), we reliably detected the distributions of histone modifications and DNA-binding factors in 100-1,000 cells. In addition, ChIL-seq successfully detected genomic regions associated with histone marks at the single-cell level. Thus, ChIL-seq offers an alternative method to ChIP-seq for epigenomic profiling using small numbers of cells, in particular, those attached to culture plates and after immunofluorescence.
Coordinated change at the colony level in fruit bat fur microbiomes through time.
Dec 13, 2018   Nature Ecology & Evolution
Kolodny O, Weinberg M, Reshef L, Harten L, Hefetz A, Gophna U, Feldman MW, Yovel Y
Coordinated change at the colony level in fruit bat fur microbiomes through time.
Dec 13, 2018
Nature Ecology & Evolution
The host-associated microbiome affects individual health and behaviour, and may be influenced by local environmental conditions. However, little is known about microbiomes' temporal dynamics in free-living species compared with their dynamics in humans and model organisms, especially in body sites other than the gut. Here, we investigate longitudinal changes in the fur microbiome of captive and free-living Egyptian fruit bats. We find that, in contrast to patterns described in humans and other mammals, the prominent dynamics is of change over time at the level of the colony as a whole. On average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats' ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats' fur, but differs from the more individualized pattern found in the bats' gut microbiome.
Quantification of protein mobility and associated reshuffling of cytoplasm during chemical fixation.
Dec 11, 2018   Scientific Reports
Huebinger J, Spindler J, Holl KJ, Koos B
Quantification of protein mobility and associated reshuffling of cytoplasm during chemical fixation.
Dec 11, 2018
Scientific Reports
To understand cellular functionalities, it is essential to unravel spatio-temporal patterns of molecular distributions and interactions within living cells. The technological progress in fluorescence microscopy now allows in principle to measure these patterns with sufficient spatial resolution. However, high resolution imaging comes with long acquisition times and high phototoxicity. Therefore, physiological live cell imaging is often unfeasible and chemical fixation is employed. Yet, fixation methods have not been rigorously investigated, in terms of pattern preservation, at the resolution at which cells can now be imaged. A key parameter for this is the time required until fixation is complete. During this time, cells are under unphysiological conditions and patterns decay. We demonstrate here that formaldehyde fixation takes more than one hour for cytosolic proteins in cultured cells. Other small aldehydes, glyoxal and acrolein, did not perform better. Associated with this, we found a distinct displacement of proteins and lipids, including their loss from cells. Fixations using glutaraldehyde were faster than four minutes and retained most cytoplasmic proteins. Surprisingly, autofluorescence produced by glutaraldehyde was almost completely absent with supplementary addition of formaldehyde without compromising fixation speed. These findings indicate, which cellular processes can actually be reliably imaged after a certain chemical fixation.
Glucocorticoid Resistance in Acute Lymphoblastic Leukemia: BIM Finally.
Dec 11, 2018   Cancer Cell
Brown JA, Ferrando A
Glucocorticoid Resistance in Acute Lymphoblastic Leukemia: BIM Finally.
Dec 11, 2018
Cancer Cell
Glucocorticoid resistance represents a major challenge in treating acute lymphoblastic leukemia. In this issue of Cancer Cell, Jing and colleagues show epigenetic deregulation of glucocorticoid-induced BIM activation in glucocorticoid-resistant leukemia cells, and restore glucocorticoid-receptor-induced BIM upregulation with DNA demethylating agents to effectively enhance glucocorticoid response.

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