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Thomas O'Loughlin, Thomas A Masters, Folma Buss
The intracellular functions of myosin motors requires a number of adaptor molecules, which control cargo attachment, but also fine-tune motor activity in time and space. These motor-adaptor-cargo interactions are often weak, transient or highly regulated. To overcome these problems, we use a proximity labelling-based proteomics strategy to map the interactome of the unique minus end-directed actin motor MYO6. Detailed biochemical and functional analysis identified several distinct MYO6-adaptor modules including two complexes containing RhoGEFs: the LIFT (LARG-Induced F-actin for Tethering) complex that controls endosome positioning and motility through RHO-driven actin polymerisation; and the DISP (DOCK7-Induced Septin disPlacement) complex, a novel regulator of the septin cytoskeleton...
February 21, 2018: EMBO Reports
Maria Vila-Casadesús, Elena Vila-Navarro, Giulia Raimondi, Cristina Fillat, Antoni Castells, Juan José Lozano, Meritxell Gironella
MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression. They play important roles in cancer but little is known about the specific functions that each miRNA exerts in each type of cancer. More knowledge about their specific targets is needed to better understand the complexity of molecular networks taking part in cancer. In this study we report the miRNA-mRNA interactome occurring in pancreatic cancer by using a bioinformatic approach called miRComb, which combines tissue expression data with miRNA-target prediction databases (TargetScan, miRSVR and miRDB)...
January 19, 2018: Oncotarget
Elizabeth Scarr, Madhara Udawela, Brian Dean
Schizophrenia (Sz) probably occurs after genetically susceptible individuals encounter a deleterious environmental factor that triggers epigenetic mechanisms to change CNS gene expression. To determine if omnibus changes in CNS gene expression are present in Sz, we compared mRNA levels in the frontal pole (Brodmann's area (BA) 10), the dorsolateral prefrontal cortex (BA 9) and cingulate cortex (BA 33) from 15 subjects with Sz and 15 controls using the Affymetrix™ Human Exon 1.0 ST Array. Differences in mRNA levels (±≥20%; p < 0...
February 20, 2018: NPJ Schizophrenia
Tao Li, Li Yi, Long Hai, Haiwen Ma, Zhennan Tao, Chen Zhang, Iruni Roshanie Abeysekera, Kai Zhao, Yihan Yang, Wei Wang, Bo Liu, Shengping Yu, Luqing Tong, Peidong Liu, Meng Zhu, Bingcheng Ren, Yu Lin, Kai Zhang, Cheng Cheng, Yubao Huang, Xuejun Yang
Numerous studies have shown that calmodulin (CaM) is a major regulator of calcium-dependent signaling, which regulates cell proliferation, programmed cell death, and autophagy in cancer. However, limited information is available on mechanisms underlying the effect of CaM on the invasive property of glioblastoma multiforme (GBM) cells, especially with respect to invadopodia formation. In this study, we find that CaM serves as a prognostic factor for GBM, and it is strongly associated with the invasive nature of this tumor...
February 20, 2018: Cell Death & Disease
Masaharu Iwasaki, Petra Minder, Yíngyún Caì, Jens H Kuhn, John R Yates, Bruce E Torbett, Juan C de la Torre
Several mammalian arenaviruses (mammarenaviruses) cause hemorrhagic fevers in humans and pose serious public health concerns in their endemic regions. Additionally, mounting evidence indicates that the worldwide-distributed, prototypic mammarenavirus, lymphocytic choriomeningitis virus (LCMV), is a neglected human pathogen of clinical significance. Concerns about human-pathogenic mammarenaviruses are exacerbated by of the lack of licensed vaccines, and current anti-mammarenavirus therapy is limited to off-label use of ribavirin that is only partially effective...
February 20, 2018: PLoS Pathogens
Jing Xia, Ling Kong, Li-Juan Zhou, Shui-Zhen Wu, Li-Jie Yao, Cheng He, Cynthia Y He, Hong-Juan Peng
Toxoplasma gondii rhoptry protein ROP18 ( Tg ROP18) is a key virulence factor secreted into the host cell during invasion, where it modulates the host cell response by interacting with its host targets. However, only a few Tg ROP18 targets have been identified. In this study, we applied a high-throughput protein-protein interaction (PPI) screening in human cells using bimolecular fluorescence complementation (BiFC) to identify the targets of Type I strain ROP18 (ROP18I ) and Type II strain ROP18 (ROP18II )...
2018: Frontiers in Immunology
Javier De Las Rivas, Diego Alonso-López, Mónica M Arroyo
Unraveling the protein interaction wiring that occurs in human cells as a scaffold of biological processes requires the identification of all elements that constitute such molecular interaction networks. Proteome-wide experimental studies and bioinformatic comprehensive efforts have provided reliable and updated compendiums of the human protein interactome. In this work, we present a current view of available databases of human protein-protein interactions (PPIs) that allow building protein interaction networks...
2018: Advances in Protein Chemistry and Structural Biology
Pedro S T Russo, Gustavo R Ferreira, Lucas E Cardozo, Matheus C Bürger, Raul Arias-Carrasco, Sandra R Maruyama, Thiago D C Hirata, Diógenes S Lima, Fernando M Passos, Kiyoshi F Fukutani, Melissa Lever, João S Silva, Vinicius Maracaja-Coutinho, Helder I Nakaya
BACKGROUND: The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions. RESULTS: In this paper, we present a fast and easy-to-use Bioconductor package named CEMiTool that unifies the discovery and the analysis of co-expression modules...
February 20, 2018: BMC Bioinformatics
Alfredo Toledo-Leyva, Julio César Villegas-Pineda, Sergio Encarnación-Guevara, Dolores Gallardo-Rincón, Patricia Talamás-Rohana
Background: Epithelial ovarian cancer is the second most lethal gynecological cancer worldwide. Ascites can be found in all clinical stages, however in advanced disease stages IIIC and IV it is more frequent and could be massive, associated with worse prognosis. Due to the above, it was our interest to understanding how the ascites of ovarian cancer patients induces the mechanisms by which the cells present in it acquire a more aggressive phenotype and to know new proteins associated to this process...
2018: Proteome Science
Maria João Freitas, Margarida Fardilha
Sertoli cells are crucial for germ cell support, create a suitable environment for spermatogenesis, and integrate information from the nervous system and germ cell line. To fully understand the role of Sertoli cells, it is necessary to characterize the protein-protein interactions. Identifying the interactome of a given protein may provide leads about the role and molecular mechanism of such protein in Sertoli cells. One of the techniques to characterize protein interactomes consists of co-immunoprecipitation followed by mass spectrometry or Western blot...
2018: Methods in Molecular Biology
Nathan P Manes, Aleksandra Nita-Lazar
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples...
February 13, 2018: Journal of Proteomics
Erasmia Rouka
Human Herpes Virus type 6 (HHV-6) is a ubiquitous virus consisting of two viral species, HHV-6A and HHV-6B that have been associated with numerous and diverse pathologies. As many other viruses HHV-6 modulates the apoptotic machinery of its host to subvert immune response to infection, yet the exact mechanisms behind this process remain under investigation. The genes encoding the CTSS, PTX3, CHI3L1, Mx1, CXCL16, BIRC3 and BST2 proteins have been linked to HHV-6Α related neurologic diseases whilst also associated with apoptosis...
March 2018: Medical Hypotheses
Branislava Gemovic, Neven Sumonja, Radoslav Davidovic, Vladimir Perovic, Nevena Veljkovic
BACKGROUND: The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology...
February 13, 2018: Current Medicinal Chemistry
Jack C-C Hsu, David W Reid, Alyson M Hoffman, Devanand Sarkar, Christopher V Nicchitta
Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs...
February 7, 2018: RNA
N Pospiech, H Cibis, L Dietrich, F Müller, T Bange, S Hennig
Interactions of long non-coding RNAs (lncRNA) with proteins play important roles in the regulation of many cellular processes. PANDAR (Promotor of CDKN1A Antisense DNA damage Activated RNA) is a lncRNA that is transcribed in a p53-dependent manner from the CDKN1A promoter and is involved in the regulation of proliferation and senescence. Overexpression of PANDAR has been observed in several tumor species and correlated with a poor prognosis for patient survival rate. Depending on the cellular state, PANDAR is known to interact with proteins such as the nuclear transcription factor Y subunit A (NF-YA) and the scaffold attachment factor A (SAF-A)...
February 12, 2018: Scientific Reports
Xichen Bao, Xiangpeng Guo, Menghui Yin, Muqddas Tariq, Yiwei Lai, Shahzina Kanwal, Jiajian Zhou, Na Li, Yuan Lv, Carlos Pulido-Quetglas, Xiwei Wang, Lu Ji, Muhammad J Khan, Xihua Zhu, Zhiwei Luo, Changwei Shao, Do-Hwan Lim, Xiao Liu, Nan Li, Wei Wang, Minghui He, Yu-Lin Liu, Carl Ward, Tong Wang, Gong Zhang, Dongye Wang, Jianhua Yang, Yiwen Chen, Chaolin Zhang, Ralf Jauch, Yun-Gui Yang, Yangming Wang, Baoming Qin, Minna-Liisa Anko, Andrew P Hutchins, Hao Sun, Huating Wang, Xiang-Dong Fu, Biliang Zhang, Miguel A Esteban
We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells...
February 12, 2018: Nature Methods
Kate E Yu, Do-Hyoung Kim, Yong-In Kim, Walton D Jones, J Eugene Lee
Animals use their odorant receptors to receive chemical information from the environment. Insect odorant receptors differ from the G protein-coupled odorant receptors in vertebrates and nematodes, and very little is known about their protein-protein interactions. Here, we introduce a mass spectrometric platform designed for the large-scale analysis of insect odorant receptor protein-protein interactions. Using this platform, we obtained the first Orco interactome from Drosophila melanogaster. From a total of 1,186 identified proteins, we narrowed the interaction candidates to 226, of which only two-thirds have been named...
February 12, 2018: Molecules and Cells
Haixiu Yang, Yunpeng Zhang, Jiasheng Wang, Tan Wu, Siyao Liu, Yanjun Xu, Desi Shang
An important challenge in drug development is to gain insight into the mechanism of drug sensitivity. Looking for insights into the global relationships between drugs and their sensitivity genes would be expected to reveal mechanism of drug sensitivity. Here we constructed a drug-sensitivity gene network (DSGN) based on the relationships between drugs and their sensitivity genes, using drug screened genomic data from the NCI-60 cell line panel, including 181 drugs and 1057 sensitivity genes, and 1646 associations between them...
January 9, 2018: Oncotarget
Feifei Wang, Songli Zhu, Laura A Fisher, Weidong Wang, Gregory G Oakley, Chunling Li, Aimin Peng
The specific function of PP2A, a major serine/threonine phosphatase, is mediated by regulatory targeting subunits, such as members of the B55 family. Although implicated in cell division and other pathways, the specific substrates and functions of B55 targeting subunits are largely undefined. In this study we identified over 100 binding proteins of B55α and B55β in Xenopus egg extracts that are involved in metabolism, mitochondria function, molecular trafficking, cell division, cytoskeleton, DNA replication, DNA repair, and cell signaling...
February 8, 2018: Scientific Reports
Petros Kolovos, Rutger W W Brouwer, Christel E M Kockx, Michael Lesnussa, Nick Kepper, Jessica Zuin, A M Ali Imam, Harmen J G van de Werken, Kerstin S Wendt, Tobias A Knoch, Wilfred F J van IJcken, Frank Grosveld
Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio...
March 2018: Nature Protocols
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