bluuebunny/crossref_metadata_2025_split huggingface dataset:
PTPN2 deletion in T cells promotes anti-tumour immunity and CAR T cell efficacy in solid tumours
Authors: Wiede Florian , Lu Kun-Hui , Du Xin , Liang Shuwei , Hochheiser Katharina , Dodd Garron T. , Goh Pei , Kearney Conor , Meyran Deborah , Beavis Paul A. , Henderson Melissa A. , Park Simone L. , Waithman Jason , Zhang Sheng , Zhang Zhong-Yin , Oliaro Jane , Gebhardt Thomas , Darcy Phillip K. , Tiganis Tony 
Published: September 2019

ABSTRACTAlthough adoptive T cell therapy has shown remarkable clinical efficacy in hematological malignancies, its success in combating solid tumours has been limited. Here we report that PTPN2 deletion in T cells enhances cancer immunosurveillance and the efficacy of adoptively transferred tumour-specific T cells. T cell-specific PTPN2 deficiency prevented tumours forming in aged mice heterozygous for the tumour suppressor p53. Adoptive transfer of PTPN2-deficient CD8+ T cells markedly repressed tumour formation in mice bearing mammary tumours. Moreover, PTPN2 deletion in T cells expressing a chimeric antigen receptor (CAR) specific for the oncoprotein HER-2 increased the activation of the Src family kinase LCK and cytokine-induced STAT-5 signalling thereby enhancing both CAR T cell activation and homing to CXCL9/10 expressing tumours to eradicate HER-2+ mammary tumoursin vivo. Our findings define PTPN2 as a target for bolstering T-cell mediated anti-tumour immunity and CAR T cell therapy against solid tumours.
Dopamine response gene pathways in dorsal striatum MSNs from a gene expression viewpoint: cAMP-mediated gene networks
Authors: Babenko Vladimir , Galyamina Anna , Rogozin Igor , Smagin Dmitry , Kudryavtseva Natalia 
Published: September 2019

AbstractA mouse model of chronic social conflicts was used to analyze dorsal striatum neurons implicated in cAMP-mediated phosphorylation activation pathways specific for Medium Spiny Neurons (MSNs). Based on expression correlation analysis, we succeeded in dissecting Drd1- and Drd2-dopaminoceptive neurons (D1 and D2, correspondingly) gene pathways. We also found that D1 neurons feature previously reported two states, passive and active ones, represented in our analysis by distinct, negatively correlated gene clusters.The correlation based gene pathways strongly corroborate the phosphorylation cascades highlighted in the previous studies, implying that the expression-based viewpoint corresponds to phosphorylation/dephosphorylation interplay in each type of neurons. Notably, D2 neurons showed the largest Ppp1r1b (encoding DARPP-32) expression modulation impact, implying that Ppp1r1b expression dynamics is mostly associated with neuroendocrine response mediated by Penk/Pdyn genes expression in D2 neurons.We observed that under defeat stress in chronic social conflicts mice exhibited reduced motor activity as well as overall depression of dopamine-mediated MSNs activity, while aggressive mice exhibited motor hyperactivity and an increase in both D1-active phase and D2 MSNs genes expression.Based on alternative transcript isoforms expression analysis, it was assumed that many genes (Drd1, Adora1, Pde10, Ppp1r1b, Gnal), specifically those in D1 neurons, apparently remain transcriptionally repressed via the reversible mechanism of promoter CpG island silencing, resulting in alternative promoter usage following profound reduction in their expression rate.Significance statementMedium Spiny Neurons (MSNs) comprise the main body of dorsal striatum neurons and represent dopaminoceptive GABAergic neurons. The cAMP- mediated cascade of excitation and inhibition responses involved in dopaminergic neurotransmission is crucial for neuroscience research due to its involvement in the motor and behavioral functions. In particular, all types of addictions are related to MSNs. Shedding the light on the mechanics of the above-mentioned cascade is of primary importance for this research domain. In this paper MSNs steady states will be elucidated based on pooled tissue RNA-Seq data not explicitly outlined before and connected with dynamic dopamine neurotransmission cycles.
Kinetics of the immune response toEimeria maximain relatively resistant and susceptible chicken lines
Authors: Bremner Abi , Kim Sungwon , Morris Katrina , Nolan Matthew J. , Borowska Dominika , Wu Zhiguang , Tomley Fiona , Blake Damer P. , Hawken Rachel , Kaiser Pete , Vervelde Lonneke 
Published: September 2019

AbstractEimeria maximais a common cause of coccidiosis in chickens, a disease which has a huge economic impact on poultry production. Knowledge of immunity toE. maximaand the specific mechanisms that contribute to differing levels of resistance observed between chicken breeds and between congenic lines derived from a single breed of chickens is required. This study aimed to define differences in the kinetics of the immune response of two inbred lines of White Leghorn chickens that exhibit differential resistance (line C.B12) or susceptibility (line 15I) to infection byE. maxima. Line C.B12 and 15I chickens were infected withE. maximaand transcriptome analysis of infected jejunal tissue was carried out at 2, 4, 6 and 8 days post-infection (dpi). RNA-Seq analysis revealed differences in the rapidity and magnitude of cytokine transcription responses post-infection between the two lines. In particular, IFN-γ and IL-10 transcripts in the jejunum accumulated earlier in line C.B12 (at 4 dpi) compared to line 15I (at 6 dpi). Line C.B12 chickens exhibited increases ofIFNGandIL10mRNA in the jejunum at 4 dpi, whereas in line 15I transcription was delayed but increased to a greater extent. RT-qPCR and ELISAs confirmed the results of the transcriptomic study. Higher serum IL-10 correlated strongly with higherE. maximareplication in line 15I compared to line C.B12 chickens. Overall, the findings suggest early induction of the IFN-γ and IL-10 responses, as well as immune-related genes at 4 dpi identified by RNA-Seq, may be key to resistance toE. maxima.
A cell-free platform based on nisin biosynthesis for discovering novel lanthipeptides and guiding their overproductionin vivo
Authors: Liu Ran , Zhang Yuchen , Zhai Guoqing , Fu Shuai , Xia Yao , Hu Ben , Cai Xuan , Zhang Yan , Li Yan , Deng Zixin , Liu Tiangang 
Published: September 2019

AbstractLanthipeptides have extensive therapeutic and industrial applications; however, since many are bactericidal, traditionalin vivoplatforms are limited in their capacity to discover and mass produce novel lanthipeptides as bacterial organisms are often critical components in these systems. We developed a cell-free protein synthesis (CFPS) platform that enables rapid genome mining, screening and guiding overproduction of lanthipeptidesin vivo. For proof-of-concept studies, the type I lanthipeptide, nisin, was selected. Four novel lanthipeptides with anti-bacterial activity were identified among all nisin analogs in the NCBI database in a single day. Further, we coupled the CFPS platform with a screening assay for gram-negative bacterial growth and identified a potent nisin mutant, M5. The titer of nisin and nisin analogs significantly improved with CFPS platform guidance. Owing to the similarities in biosynthesis, our CFPS platform is broadly applicable to other lanthipeptides, provides a universal method for lanthipeptides discovery and overproduction.
PD-L1 expression in 522 selected sarcomas with subset analysis of recurrent or metastatic matched samples and association with tumour-infiltrating lymphocytes
Authors: Vargas Ana Cristina , Maclean Fiona M , Sioson Loretta , Tran Dinh , Bonar Fiona , Mahar Annabelle , Cheah Alison L. , Russell Peter , Grimison Peter , Richardson Louise , Gill Anthony J 
Published: September 2019

AbstractWe assessed the frequency of programmed death-ligand 1 (PD-L1) expression by immunohistochemistry (IHC) in a cohort of 522 sarcomas from 457 patients, incuding a subset of 46 patients with 63 matched samples from local recurrence or metastases with primary tumours and/or metachronous metastases. We also investigated the correlation of PD-L1 with the presence and degree of tumour-infiltrating lymphocytes (TILs) in a subset of cases. IHC was performed using the PD-L1 SP263 companion kit (VENTANA) on tissue microarrays from an archival cohort. Evaluation of PD-L1 and TILs was performed on full sections for a subset of 23 cases. Fisher’s exact and Mann Whitney test were used to establish significance (P <0.05). PD-L1 positive expression (≥1%) was identified in 31% of undifferentiated pleomorphic sarcomas, 29% of angiosarcomas, 26% of rhabdomyosarcomas, 18% of myxofibrosarcomas, 11% of leiomyosarcomas and 10% of dedifferentiated liposarcomas. Negative expression was present in all atypical lipomatous tumous/well-differentiated lipoasarcomas, myxoid liposarcomas, synovial sarcomas, pleomorphic liposarcomas, and Ewing sarcomas. PD-L1 IHC was concordant in 81% (38 of 47) of matched/paired samples. PD-L1 IHC was discordant in 19% (9 of 47 matched/paired samples), displaying differences in the proportion of cells expressing PD-L1 amongst paired samples with the percentage of PD-L1-positive cells increasing in the metastatic/recurrent site compared to the primary in 6 of 9 cases (67%). Significant correlation between PD-L1 expression and the degree of TILs was exclusively identified in the general cohort of leiomyosarcomas, but not in other sarcoma subtypes or in metastatic/recurrent samples. We conclude that the prevalence of PD-L1 expression in selected sarcomas is variable and likely to be clone dependent. Importantly, we demonstrated that PD-L1 can objectively increase in a small proportion of metastases/recurrent sarcomas, offering the potential of treatment benefit to immune checkpoint inhibitors in this metastatic setting.
Lgr5 Controls Extracellular Matrix Production By Stem Cells In The Developing Intestine
Authors: Vallone Valeria Fernandez , Leprovots Morgane , Gerbier Romain , Ribatallada-Soriano Didac , Lefort Anne , Libert Frédérick , Vassart Gilbert , Garcia Marie-Isabelle 
Published: September 2019

AbstractThe Lgr5 receptor is a marker of intestinal stem cells (ISCs) that regulates Wnt/b-catenin signaling. In this study, phenotype analysis of knockin/knockout Lgr5-eGFP-IRES-Cre and Lgr5-DTReGFP embryos revealed that Lgr5 deficiency during Wnt-mediated cytodifferentiation results in amplification of ISCs and early differentiation into Paneth cells, which can be counteracted by in utero treatment with the Wnt inhibitor LGK974. Conditional ablation of Lgr5 postnatally, but not in adults, altered stem cell fate towards the Paneth lineage. Together, these in vivo studies suggest that Lgr5 is part of a feedback loop to adjust the Wnt tone in ISCs. Moreover, transcriptome analyses revealed that fetal ISCs generate their own extracellular matrix components, a property lost in adult ISCs, which adopt a definitive epithelialized phenotype and an inflammatory response signature. Absence of Lgr5 in fetal ISCs resulted in reduced extracellular matrix production and accelerated ISC maturation, indicating that Lgr5 regulates the ISC niche. Finally, evidences are provided that Rspondin 2 negatively regulates the pool of ISCs in organoids via Lgr5, revealing a sophisticated regulatory process for Wnt signaling in ISC.
Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins
Authors: Qin Liang , Ben Bdira Fredj , Sterckx Yann G. J. , Volkov Alexander N. , Vreede Jocelyne , Giachin Gabriele , van Schaik Peter , Ubbink Marcellus , Dame Remus T. 
Published: September 2019

AbstractH-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The molecular mechanism underlying the switching process and its conservation among H-NS family members remains elusive.Here, we focus on the H-NS family protein MvaT from P. aeruginosa and demonstrate experimentally that its protomer exists in two different conformations, corresponding to two different functional states. In the half-opened state (dominant at low salt) the protein forms filaments along DNA, in the fully opened state (dominant at high salt) the protein bridges DNA. This switching is a direct effect of ionic strengths on electrostatic interactions between the appositively charged DNA binding and N-terminal domains of MvaT. The asymmetric charge distribution and intramolecular interactions are conserved among the H-NS family of proteins. Therefore, our study establishes a general paradigm for the molecular mechanistic basis of the osmosensitivity of H-NS proteins.
Biochemical and structural analysis reveals the Neurofibromin (NF1) protein forms a high-affinity dimer
Authors: Sherekar Mukul , Han Sae-Won , Ghirlando Rodolfo , Messing Simon , Drew Matthew , Juneja Puneet , O’Neill Hugh , Stanley Christopher , Bhowmik Debsindhu , Ramanathan Arvind , Subramaniam Sriram , Nissley Dwight V. , Gillette William , McCormick Frank , Esposito Dominic 
Published: September 2019

ABSTRACTNeurofibromin is the protein product of the NF1 gene which is mutated in the Rasopathy disease Neurofibromatosis Type I. Defects in NF1 lead to aberrant signaling through the RAS-MAPK pathway due to disruption of the Neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of the majority of Neurofibromin—to date, biochemical and structural data exist only for the GAP domain and the region containing a Sec-PH motif. To better understand the role of this large protein, we carried out a series of biochemical and biophysical studies which demonstrate that full length Neurofibromin forms a high-affinity dimer. Neurofibromin dimerization also occurs in cells, and likely has biological and clinical implications. Analysis of purified full-length and truncated variants of Neurofibromin by negative stain electron microscopy reveals the overall architecture of the dimer and predicts the potential interactions which contribute to the dimer interface. Structures resembling high-affinity full-length dimers could be reconstituted by mixing N- and C-terminal protein domains in vitro. Taken together these data suggest how Neurofibromin dimers might form and be stabilized within the cell.
The kinesin-14, Ncd, drives a right-handed, helical motion of antiparallel microtubules around each other
Authors: Mitra Aniruddha , Gandhimathi Rojapriyadharshini , Ruhnow Felix , Renger Roman , Diez Stefan 
Published: September 2019

AbstractWithin the mitotic spindle, several kinesin motors crosslink and slide microtubules. While some of them (e.g. kinesin-5, kinesin-8 and kinesin-14) have been shown to exhibit sideways components in their step cycles, the impact of the resulting off-axis power strokes on motility and force generation in the spindle has not been investigated so far. Here, we develop and utilize a novel three-dimensional in vitro motility assay to explore the kinesin-14, Ncd, driven sliding of crosslinked, fluorescently-labeled microtubules. We find that free microtubules, sliding in an antiparallel orientation on microtubules suspended between nanofabricated ridges, not only rotate around their own axis but also move around the suspended microtubules with right-handed helical trajectories. In contrast, microtubules crosslinked in parallel orientation are static with neither longitudinal nor helical motion. Further, our technique allows us to measure the in situ spatial extension of the motors between the crosslinked microtubules to be about 20 nm. We argue that the capability of microtubule-crosslinking kinesins to cause helical motion of microtubules around each other allows for flexible filament organization, roadblock circumvention and torque generation in the mitotic spindle.
Comparative analysis of inducible promoters in cyanobacteria
Authors: Behle Anna , Saake Pia , Axmann Ilka M. 
Published: September 2019

AbstractResearch in the field of synthetic biology highly depends on efficient, well-characterized promoters. While great progress has been made with other model organisms such asEscherichia coli, photosynthetic cyanobacteria still lag behind. Commonly used promoters that have been tested in cyanobacteria show weaker dynamic range or no regulation at all. Alternatives such as native metal-inducible promoters pose the problem of inducer toxicity.Here, we evaluate four different inducible promoters, both previously published and new, using the modular plasmid pSHDY, in the model cyanobacteriumSynechocystis sp. PCC 6803 - namely the vanillate-inducible promoter PvanCC, the rhamnose-inducible Prha, and the aTc-inducible PL03, and the Co2+-inducible PcoaT. We estimate individual advantages and disadvantages, as well as dynamic range and strength of each promoter in comparison with well-established constitutive systems. We observed a delicate balance between transcription factor toxicity and sufficient expression to obtain a dose-dependent response to the inducer. In summary, we expand the current understanding and employability of inducible promoters in order to facilitate the construction of more complex regulatory synthetic networks, as well as more complicated biotechnological pathways for cyanobacteria.
Serotonin receptor 4 in mature excitatory hippocampal neurons modulates mood and anxiety
Authors: Karayol Remzi , Medrihan Lucian , Warner-Schmidt Jennifer L. , Rao Meghana N. , Holzner Eva B. , Greengard Paul , Heintz Nathaniel , Schmidt Eric F. 
Published: September 2019

AbstractSerotonin receptor 4 (5-HT4R) plays an important role in regulating mood, anxiety, and cognition, and drugs that activate this receptor have fast-acting antidepressant (AD)-like effects in preclinical models. However, 5-HT4R is widely expressed throughout the central nervous system (CNS) and periphery, making it a poor therapeutic target and difficult to pinpoint the cell types and circuits underlying its effects. Therefore, we generated a Cre-dependent 5-HT4R knockout mouse line to dissect the function of 5-HT4R in specific brain regions and cell types. We show that the loss of functional 5-HT4R specifically in the mature excitatory neurons of hippocampus led to robust AD-like behavioral responses and an elevation in baseline anxiety. 5-HT4R was necessary to maintain the proper excitability of mature dentate gyrus (DG) granule cells and cell type specific molecular profiling revealed a dysregulation of genes necessary for normal neural function and plasticity in cells lacking 5-HT4R. These adaptations were accompanied by an increase in the number of immature neurons in ventral, but not dorsal, dentate gyrus, indicating a broad impact of 5-HT4R loss on the local cellular environment. This study is the first to use conditional genetic targeting to demonstrate a direct role for hippocampal 5-HT4R signaling in modulating mood and anxiety. Our findings also underscore the need for cell type-based approaches to elucidate the complex action of neuromodulatory systems on distinct neural circuits.
Molecular Mechanism Underlying Inhibition of Intrinsic ATPase Activity in a Ski2-like RNA Helicase
Authors: Absmeier Eva , Santos Karine F. , Wahl Markus C. 
Published: September 2019

SUMMARYRNA-dependent NTPases can act as RNA/RNA-protein remodeling enzymes and typically exhibit low NTPase activity in the absence of RNA/RNA-protein substrates. How futile intrinsic NTP hydrolysis is prevented is frequently not known. The ATPase/RNA helicase Brr2 belongs to the Ski2-like family of nucleic acid-dependent NTPases and is an integral component of the spliceosome. Comprehensive nucleotide binding and hydrolysis studies are not available for a member of the Ski2-like family. We present crystal structures of Chaetomium thermophilum Brr2 in the apo, ADP-bound and ATPyS-bound states, revealing nucleotide-induced conformational changes and a hitherto unknown ATPyS binding mode. Our results in conjunction with Brr2 structures in other molecular contexts reveal multiple molecular mechanisms that contribute to the inhibition of intrinsic ATPase activity, including an N-terminal region that restrains the RecA-like domains in an open conformation and exclusion of an attacking water molecule, and suggest how RNA substrate binding can lead to ATPase stimulation.HIGHLIGHTSCrystal structures of Brr2 in complex with different adenine nucleotides.The Brr2 N-terminal region counteracts conformational changes induced by ATP binding.Brr2 excludes an attacking water molecule in the absence of substrate RNA.Different helicase families resort to different NTPase mechanisms.
Bidirectional Wnt signaling between endoderm and mesoderm confer tracheal identity in mouse and human
Authors: Kishimoto Keishi , Furukawa Kana T. , Madrigal Agustin Luz , Yamaoka Akira , Matsuoka Chisa , Habu Masanobu , Alev Cantas , Zorn Aaron M. , Morimoto Mitsuru 
Published: September 2019

AbstractThe periodic cartilage and smooth muscle structures in mammalian trachea are derived from tracheal mesoderm, and tracheal malformations result in serious respiratory defects in neonates. Here we show that canonical Wnt signaling in mesoderm is critical to confer trachea mesenchymal identity in human and mouse. Loss of β-catenin in fetal mouse mesoderm caused loss of Tbx4+tracheal mesoderm and tracheal cartilage agenesis. The Tbx4 expression relied on endodermal Wnt activity and its downstream Wnt ligand but independent of known Nkx2.1-mediated respiratory development, suggesting that bidirectional Wnt signaling between endoderm and mesoderm promotes trachea development. Repopulatingin vivomodel, activating Wnt, Bmp signaling in mouse embryonic stem cell (ESC)-derived lateral plate mesoderm (LPM) generated tracheal mesoderm containing chondrocytes and smooth muscle cells. For human ESC-derived LPM, SHH activation was required along with Wnt to generate proper tracheal mesoderm. Together, these findings may contribute to developing applications for human tracheal tissue repair.
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
Authors: Musser Jacob M. , Schippers Klaske J. , Nickel Michael , Mizzon Giulia , Kohn Andrea B. , Pape Constantin , Hammel Jörg U. , Wolf Florian , Liang Cong , Hernández-Plaza Ana , Achim Kaia , Schieber Nicole L. , Francis Warren R. , Vargas R. Sergio , Kling Svenja , Renkert Maike , Feuda Roberto , Gaspar Imre , Burkhardt Pawel , Bork Peer , Beck Martin , Kreshuk Anna , Wörheide Gert , Huerta-Cepas Jaime , Schwab Yannick , Moroz Leonid L. , Arendt Detlev 
Published: September 2019

AbstractThe evolutionary origin of metazoan cell types such as neurons, muscles, digestive, and immune cells, remains unsolved. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identify 18 distinct cell types comprising four major families. This includes nitric-oxide sensitive contractile cells, digestive cells active in macropinocytosis, and a family of amoeboid-neuroid cells involved in innate immunity. We uncover ‘presynaptic’ genes in an amoeboid-neuroid cell type, and ‘postsynaptic’ genes in digestive choanocytes, suggesting asymmetric and targeted communication. Corroborating this, long neurite-like extensions from neuroid cells directly contact and enwrap choanocyte microvillar collars. Our data indicate a link between neuroid and immune functions in sponges, and suggest that a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.