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https://www.readbyqxmd.com/read/30050954/obesity-related-asthma-immune-regulation-and-potential-targeted-therapies
#1
REVIEW
Yuze Yuan, Nan Ran, Lingxin Xiong, Guoqiang Wang, Xuewa Guan, Ziyan Wang, Yingqiao Guo, Zhiqiang Pang, Keyong Fang, Junying Lu, Chao Zhang, Ruipeng Zheng, Jingtong Zheng, Jie Ma, Fang Wang
Obesity, one of the most severe public health problems of the 21st century, is a common metabolic syndrome due to excess body fat. The incidence and severity of obesity-related asthma have undergone a dramatic increase. Because obesity-related asthma is poorly controlled using conventional therapies, alternative and complementary therapies are urgently needed. Lipid metabolism may be abnormal in obesity-related asthma, and immune modulation therapies need to be investigated. Herein, we describe the immune regulators of lipid metabolism in obesity as well as the interplay of obesity and asthma...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29955050/parkin-regulates-nf-%C3%AE%C2%BAb-by-mediating-site-specific-ubiquitination-of-ripk1
#2
Yu Wang, Bing Shan, Yaosi Liang, Huiting Wei, Junying Yuan
Parkin (Park2), a RING-between-RING-type E3 ubiquitin ligase, has been implicated in regulating NF-κB. Mutations in Parkin are associated with Parkinson's disease. Here we investigated the interaction of Parkin with Receptor-interacting protein kinase 1 (RIPK1) kinase, a key mediator of multiple signaling pathways activated by TNFR1 including NF-κB pathway. We report that Parkin interacts with RIPK1 and mediates K63 ubiquitination of RIPK1 on K376 in TNFR1-signaling pathway. The expression of Parkin promotes the recruitment of transforming growth factor β (TGF-β)-activated kinase 1 (TAK1), nuclear factor-κB (NF-κB) essential molecule (NEMO), Sharpin and A20 in complex I associated with TNFR1 upon TNFα stimulation...
June 28, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29891719/regulation-of-a-distinct-activated-ripk1-intermediate-bridging-complex-i-and-complex-ii-in-tnf%C3%AE-mediated-apoptosis
#3
Palak Amin, Marcus Florez, Ayaz Najafov, Heling Pan, Jiefei Geng, Dimitry Ofengeim, Slawomir A Dziedzic, Huibing Wang, Vica Jean Barrett, Yasushi Ito, Matthew J LaVoie, Junying Yuan
Stimulation of cells with TNFα can promote distinct cell death pathways, including RIPK1-independent apoptosis, necroptosis, and RIPK1-dependent apoptosis (RDA)-the latter of which we still know little about. Here we show that RDA involves the rapid formation of a distinct detergent-insoluble, highly ubiquitinated, and activated RIPK1 pool, termed "iuRIPK1." iuRIPK1 forms after RIPK1 activation in TNF-receptor-associated complex I, and before cytosolic complex II formation and caspase activation...
June 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29725272/the-role-of-regulatory-t-cell-in-nontypeable-haemophilus-influenzae-induced-acute-exacerbation-of-chronic-obstructive-pulmonary-disease
#4
Xuewa Guan, Yanjiao Lu, Guoqiang Wang, Peter Gibson, Fang Chen, Keyong Fang, Ziyan Wang, Zhiqiang Pang, Yingqiao Guo, Junying Lu, Yuze Yuan, Nan Ran, Fang Wang
Chronic obstructive pulmonary disease (COPD) is associated with irreversible persistent airflow limitation and enhanced inflammation. The episodes of acute exacerbation (AECOPD) largely depend on the colonized pathogens such as nontypeable Haemophilus influenzae (NTHi), one of the most commonly isolated bacteria. Regulatory T cells (Tregs) are critical in controlling inflammatory immune responses and maintaining tolerance; however, their role in AECOPD is poorly understood. In this study, we hypothesized a regulatory role of Tregs, as NTHi participated in the progress of COPD...
2018: Mediators of Inflammation
https://www.readbyqxmd.com/read/29703889/necroptosis-promotes-cell-autonomous-activation-of-proinflammatory-cytokine-gene-expression
#5
Kezhou Zhu, Wei Liang, Zaijun Ma, Daichao Xu, Shuangyi Cao, Xiaojuan Lu, Nan Liu, Bing Shan, Lihui Qian, Junying Yuan
Necroptosis, a form of regulated necrotic cell death, is mediated by receptor interacting protein 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein (MLKL). However, the mechanism by which necroptosis promotes inflammation is still unclear. Here we report that the expression of cytokines is robustly upregulated in a cell-autonomous manner during necroptosis induced by tumor necrosis factor alpha (TNFα). We demonstrate that TNFα-induced necroptosis leads to two waves of cytokine production. The first wave, more transient and weaker than the second, is in response to TNFα alone; whereas the second wave depends upon the necroptotic signaling...
May 1, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29693254/microrna-224-suppresses-osteoblast-differentiation-by-inhibiting-smad4
#6
Yuan Luo, Xiaodong Cao, Junfeng Chen, Jianwei Gu, Jitong Zhao, Junying Sun
Osteoblast differentiation was found to be regulated by a variety of cell signaling and intracellular regulatory factors. In this study, we aimed at investigating the regulatory effect of microRNA-224 on osteoblast differentiation and its molecular mechanism. Expression of miR-224 in the osteoblasts, adipose-derived mesenchymal stem cells (MSC-A), bone marrow-derived mesenchymal stem cells (MSC-B) and mbilical cord-derived mesenchymal stem cells (MSC-U) were detected using RT-PCR. Expression of miR-224 was lower in osteoblast than in the three mesenchymal stem cells and it revealed a decreasing time-dependent trend from 0 day to 28 days during osteoblast differentiation...
October 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29662181/author-correction-niche-harmony-search-algorithm-for-detecting-complex-disease-associated-high-order-snp-combinations
#7
Shouheng Tuo, Junying Zhang, Xiguo Yuan, Zongzhen He, Yajun Liu, Zhaowen Liu
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29593066/necroptosis-in-development-and-diseases
#8
REVIEW
Bing Shan, Heling Pan, Ayaz Najafov, Junying Yuan
Necroptosis, a form of regulated necrotic cell death mediated by RIPK1 (receptor-interacting protein kinase 1) kinase activity, RIPK3, and MLKL (mixed-lineage kinase domain-like pseudokinase), can be activated under apoptosis-deficient conditions. Modulating the activation of RIPK1 by ubiquitination and phosphorylation is critical to control both necroptosis and apoptosis. Mutant mice with kinase-dead RIPK1 or RIPK3 and MLKL deficiency show no detrimental phenotype in regard to development and adult homeostasis...
March 1, 2018: Genes & Development
https://www.readbyqxmd.com/read/29570071/detection-of-significant-copy-number-variations-from-multiple-samples-in-next-generation-sequencing-data
#9
Xiguo Yuan, Junying Zhang, Liying Yang, Jun Bai, Peizhen Fan
Analyzing copy number variations (CNVs) from next-generation sequencing (NGS) data has become a common approach to detect disease susceptibility genes. The main challenge is how to utilize the NGS data with limited coverage depth to detect significant CNVs. Here, we introduce a new statistical method, the derivative of correlation coefficient (DCC), to detect significant CNVs that recurrently occur in multiple samples using read depth signals. We use a sliding window to calculate a correlation coefficient for each genome bin, and compute corresponding derivatives by fitting curves to the correlation coefficient...
March 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/29467542/tubulation-repair-mitigates-misdirection-of-regenerating-motor-axons-across-a-sciatic-nerve-gap-in-rats
#10
Dan Liu, Daguo Mi, Tuanjie Zhang, Yanping Zhang, Junying Yan, Yaxian Wang, Xuefeng Tan, Ying Yuan, Yumin Yang, Xiaosong Gu, Wen Hu
The repair of peripheral nerve laceration injury to obtain optimal function recovery remains a big challenge in the clinic. Misdirection of regenerating axons to inappropriate target, as a result of forced mismatch of endoneurial sheaths in the case of end-to-end nerve anastomosis or nerve autografting, represents one major drawback that limits nerve function recovery. Here we tested whether tubulation repair of a nerve defect could be beneficial in terms of nerve regeneration accuracy and nerve function. We employed sequential retrograde neuronal tracing to assess the accuracy of motor axon regeneration into the tibial nerve after sciatic nerve laceration and entubulation in adult Sprague-Dawley rats...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29440439/death-domain-dimerization-mediated-activation-of-ripk1-controls-necroptosis-and-ripk1-dependent-apoptosis
#11
Huyan Meng, Zhen Liu, Xingyan Li, Huibing Wang, Taijie Jin, Guowei Wu, Bing Shan, Dana E Christofferson, Chunting Qi, Qiang Yu, Ying Li, Junying Yuan
RIPK1 is a critical mediator of cell death and inflammation downstream of TNFR1 upon stimulation by TNFα, a potent proinflammatory cytokine involved in a multitude of human inflammatory and degenerative diseases. RIPK1 contains an N-terminal kinase domain, an intermediate domain, and a C-terminal death domain (DD). The kinase activity of RIPK1 promotes cell death and inflammation. Here, we investigated the involvement of RIPK1-DD in the regulation of RIPK1 kinase activity. We show that a charge-conserved mutation of a lysine located on the surface of DD (K599R in human RIPK1 or K584R in murine RIPK1) blocks RIPK1 activation in necroptosis and RIPK1-dependent apoptosis and the formation of complex II...
February 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29394115/structural-insights-into-the-ubiquitin-recognition-by-optn-optineurin-and-its-regulation-by-tbk1-mediated-phosphorylation
#12
Faxiang Li, Daichao Xu, Yingli Wang, Zixuan Zhou, Jianping Liu, Shichen Hu, Yukang Gong, Junying Yuan, Lifeng Pan
OPTN (optineurin), a ubiquitin-binding scaffold protein, functions as an important macroautophagy/autophagy receptor in selective autophagy processes. Mutations in OPTN have been linked with human neurodegenerative diseases including ALS and glaucoma. However, the mechanistic basis underlying the recognition of ubiquitin by OPTN and its regulation by TBK1-mediated phosphorylation are still elusive. Here, we demonstrate that the UBAN domain of OPTN preferentially recognizes linear ubiquitin chain and forms an asymmetric 2:1 stoichiometry complex with the linear diubiquitin...
2018: Autophagy
https://www.readbyqxmd.com/read/29374185/synergistic-effect-of-a-novel-autophagy-inhibitor-and-quizartinib-enhances-cancer-cell-death
#13
Amanda Tomie Ouchida, Yingbo Li, Jiefei Geng, Ayaz Najafov, Dimitry Ofengeim, Xiaoxiao Sun, Qiang Yu, Junying Yuan
Drug combinations have been increasingly applied in chemotherapy as a strategy to enhance the efficacy of anti-cancer treatment. The appropriate drug combinations may achieve synergistic effects beyond monotherapies alone. AC220 (Quizartinib), an FLT3 receptor tyrosine kinase inhibitor, developed for the treatment of AML, has been tested in phase II human clinical trials. However, AC220 as a monotherapy is not efficacious enough. In this study, we performed a small-molecule screening of 12 640 compounds in order to find a compound that increase the AC220 efficacy in chemotherapy...
January 26, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29362479/molecular-mechanisms-of-cell-death-recommendations-of-the-nomenclature-committee-on-cell-death-2018
#14
REVIEW
Lorenzo Galluzzi, Ilio Vitale, Stuart A Aaronson, John M Abrams, Dieter Adam, Patrizia Agostinis, Emad S Alnemri, Lucia Altucci, Ivano Amelio, David W Andrews, Margherita Annicchiarico-Petruzzelli, Alexey V Antonov, Eli Arama, Eric H Baehrecke, Nickolai A Barlev, Nicolas G Bazan, Francesca Bernassola, Mathieu J M Bertrand, Katiuscia Bianchi, Mikhail V Blagosklonny, Klas Blomgren, Christoph Borner, Patricia Boya, Catherine Brenner, Michelangelo Campanella, Eleonora Candi, Didac Carmona-Gutierrez, Francesco Cecconi, Francis K-M Chan, Navdeep S Chandel, Emily H Cheng, Jerry E Chipuk, John A Cidlowski, Aaron Ciechanover, Gerald M Cohen, Marcus Conrad, Juan R Cubillos-Ruiz, Peter E Czabotar, Vincenzo D'Angiolella, Ted M Dawson, Valina L Dawson, Vincenzo De Laurenzi, Ruggero De Maria, Klaus-Michael Debatin, Ralph J DeBerardinis, Mohanish Deshmukh, Nicola Di Daniele, Francesco Di Virgilio, Vishva M Dixit, Scott J Dixon, Colin S Duckett, Brian D Dynlacht, Wafik S El-Deiry, John W Elrod, Gian Maria Fimia, Simone Fulda, Ana J García-Sáez, Abhishek D Garg, Carmen Garrido, Evripidis Gavathiotis, Pierre Golstein, Eyal Gottlieb, Douglas R Green, Lloyd A Greene, Hinrich Gronemeyer, Atan Gross, Gyorgy Hajnoczky, J Marie Hardwick, Isaac S Harris, Michael O Hengartner, Claudio Hetz, Hidenori Ichijo, Marja Jäättelä, Bertrand Joseph, Philipp J Jost, Philippe P Juin, William J Kaiser, Michael Karin, Thomas Kaufmann, Oliver Kepp, Adi Kimchi, Richard N Kitsis, Daniel J Klionsky, Richard A Knight, Sharad Kumar, Sam W Lee, John J Lemasters, Beth Levine, Andreas Linkermann, Stuart A Lipton, Richard A Lockshin, Carlos López-Otín, Scott W Lowe, Tom Luedde, Enrico Lugli, Marion MacFarlane, Frank Madeo, Michal Malewicz, Walter Malorni, Gwenola Manic, Jean-Christophe Marine, Seamus J Martin, Jean-Claude Martinou, Jan Paul Medema, Patrick Mehlen, Pascal Meier, Sonia Melino, Edward A Miao, Jeffery D Molkentin, Ute M Moll, Cristina Muñoz-Pinedo, Shigekazu Nagata, Gabriel Nuñez, Andrew Oberst, Moshe Oren, Michael Overholtzer, Michele Pagano, Theocharis Panaretakis, Manolis Pasparakis, Josef M Penninger, David M Pereira, Shazib Pervaiz, Marcus E Peter, Mauro Piacentini, Paolo Pinton, Jochen H M Prehn, Hamsa Puthalakath, Gabriel A Rabinovich, Markus Rehm, Rosario Rizzuto, Cecilia M P Rodrigues, David C Rubinsztein, Thomas Rudel, Kevin M Ryan, Emre Sayan, Luca Scorrano, Feng Shao, Yufang Shi, John Silke, Hans-Uwe Simon, Antonella Sistigu, Brent R Stockwell, Andreas Strasser, Gyorgy Szabadkai, Stephen W G Tait, Daolin Tang, Nektarios Tavernarakis, Andrew Thorburn, Yoshihide Tsujimoto, Boris Turk, Tom Vanden Berghe, Peter Vandenabeele, Matthew G Vander Heiden, Andreas Villunger, Herbert W Virgin, Karen H Vousden, Domagoj Vucic, Erwin F Wagner, Henning Walczak, David Wallach, Ying Wang, James A Wells, Will Wood, Junying Yuan, Zahra Zakeri, Boris Zhivotovsky, Laurence Zitvogel, Gerry Melino, Guido Kroemer
Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes...
March 2018: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29219397/thermodynamic-evidence-for-the-fulde-ferrell-larkin-ovchinnikov-state-in-the-kfe_-2-as_-2-superconductor
#15
Chang-Woo Cho, Jonathan Haiwei Yang, Noah F Q Yuan, Junying Shen, Thomas Wolf, Rolf Lortz
We investigate the magnetic phase diagram near the upper critical field of KFe_{2}As_{2} by magnetic torque and specific heat experiments using a high-resolution piezorotary positioner to precisely control the parallel alignment of the magnetic field with respect to the FeAs layers. We observe a clear double transition when the field is strictly aligned in the plane and a characteristic upturn of the upper critical field line, which goes far beyond the Pauli limit at 4.8 T. This provides firm evidence that a Fulde-Ferrell-Larkin-Ovchinnikov state exists in this iron-based KFe_{2}As_{2} superconductor...
November 24, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29203883/abin-1-regulates-ripk1-activation-by-linking-met1-ubiquitylation-with-lys63-deubiquitylation-in-tnf-rsc
#16
Slawomir A Dziedzic, Zhenyi Su, Vica Jean Barrett, Ayaz Najafov, Adnan K Mookhtiar, Palak Amin, Heling Pan, Li Sun, Hong Zhu, Averil Ma, Derek W Abbott, Junying Yuan
Ubiquitylation of the TNFR1 signalling complex (TNF-RSC) controls the activation of RIPK1, a kinase critically involved in mediating multiple TNFα-activated deleterious events. However, the molecular mechanism that coordinates different types of ubiquitylation modification to regulate the activation of RIPK1 kinase remains unclear. Here, we show that ABIN-1/NAF-1, a ubiquitin-binding protein, is recruited rapidly into TNF-RSC in a manner dependent on the Met1-ubiquitylating complex LUBAC to regulate the recruitment of A20 to control Lys63 deubiquitylation of RIPK1...
January 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29137596/analysis-of-breast-cancer-subtypes-by-ap-isa-biclustering
#17
Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang, Jianhua Wei
BACKGROUND: Gene expression profiling has led to the definition of breast cancer molecular subtypes: Basal-like, HER2-enriched, LuminalA, LuminalB and Normal-like. Different subtypes exhibit diverse responses to treatment. In the past years, several traditional clustering algorithms have been applied to analyze gene expression profiling. However, accurate identification of breast cancer subtypes, especially within highly variable LuminalA subtype, remains a challenge. Furthermore, the relationship between DNA methylation and expression level in different breast cancer subtypes is not clear...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29078411/peli1-functions-as-a-dual-modulator-of-necroptosis-and-apoptosis-by-regulating-ubiquitination-of-ripk1-and-mrna-levels-of-c-flip
#18
Huibing Wang, Huyan Meng, Xingyan Li, Kezhou Zhu, Kangyun Dong, Adnan K Mookhtiar, Huiting Wei, Ying Li, Shao-Cong Sun, Junying Yuan
Apoptosis and necroptosis are two distinct cell death mechanisms that may be activated in cells on stimulation by TNFα. It is still unclear, however, how apoptosis and necroptosis may be differentially regulated. Here we screened for E3 ubiquitin ligases that could mediate necroptosis. We found that deficiency of Pellino 1 (PELI1), an E3 ubiquitin ligase, blocked necroptosis. We show that PELI1 mediates K63 ubiquitination on K115 of RIPK1 in a kinase-dependent manner during necroptosis. Ubiquitination of RIPK1 by PELI1 promotes the formation of necrosome and execution of necroptosis...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29023097/isolation-and-characterization-of-few-layer-manganese-thiophosphite
#19
Gen Long, Ting Zhang, Xiangbin Cai, Jin Hu, Chang-Woo Cho, Shuigang Xu, Junying Shen, Zefei Wu, Tianyi Han, Jiangxiazi Lin, Jingwei Wang, Yuan Cai, Rolf Lortz, Zhiqiang Mao, Ning Wang
This work reports an experimental study on an antiferromagnetic honeycomb lattice of MnPS3 that couples the valley degree of freedom to a macroscopic antiferromagnetic order. The crystal structure of MnPS3 is identified by high-resolution scanning transmission electron microscopy. Layer-dependent angle-resolved polarized Raman fingerprints of the MnPS3 crystal are obtained, and the Raman peak at 383 cm-1 exhibits 100% polarity. Temperature dependences of anisotropic magnetic susceptibility of the MnPS3 crystal are measured in a superconducting quantum interference device...
November 28, 2017: ACS Nano
https://www.readbyqxmd.com/read/28912584/niche-harmony-search-algorithm-for-detecting-complex-disease-associated-high-order-snp-combinations
#20
Shouheng Tuo, Junying Zhang, Xiguo Yuan, Zongzhen He, Yajun Liu, Zhaowen Liu
Genome-wide association study is especially challenging in detecting high-order disease-causing models due to model diversity, possible low or even no marginal effect of the model, and extraordinary search and computations. In this paper, we propose a niche harmony search algorithm where joint entropy is utilized as a heuristic factor to guide the search for low or no marginal effect model, and two computationally lightweight scores are selected to evaluate and adapt to diverse of disease models. In order to obtain all possible suspected pathogenic models, niche technique merges with HS, which serves as a taboo region to avoid HS trapping into local search...
September 14, 2017: Scientific Reports
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