scholarly journals Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain

2018 ◽  
Author(s):  
Salim Megat ◽  
Pradipta R. Ray ◽  
Jamie K. Moy ◽  
Tzu-Fang Lou ◽  
Paulino Barragan-Iglesias ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neuropathic Pain ◽  
Signaling Pathways ◽  
Affinity Purification ◽  
Mrna Translation ◽  
Underlying Mechanism ◽  
Genetic Ablation ◽  
Key Drivers ◽  
Novel Target ◽  
Mtorc1 Activation

AbstractPain sensing neurons, nociceptors, are key drivers of neuropathic pain. We used translating ribosome affinity purification (TRAP) to comprehensively characterize up-and down-regulated mRNA translation in Scn10a-positive nociceptors in chemotherapy-induced neuropathic pain. We provide evidence that an underlying mechanism driving these changes in gene expression is a sustained mTORC1 activation driven by MNK1-eIF4E signaling. RagA, a GTPase controlling mTORC1 activity, is identified as a novel target of MNK1-eIF4E signaling, demonstrating a new link between these distinct signaling pathways. Neuropathic pain and RagA translation are strongly attenuated by genetic ablation of eIF4E phosphorylation, MNK1 elimination or treatment with the MNK inhibitor eFT508. We reveal a novel translational circuit for the genesis of neuropathic pain with important implications for next generation neuropathic pain therapeutics.One Sentence SummaryCell-specific sequencing of translating mRNAs elucidates signaling pathology that can be targeted to reverse neuropathic pain

scholarly journals A potential role for a novel ZC3H5 complex in regulating mRNA translation in Trypanosoma brucei

2020 ◽  
Vol 295 (42) ◽  
pp. 14291-14304
Author(s):  
Kathrin Bajak ◽  
Kevin Leiss ◽  
Christine Clayton ◽  
Esteban Erben
Keyword(s):  
Gene Expression ◽  
Trypanosoma Brucei ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Affinity Purification ◽  
Critical Role ◽  
Rna Binding Protein ◽  
Mrna Translation

In Trypanosoma brucei and related kinetoplastids, gene expression regulation occurs mostly posttranscriptionally. Consequently, RNA-binding proteins play a critical role in the regulation of mRNA and protein abundance. Yet, the roles of many RNA-binding proteins are not understood. Our previous research identified the RNA-binding protein ZC3H5 as possibly involved in gene repression, but its role in controlling gene expression was unknown. We here show that ZC3H5 is an essential cytoplasmic RNA-binding protein. RNAi targeting ZC3H5 causes accumulation of precytokinetic cells followed by rapid cell death. Affinity purification and pairwise yeast two-hybrid analysis suggest that ZC3H5 forms a complex with three other proteins, encoded by genes Tb927.11.4900, Tb927.8.1500, and Tb927.7.3040. RNA immunoprecipitation revealed that ZC3H5 is preferentially associated with poorly translated, low-stability mRNAs, the 5′-untranslated regions and coding regions of which are enriched in the motif (U/A)UAG(U/A). As previously found in high-throughput analyses, artificial tethering of ZC3H5 to a reporter mRNA or other complex components repressed reporter expression. However, depletion of ZC3H5 in vivo caused only very minor decreases in a few targets, marked increases in the abundances of very stable mRNAs, an increase in monosomes at the expense of large polysomes, and appearance of “halfmer” disomes containing two 80S subunits and one 40S subunit. We speculate that the ZC3H5 complex might be implicated in quality control during the translation of suboptimal open reading frames.

Translation of IGBP1 mRNA Contributes to the Regulation of Expansion and Differentiation of Erythroid Progenitors.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 72-72
Author(s):  
Godfrey Grech ◽  
Montserrat Blazquez-Domingo ◽  
Andrea Kolbus ◽  
Hartmut Beug ◽  
Bob Lowenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Binding Protein ◽  
Expression Profiles ◽  
Constitutive Expression ◽  
Mrna Translation ◽  
Erythroid Differentiation ◽  
Scaffolding Protein ◽  
Initiation Factor ◽  
Erythroid Progenitors

Abstract Erythroid progenitors can be expanded in vitro in the presence of erythropoietin (Epo), stem cell factor (SCF) and dexamethasone, while they differentiate to enucleated erythrocytes in presence of Epo only. Our study aims to identify (i) signaling pathways that control expansion of erythroid progenitors and (i) genes regulated by these signaling pathways. Since (i) SCF strongly activates phosphotidylinositol 3 kinase (PI3K) and (ii) inhibition of PI3K with LY294002 induces terminal differentiation of erythroid progenitors under Epo and SCF stimulation, SCF seems to enhance renewal divisions of erythroid progenitors via a PI3K-dependent mechanism. An important PI3K-dependent process in cell proliferation is regulation of mRNA translation. PI3K controls the activity of mTOR (mammalian target of rapamycin), whose activation results in phosphorylation of eIF4E (eukaryote Initiation Factor 4E)-binding protein (4E-BP). Fully phosphorylated 4E-BP releases eIF4E, which can subsequently bind eIF4G, the scaffolding protein of the eIF4F cap-binding and scanning complex. In particular mRNAs with a structured UTR (untranslated region) require optimal availability of eIF4E to be translated. SCF, but not Epo can induce full phosphorylation of 4E-BP and efficient formation of the eIF4F cap-binding complex. Overexpression of eIF4E inhibited erythroid differentiation as if SCF were present, indicating that SCF-induced release of eIF4E from 4E-BP is an important mechanism regulating the balance between progenitor expansion and differentiation. A major step in mRNA translation controlled by eIF4F is polysome recruitment. To identify genes whose expression is regulated by signaling-induced polysome recruitment, we compared total and polysome-bound mRNA from factor deprived and Epo-, SCF- or Epo plus SCF restimulated progenitors on gene-expression micro-arrays (Affymetrix). The profiling was performed with 4 biological replicates and candidate genes were selected using ANOVA. In subsequent cluster analysis we combined these data with (polysomal) expression profiles of differentiating erythroid cells. Thus we identified a cluster containing genes, upregulated in part or completely at the level of mRNA polysome recruitment and downregulated during erythroid differentiation. Targets involved in signal transduction and gene expression were analyzed in more detail. Polysome recruitment of 15/17 targets tested so far appeared to be dependent on PI3K activation and eIF4E expression. Constitutive expression of these targets in erythroid progenitors revealed that one target in particular was able to inhibit erythroid differentiation comparable to overexpression of eIF4E. This target was IGBP1 (Immunoglobulin binding protein 1). IGBP1 binds to and modulates the activity of the catalytic subunit of PP2A, a major cellular serine/threonine phosphatase, which also dephosphorylates 4E-BP. Overexpression of IGBP1 does not inhibit 4E-BP dephosphorylation in absence of factor, but enhances phosphorylation of 4E-BP in presence of Epo. Nevertheless, constitutive expression of IGBP1 does not increase polysome association of structured mRNAs. The multiple functions of PP2A suggest that the potent inhibition of erythroid differentiation by IGBP1 may be due to deregulation of several cellular mechanisms.

ZmCLA4 regulates leaf angle through multiple hormone signaling pathways in maize

2020 ◽  
Author(s):  
Dandan Dou ◽  
Shengbo Han ◽  
Liru Cao ◽  
Lixia Ku ◽  
Huafeng Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Target Genes ◽  
Acid Metabolism ◽  
Affinity Purification ◽  
Underlying Mechanism ◽  
Leaf Angle ◽  
Hormone Signaling ◽  
Transport Pathway ◽  
Close Relationship ◽  
Plant Hormone Signaling

Abstract Leaf angle (LA) is an important agronomic trait in cereals that shares a close relationship with crop architecture and grain yield. Although it has been previously reported that ZmCLA4 can influence LA, the underlying mechanism of it remains unclear. In this study, we used Gal4-LexA/UAS system and transactivation analysis to demonstrate that ZmCLA4 is a transcriptional repressor that regulates LA. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmCLA4 mainly binds to the promoters containing the EAR motif (CACCGGAC) as well as two motifs (CCGARGS and CDTCNTC) to inhibit the expression of its target genes. Further analysis of ZmCLA4 target genes indicated that ZmCLA4 functions as a hub of multiple plant hormone signaling pathways because ZmCLA4 was found to directly bind to the promoters of multiple genes including ZmARF22 and ZmIAA26 in the auxin transport pathway, ZmBZR3 in the brassinosteroid signaling pathway, two ZmWRKY genes involved in abscisic acid metabolism, ZmCYP genes (ZmCYP75B1, ZmCYP93D1) related to jasmonic acid metabolism, and ZmABI3 involved in the ethylene response pathway. Overall, our work provides deep insights into the regulatory network of ZmCLA4 in controlling LA in maize.

scholarly journals RPL-4 and RPL-9 ̶Mediated Ribosome Purifications Facilitate the Efficient Analysis of Gene Expression in Caenorhabditis elegans Germ Cells

2020 ◽  
Vol 10 (11) ◽  
pp. 4063-4069
Author(s):  
Marco Nousch
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Germ Cell ◽  
Germ Cells ◽  
Ribosomal Proteins ◽  
Affinity Purification ◽  
Mrna Translation ◽  
Target Tissue ◽  
Purification Method ◽  
Cell Functions

In many organisms, tissue complexity and cellular diversity create a barrier that can hinder our understanding of gene expression programs. To address this problem, methods have been developed that allow for easy isolation of translated mRNAs from genetically defined cell populations. A prominent example is the Translating Ribosome Affinity Purification method also called TRAP. Here, ribosome associated mRNAs are isolated via purification of the ribosomal protein RPL10A/uL1, which is expressed under the control of a tissue specific promoter. Originally developed to investigate gene expression in mouse neurons, it has by now been adopted to many different organisms and tissues. Interestingly, TRAP has never been used successfully to analyze mRNA translation in germ cells. Employing a combination of genetic and biochemical approaches, I assessed several ribosomal proteins for their suitability for TRAP using the Caenorhabditis elegans germline as a target tissue. Surprisingly, I found that RPL10A/uL1 is not the ideal ribosomal component to perform such an analysis in germ cells. Instead other proteins such as RPL4/uL4 or RPL9/eL6 are much better suited for this task. Tagged variants of these proteins are well expressed in germ cells, integrated into translating ribosomes and do not influence germ cell functions. Furthermore, germ cell-specific mRNAs are much more efficiently co-purified with RPL4/uL4 and RPL9/uL6 compared to RPL10A/uL1. This study provides a solid basis upon which future germ cell TRAP experiments can be built, and it highlights the need for rigorous testing when adopting such methods to a new biological system.

Comprehensive assessment of PD-L1 and PD-L2 dysregulation in gastrointestinal cancers

Epigenomics ◽  
2020 ◽  
Author(s):  
Qijie Zhao ◽  
Jinan Guo ◽  
Yueshui Zhao ◽  
Jing Shen ◽  
Parham Jabbarzadeh Kaboli ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Signaling Pathways ◽  
Underlying Mechanism ◽  
Comprehensive Analysis ◽  
The Cancer Genome Atlas ◽  
Gastrointestinal Cancers ◽  
Tumor Mutation Burden ◽  
Mutation Burden ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Background: PD-L1 and PD-L2 are ligands of PD-1. Their overexpression has been reported in different cancers. However, the underlying mechanism of PD-L1 and PD-L2 dysregulation and their related signaling pathways are still unclear in gastrointestinal cancers. Materials & methods: The expression of PD-L1 and PD-L2 were studied in The Cancer Genome Atlas and Genotype-Tissue Expression databases. The gene and protein alteration of PD-L1 and PD-L2 were analyzed in cBioportal. The direct transcription factor regulating PD-L1/ PD-L2 was determined with ChIP-seq data. The association of PD-L1/PD-L2 expression with clinicopathological parameters, survival, immune infiltration and tumor mutation burden were investigated with data from The Cancer Genome Atlas. Potential targets and pathways of PD-L1 and PD-L2 were determined by protein enrichment, WebGestalt and gene ontology. Results: Comprehensive analysis revealed that PD-L1 and PD-L2 were significantly upregulated in most types of gastrointestinal cancers and their expressions were positively correlated. SP1 was a key transcription factor regulating the expression of PD-L1. Conclusion: Higher PD-L1 or PD-L2 expression was significantly associated with poor overall survival, higher tumor mutation burden and more immune and stromal cell populations. Finally, HIF-1, ERBB and mTOR signaling pathways were most significantly affected by PD-L1 and PD-L2 dysregulation. Altogether, this study provided comprehensive analysis of the dysregulation of PD-L1 and PD-L2, its underlying mechanism and downstream pathways, which add to the knowledge of manipulating PD-L1/PD-L2 for cancer immunotherapy.

scholarly journals CircFAM13B promotes the proliferation of hepatocellular carcinoma by sponging miR-212, upregulating E2F5 expression and activating the P53 pathway

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Xie ◽  
Xiaofeng Hang ◽  
Wensheng Xu ◽  
Jing Gu ◽  
Yuanjing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
In Vivo Studies ◽  
Circular Rnas ◽  
Novel Target ◽  
Underlying Mechanisms

Abstract Background Most of the biological functions of circular RNAs (circRNAs) and the potential underlying mechanisms in hepatocellular carcinoma (HCC) have not yet been discovered. Methods In this study, using circRNA expression data from HCC tumor tissues and adjacent tissues from the Gene Expression Omnibus database, we identified out differentially expressed circRNAs and verified them by qRT-PCT. Functional experiments were performed to evaluate the effects of circFAM13B in HCC in vitro and in vivo. Results We found that circFAM13B was the most significantly differentially expressed circRNA in HCC tissue. Subsequently, in vitro and in vivo studies also demonstrated that circFAM13B promoted the proliferation of HCC. Further studies revealed that circFAM13B, a sponge of miR-212, is involved in the regulation of E2F5 gene expression by competitively binding to miR-212, inhibits the activation of the P53 signalling pathway, and promotes the proliferation of HCC cells. Conclusions Our findings revealed the mechanism underlying the regulatory role played by circFAM13B, miR-212 and E2F5 in HCC. This study provides a new theoretical basis and novel target for the clinical prevention and treatment of HCC.

scholarly journals 975. Why Sex Make a Difference in HIV Clinical Course? Bioinformatics Analysis of Differential Expressed Gene in Females and Males with HIV Disease

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S516-S517
Author(s):  
Kulachanya Suwanwongse ◽  
Nehad Shabarek
Keyword(s):  
Gene Expression ◽  
Bioinformatics Analysis ◽  
Underlying Mechanism ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Gender Inequalities ◽  
Hiv Disease ◽  
Go Analysis ◽  
Hiv Progression ◽  
Pathway Analyses

Abstract Background Human immunodeficiency virus (HIV) disease progression are different among genders, in which women usually progress to acquired immunodeficiency syndrome (AIDS) faster than men. The mechanisms resulting in the gender biases of HIV progression are unclear. We conducted a bioinformatics analysis of differentially expressed genes (DEGs) in women and men with HIV disease to understand the sex-based differences in HIV pathogenesis. Methods We obtained microarray data from the Gene Expression Omnibus (GEO) database using our pre-defined search strategy and analyzed data using the GEO2R platform. The t-test was done to compare DEGs between females and males with HIV diseases. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was implemented to systematically extract biological features and processes of retrieving DEGs via gene ontology (GO) analysis. A Systemic search was performed to evaluate each DEG function and its possible association with HIV. Results One gene expression profiling data were retrieved: GSE 140713, composed of 40 males and 10 females with HIV1 infected samples. A GEO2R analysis yielded 19 DEGs (Table 1). The GO analysis result was demonstrated in Tables 2 and 3. Following a systemic search, we found two DEGs, which have previous studies reported an association with HIV: DDX3X (20 studies) and PDS5 (1 study). We proposed DDX3X (t 5.3, p 0.0037) is responsible for gender inequalities of HIV progression because of: 1. DDX3X is needed in the HIV1 life cycle. 2. Several studies confirmed a positive correlation between DDX3X expression and HIV1 replication. 3. Our study found an up-regulated DDX3X expression in women corresponded to the fact that women progress to AIDS faster than men. 4. Our GO analysis showed female up-regulated genes were enriched in positive regulation of the gene expression pathway, which can be explained by DDX3X and its underlying mechanism. Table 1: DEGs in women and men with HIV1 disease Table 2: GO functional enrichment pathway analyses of overall retrieving DEGs Table 3: GO functional enrichment pathway analyses of down- and up-regulated clusters of DEGs Conclusion Aberrant DDX3X expression may contribute to sex-based differences in HIV disease. Drugs modifying DDX3X gene expression will be beneficial in the treatment of HIV especially resolving the HIV drug resistance problem because current anti-HIV drugs target viral components posed the risk of viral mutation. Disclosures All Authors: No reported disclosures

scholarly journals Challenges with Methods for Detecting and Studying the Transcription Factor Nuclear Factor Kappa B (NF-κB) in the Central Nervous System

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1335
Author(s):  
Marina Mostafizar ◽  
Claudia Cortes-Pérez ◽  
Wanda Snow ◽  
Jelena Djordjevic ◽  
Aida Adlimoghaddam ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Signaling Pathways ◽  
Quantitative Methods ◽  
Nuclear Factor Kappa B ◽  
Inflammatory Responses ◽  
Nuclear Factor ◽  
Nuclear Factor Kappa ◽  
Regulated Gene Expression ◽  
Transcription Factor Nuclear Factor

The transcription factor nuclear factor kappa B (NF-κB) is highly expressed in almost all types of cells. NF-κB is involved in many complex biological processes, in particular in immunity. The activation of the NF-κB signaling pathways is also associated with cancer, diabetes, neurological disorders and even memory. Hence, NF-κB is a central factor for understanding not only fundamental biological presence but also pathogenesis, and has been the subject of intense study in these contexts. Under healthy physiological conditions, the NF-κB pathway promotes synapse growth and synaptic plasticity in neurons, while in glia, NF-κB signaling can promote pro-inflammatory responses to injury. In addition, NF-κB promotes the maintenance and maturation of B cells regulating gene expression in a majority of diverse signaling pathways. Given this, the protein plays a predominant role in activating the mammalian immune system, where NF-κB-regulated gene expression targets processes of inflammation and host defense. Thus, an understanding of the methodological issues around its detection for localization, quantification, and mechanistic insights should have a broad interest across the molecular neuroscience community. In this review, we summarize the available methods for the proper detection and analysis of NF-κB among various brain tissues, cell types, and subcellular compartments, using both qualitative and quantitative methods. We also summarize the flexibility and performance of these experimental methods for the detection of the protein, accurate quantification in different samples, and the experimental challenges in this regard, as well as suggestions to overcome common challenges.

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