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Yibo Zhang, Zhiwei Zhang, Wei Ge
Homology-directed recombination (HDR)-mediated genome editing is a powerful approach for both basic functional study and disease modeling. Although some studies have reported HDR-mediated precise editing in non-rodent models, the efficiency of establishing pure mutant animal lines that carry specific amino acid substitutions remains low. Furthermore, because the efficiency of nonhomologous end joining (NHEJ)-induced insertion and deletion (indel) mutations is normally much higher than that of HDR-induced point mutations, it is often difficult to identify the latter in the background of indel mutations...
March 2, 2018: Journal of Biological Chemistry
Mohamad Moustafa Ali, Vijay Suresh Akhade, Subazini Thankaswamy Kosalai, Santhilal Subhash, Luisa Statello, Matthieu Meryet-Figuiere, Jonas Abrahamsson, Tanmoy Mondal, Chandrasekhar Kanduri
Despite improvement in our understanding of long noncoding RNAs (lncRNAs) role in cancer, efforts to find clinically relevant cancer-associated lncRNAs are still lacking. Here, using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets. Systematic clinical investigation of 14 Pan-Cancer data sets identified 633 independent prognostic markers. Silencing of the top differentially expressed and clinically relevant S-phase-enriched lncRNAs in several cancer models affects crucial cancer cell hallmarks...
February 28, 2018: Nature Communications
Padmanaban S Suresh, Rie Tsutsumi, Thejaswini Venkatesh
YBX1 (Y box binding protein 1) is an RNA-/DNA-binding multifunctional protein harboring the classical cold shock protein (CSD) domain, an A/P domain, and a long C-terminal domain with alternating positively and negatively charged amino acids. It is a well-established oncogenic transcriptional factor, and regulates apoptosis, translation, cell proliferation, mRNA splicing, repair, differentiation, and stress response. The non-coding transcriptome has added yet another layer of complexity to the YBX1-mediated master regulation of cellular functions...
February 19, 2018: European Journal of Cell Biology
Yong Wang, Yiting Wang, Liang Xu, Xianqi Lu, Donghe Fu, Jing Su, Hua Geng, Guoxuan Qin, Ruibing Chen, Changyi Quan, Yuanjie Niu, Dan Yue
Renal cell carcinoma (RCC) is a common urologic tumor and the third leading cause of death among urological tumors. Recent studies demonstrate that RCC tumors are more heavily infiltrated by lymphocytes than other cancers. However, the exact roles played by CD4 + T cells in RCC proliferation remain unknown. In this study, we cocultured RCC cells with CD4 + T cells. Stable knockdown of YBX1 in RCC cells was constructed. The effects of CD4 + T cells, TGFβ1 and YBX1 on RCC cells were investigated using cell viability assays...
December 28, 2017: Experimental Cell Research
Queenie Wing-Lei Wong, Ming-An Sun, Shuk-Wa Lau, Chirag Parsania, Shaolong Zhou, Silin Zhong, Wei Ge
Ovarian folliculogenesis is always of great interest in reproductive biology. However, the molecular mechanisms that control follicle development, particularly the early phase of follicle activation or recruitment, still remain poorly understood. In an attempt to decipher the gene networks and signaling pathways involved in such transition, we conducted a transcriptomic analysis (RNA-seq) on zebrafish primary growth (PG, stage I; inactive) and previtellogenic (PV, stage II; activated) follicles. A total of 118 unique microRNAs (miRNAs) (11 downregulated and 83 upregulated during PG/PV transition) and 56711 unique messenger RNAs (mRNAs) (1839 downregulated and 7243 upregulated during PG/PV transition) were identified...
January 1, 2018: Biology of Reproduction
Thomas M Campbell, Mauro A A Castro, Kelin Gonçalves de Oliveira, Bruce A J Ponder, Kerstin B Meyer
Two opposing clusters of transcription factors (TF) have been associated with the differential risks of estrogen receptor positive or negative breast cancers, but the mechanisms underlying the opposing functions of the two clusters are undefined. In this study, we identified NFIB and YBX1 as novel interactors of the estrogen receptor (ESR1). NFIB and YBX1 are both risk TF associated with progression of ESR1-negative disease. Notably, they both interacted with the ESR1-FOXA1 complex and inhibited the transactivational potential of ESR1...
January 15, 2018: Cancer Research
Xiaolan Yu, Yingcheng Yang, Yan Li, Yong Cao, Li Tang, Feng Chen, Jiyi Xia
Baicalein, an active flavonoid extracted from the root of Scutellaria baicalensis Georgi, has fascinating anti-cancer effects on many cancers. Our previous study also found that baicalein inhibited cervical cancer cell proliferation and migration, and induced cervical cancer cell apoptosis and cell cycle arrest. However, the molecular mechanisms underlying the anti-cancer effects of baicalein are largely unknown. In this study, we identified a novel long noncoding RNA (lncRNA), which is downregulated by baicalein in a dose- and time-dependent manner in cervical cancer...
January 2018: International Journal of Biochemistry & Cell Biology
Sofía Torres, Irene García-Palmero, Consuelo Marín-Vicente, Rubén A Bartolomé, Eva Calviño, María Jesús Fernández-Aceñero, J Ignacio Casal
We investigated new transcription and splicing factors associated with the metastatic phenotype in colorectal cancer. A concatenated tandem array of consensus transcription factor (TF)-response elements was used to pull down nuclear extracts in two different pairs of colorectal cancer cells, KM12SM/KM12C and SW620/480, genetically related but differing in metastatic ability. Proteins were analyzed by label-free LC-MS and quantified with MaxLFQ. We found 240 proteins showing a significant dysregulation in highly metastatic KM12SM cells relative to nonmetastatic KM12C cells and 257 proteins in metastatic SW620 versus SW480...
November 21, 2017: Journal of Proteome Research
Thomas G Johnson, Karin Schelch, Yuen Y Cheng, Marissa Williams, Kadir H Sarun, Michaela B Kirschner, Steven Kao, Anthony Linton, Sonja Klebe, Brian C McCaughan, Ruby Cy Lin, Christine Pirker, Walter Berger, Annette Lasham, Nico van Zandwijk, Glen Reid
BACKGROUND: Malignant pleural mesothelioma (MPM) is an aggressive malignancy linked to asbestos exposure. On a genomic level, MPM is characterised by frequent chromosomal deletions of tumour suppressors, including microRNAs. MiR-137 plays a tumour suppressor role in other cancers, so the aim of this study was to characterise it and its target Y-box binding protein-1 (YB-1) in MPM. BASIC PROCEDURES: Expression, methylation and copy number status of miR-137 and its host gene MIR137HG were assessed by PCR...
November 4, 2017: Journal of Thoracic Oncology
Matthew J Shurtleff, Jun Yao, Yidan Qin, Ryan M Nottingham, Morayma M Temoche-Diaz, Randy Schekman, Alan M Lambowitz
RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
Andreas Zaucker, Agnieszka Nagorska, Pooja Kumari, Nikolai Hecker, Yin Wang, Sizhou Huang, Ledean Cooper, Lavanya Sivashanmugam, Shruthi VijayKumar, Jan Brosens, Jan Gorodkin, Karuna Sampath
In many organisms, transcriptional and post-transcriptional regulation of components of pathways or processes has been reported. However, to date, there are few reports of translational co-regulation of multiple components of a developmental signaling pathway. Here, we show that an RNA element which we previously identified as a dorsal localization element (DLE) in the 3'UTR of zebrafish nodal-related1/squint (ndr1/sqt) ligand mRNA, is shared by the related ligand nodal-related2/cyclops (ndr2/cyc) and the nodal inhibitors, lefty1 (lft1) and lefty2 mRNAs...
October 20, 2017: Nucleic Acids Research
Liuyu Xu, Hongyun Li, Longchao Wu, Shiming Huang
Aerobic glycolysis, also known as Warburg effect, is a key hallmark of cancers. The Y-box-binding protein 1 (YBX1) is a well-known oncoprotein implicated in multiple malignant phenotypes of cancers. Meanwhile, little is known about the oncogenic functions and mechanisms of YBX1 in bladder cancer. Based on gene set enrichment analysis (GSEA) of TCGA RNAseq data, we find that YBX1 was profoundly involved in the glycolysis part of glucose metabolism. Loss- and gain-of-function studies show that YBX1 can enhance glycolysis as revealed by expression of glycolytic enzymes, glucose uptake, lactate secretion and extracellular acidification rate (ECAR)...
September 12, 2017: Oncotarget
Florian Hinze, Philipp Drewe-Boß, Miha Milek, Uwe Ohler, Markus Landthaler, Michael Gotthardt
PAR-CLIP (photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation) facilitates the identification and mapping of protein/RNA interactions. So far, it has been limited to select cell-lines as it requires efficient 4SU uptake. To increase transcriptome complexity and thus identify additional RNA-protein interaction sites we fused HEK 293 T-Rex cells (HEK293-Y) that express the RNA binding protein YBX1 with PC12 cells expressing eGFP (PC12-eGFP). The resulting hybrids enable PAR-CLIP on a neuronally expanded transcriptome (Fusion-CLIP) and serve as a proof of principle...
October 13, 2017: RNA Biology
Lei-Lei Zhou, Jie Ni, Wan-Ting Feng, Rong Yao, Shun Yue, Ya-Ning Zhu, Hai-Yan Tang, Ling-Yun Lv, Ji-Feng Feng, Wei-Guo Zhu
Y-box binding protein-1 (YBX1) is a multifunctional protein and often acts as an indicator of poor prognosis in cancers. Increasing evidence has shown that the levels of YBX1 protein were closely associated with multidrug resistance, relapse, metastasis and poor prognosis in cancers. However, its role in nasopharyngeal carcinoma (NPC) metastasis remains unknown. In our study, we discovered that the expression of YBX1 was increased in nasopharyngeal carcinoma tissues. YBX1 protein levels positively correlated with T stage and metastasis of NPC patients...
December 1, 2017: Experimental Cell Research
Ryenne N Ogburn, Lorrain Jin, He Meng, Michael C Fitzgerald
The proteins in an MCF-7 cell line were probed for tamoxifen (TAM) and n-desmethyl tamoxifen (NDT) induced stability changes using the Stability of Proteins from Rates of Oxidation (SPROX) technique in combination with two different quantitative proteomics strategies, including one based on SILAC and one based on isobaric mass tags. Over 1000 proteins were assayed for TAM- and NDT-induced protein stability changes, and a total of 163 and 200 protein hits were identified in the TAM and NDT studies, respectively...
November 3, 2017: Journal of Proteome Research
Corinna Patzina, Catherine H Botting, Adolfo García-Sastre, Richard E Randall, Benjamin G Hale
NS1 proteins of influenza A and B viruses share limited sequence homology, yet both are potent manipulators of host cell processes, particularly interferon (IFN) induction. Although many cellular partners are reported for A/NS1, only a few (e.g. PKR and ISG15) have been identified for B/NS1. Here, affinity-purification and mass spectrometry were used to expand the known host interactome of B/NS1. We identified 22 human proteins as new putative targets for B/NS1, validating several, including DHX9, ILF3, YBX1 and HNRNPC...
September 2017: Journal of General Virology
Anja Bernhardt, Alexander Fehr, Sabine Brandt, Saskia Jerchel, Tobias M Ballhause, Lars Philipsen, Saskia Stolze, Robert Geffers, Honglei Weng, Klaus-Dieter Fischer, Berend Isermann, Monika C Brunner-Weinzierl, Arvind Batra, Britta Siegmund, Cheng Zhu, Jonathan A Lindquist, Peter R Mertens
Tubular cells recruit monocytic cells in inflammatory tubulointerstitial kidney diseases. The cell-cell communication that establishes pro- or anti-inflammatory activities is mainly influenced by cytokines, reactive oxygen species, nitric oxide, and phagocytosis. Key proteins orchestrating these processes such as cold-shock proteins linked with chemoattraction and cell maturation have been identified. The prototypic member of the cold-shock protein family, Y-box binding protein (YB)-1, governs specific phenotypic alterations in monocytic cells and was explored in the present study...
November 2017: Kidney International
Xiaodong Zhao, Yanbo Liu, Shuo Yu
Long noncoding RNAs (lncRNAs) have been shown to play important roles in various cancers. However, the clinical significances and biological roles of lncRNAs in hepatocellular carcinoma (HCC) remain largely unknown. In this study, using online-available data sets and quantitative real-time PCR, we identified a novel lncRNA termed lncRNA-AWPPH, which is highly expressed in HCC tissues. Its upregulation is correlated with encapsulation incomplete, microvascular invasion, advanced TNM stage and BCLC stage. Cox proportional hazards regression analysis revealed that high lncRNA-AWPPH expression is an independent prognostic factor for poor recurrence-free and overall survival...
April 18, 2017: Biochimica et Biophysica Acta
Tao Guo, Jing Kong, Yang Liu, Zhuoshi Li, Jianglong Xia, Yan Zhang, Shilei Zhao, Fengzhou Li, Jinxiu Li, Chundong Gu
Aberrant overexpression of the transcription/translation factor Y-box-binding protein-1 (YBX1) is associated with non-small cell lung cancer (NSCLC) aggressiveness. Cancer stem cells (CSCs) contribute to the tumorigenesis and metastasis of NSCLC. Hitherto, the mechanism by which YBX1 regulates CSCs and metastasis in NSCLC remains unclear. Here, we demonstrated that YBX1 levels were elevated in NSCLC tissues and cell lines. Enforced expression of YBX1 promoted NSCLC cells invasion, sphere forming ability and ALDH1(+) population...
May 20, 2017: Biochemical and Biophysical Research Communications
Jia Pei Lim, Sukanya Shyamasundar, Jayantha Gunaratne, Olivia Jane Scully, Ken Matsumoto, Boon Huat Bay
BACKGROUND: Y-box binding protein-1 is an evolutionary conserved transcription and translation regulating protein that is overexpressed in various human malignancies, including breast cancer. Despite reports of YB-1 and its association with distant spread of breast cancer, the intrinsic mechanism underlying this observation remains elusive. This study investigates the role of YB-1 in mediating metastasis in highly invasive breast cancer cell lines. METHODS: Silencing the YBX1 gene (which encodes the YB-1 protein) by small interfering RNA (siRNA) was performed in MDA-MB-231 and Hs578T breast cancer cell lines, followed by phenotypic assays including cell migration and invasion assays...
March 16, 2017: BMC Cancer
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