Protein Translation Initiation Research Articles

5'ValCAC tRNA fragment generated as part of a protective angiogenin response provides prognostic value in amyotrophic lateral sclerosis.

Loss-of-function mutations in the ribonuclease angiogenin are associated with amyotrophic lateral sclerosis. Angiogenin has been shown to cleave transfer RNAs during stress to produce ‘transfer-derived stress-induced RNAs’. Stress-induced tRNA cleavage is preserved from single-celled organisms to humans indicating it represents part of a highly conserved stress response. However, to date, the role of tRNA cleavage in amyotrophic lateral sclerosis remains to be fully elucidated. To this end, we performed small RNA sequencing on a human astrocytoma cell line to identify the complete repertoire of tRNA fragments generated by angiogenin. We found that only a specific subset of tRNAs is cleaved by angiogenin and identified 5′ValCAC transfer-derived stress-induced RNA to be secreted from neural cells. 5′ValCAC was quantified in spinal cord and serum from SOD1G93A amyotrophic lateral sclerosis mouse models where we found it to be significantly elevated at symptom onset correlating with increased angiogenin expression, imbalanced protein translation initiation factors and slower disease progression. In amyotrophic lateral sclerosis patient serum samples, we found 5′ValCAC to be significantly higher in patients with slow disease progression, and interestingly, we find 5′ValCAC to hold prognostic value for amyotrophic lateral sclerosis patients. Here, we report that angiogenin cleaves a specific subset of tRNAs and provide evidence for 5′ValCAC as a prognostic biomarker in amyotrophic lateral sclerosis. We propose that increased serum 5′ValCAC levels indicate an enhanced angiogenin-mediated stress response within motor neurons that correlates with increased survival. These data suggest that the previously reported beneficial effects of angiogenin in SOD1G93A mice may result from elevated levels of 5′ValCAC transfer RNA fragment.

Redox States of Protein Cysteines in Pathways of Protein Turnover and Cytoskeleton Dynamics Are Changed with Aging and Reversed by Slc7a11 Restoration in Mouse Lung Fibroblasts.

Slc7a11 is the key component of system Xc−, an antiporter that imports cystine (CySS) and exports glutamate. It plays an important role in cellular defense against oxidative stress because cysteine (Cys), reduced from CySS, is used for and limits the synthesis of glutathione (GSH). We have shown that downregulation of Slc7a11 is responsible for oxidation of extracellular Cys/CySS redox potential in lung fibroblasts from old mice. However, how age-related change of Slc7a11 expression affects the intracellular redox environment of mouse lung fibroblasts remains unexplored. The purpose of this study is to evaluate the effects of aging on the redox states of intracellular proteins and to examine whether Slc7a11 contributes to the age-dependent effects. Iodoacetyl Tandem Mass Tags were used to differentially label reduced and oxidized forms of Cys residues in primary lung fibroblasts from young and old mice, as well as old fibroblasts transfected with Slc7a11. The ratio of oxidized/reduced forms (i.e., redox state) of a Cys residue was determined via multiplexed tandem mass spectrometry. Redox states of 151 proteins were different in old fibroblasts compared to young fibroblasts. Slc7a11 overexpression restored redox states of 104 (69%) of these proteins. Ingenuity Pathway Analysis (IPA) showed that age-dependent Slc7a11-responsive proteins were involved in pathways of protein translation initiation, ubiquitin-proteasome-mediated degradation, and integrin-cytoskeleton-associated signaling. Gene ontology analysis showed cell adhesion, protein translation, and organization of actin cytoskeleton were among the top enriched terms for biological process. Protein-protein interaction network demonstrated the interactions between components of the three enriched pathways predicted by IPA. Follow-up experiments confirmed that proteasome activity was lower in old cells than in young cells and that upregulation of Slc7a11 expression by sulforaphane restored this activity. This study finds that aging results in changes of redox states of proteins involved in protein turnover and cytoskeleton dynamics, and that upregulating Slc7a11 can partially restore the redox states of these proteins.

Palmitoylome profiling indicates that androgens promote the palmitoylation of metabolism-related proteins in prostate cancer-derived LNCaP cells

To explore potential therapeutic targets other than androgen-deprivation treatment for prostate cancer by screening the proteins induced by androgen at palmitoylation modification level in LNCaP cells. The LNCaP cells were treated with androgen (Methyltrienolone, R1881, 5 nmol/L) or dimethyl sulfoxide (DMSO) for 24 h, and then labeled with alkynyl palmitic acid Alk-C16 (100 μmol/L). After that, the cells were collected, lysed, the total protein was extracted, agarose beads labeled with azide (1 mmol/L) were added, and the click-chemistry reaction was carried out at room temperature for 1 h. The covalent bond formed by click-chemistry reaction of azide and alkynyl group was used to enrich the palmitoylated proteins on agarose beads. Label-free quantitation (LFQ) was used to compare the protein palmitoylation level of R1881 treated and untreated cells to screen the proteins induced by androgen at palmitoylation modification level. In this experiment, 907 potential palmitoylated proteins (mascot score>2, P<0.05) were identified, among which 430 proteins had LFQ values not zero at least twice. Among the 430 proteins, the palmitoylation levels of 92 candidates were increased by androgen treatment, and their LFQ values were significantly upregulated (>1.5-fold, P<0.05) in ≥2 samples of androgen-treated vs. untreated LNCaP cells. We also used the software of cytoscape to classify the 92 proteins, and found that the known functional proteins of them could be divided into three categories: metabolism related, protein folding related and translation initiation related. Among them, metabolism related proteins included lipid metabolism (6), glucose metabolism (7) and respiratory electron transport chain (8), and a small amount of amino acid metabolism (2) and other metabolism related proteins (2). Notably, the ratio of LFQ of cytochrome b-c1 complex subunit 2 (UQCRC2) was significantly (>3-fold, P<0.05) higher in androgen-treated cells compared with untreated cells, indicating that the palmitoylation level of UQCRC2 was enhanced by androgen most significantly than that of others. The second was long-chain acyl CoA dehydrogenase (ACADVL) related to lipid metabolism and glucose 6-phosphate dehydrogenase (PGD) related to glucose metabolism, but the LFQ ratio of them was less than 3-fold. The research on palmitoylation mechanism of metabolism, especially the proteins related to respiratory electron transport chain, will provide a new guidance for the diagnosis and treatment of prostate cancer and the development of targeted drugs.

Prediction of secondary, tertiary protein structure and interaction eIF4E from Capsicum annum with Rep Geminivirus

The eIF4E gene is a gene that plays a role in the initiation of protein translation. This gene is relatively conserved and is present in all organisms. In humans, this gene functions as a proto-oncogene, its expression and activation are associated with transformation and tumorigenesis. The eIF4E protein takes a role in the translation initiation by recruiting ribosomes to the 5’-cap structure. In some conditions, it functions as an initiator in the process of translation and co-factor of the plant’s defense system from virus attacks. The eIF4E protein also can bind with the genome linked viral protein to turnip mosaic virus [TuMV] in Capsicum annum. Their interaction is effective for virus infectivity and upregulated genome amplification. Understanding the tertiary structure of the eIF4E protein and its ligands will help in elucidating its interactions with viruses. So that it can be used to avoid spreading the virus in chili plants.

A conserved motif in three viral movement proteins from different genera is required for host factor recruitment and cell-to-cell movement

Due to their minimal genomes, plant viruses are forced to hijack specific cellular pathways to ensure host colonization, a condition that most frequently involves physical interaction between viral and host proteins. Among putative viral interactors are the movement proteins, responsible for plasmodesma gating and genome binding during viral transport. Two of them, DGBp1 and DGBp2, are required for alpha-, beta- and gammacarmovirus cell-to-cell movement, but the number of DGBp-host interactors identified at present is limited. By using two different approaches, yeast two-hybrid and bimolecular fluorescence complementation assays, we found three Arabidopsis factors, eIF3g1, RPP3A and WRKY36, interacting with DGBp1s from each genus mentioned above. eIF3g1 and RPP3A are mainly involved in protein translation initiation and elongation phases, respectively, while WRKY36 belongs to WRKY transcription factor family, important regulators of many defence responses. These host proteins are not expected to be associated with viral movement, but knocking out WRKY36 or silencing either RPP3A or eIF3g1 negatively affected Arabidopsis infection by Turnip crinkle virus. A highly conserved FNF motif at DGBp1 C-terminus was required for protein-protein interaction and cell-to-cell movement, suggesting an important biological role.

Induction of Autophagy and Changes in Cellular Metabolism in Glucose Starved C2C12 Myotubes.

Mouse myoblast C2C12 cells are commonly used as a model system for investigating the metabolic regulation of skeletal muscle. As it is therefore important to understand the metabolic features of C2C12 cells, we examined the effect of glucose starvation on autophagy in C2C12 myotubes. After culture of C2C12 myotubes with high (HG, 25.0 mM) or low (LG, 5.6 mM) glucose concentrations, the concentration of glucose in the LG group had decreased to 0 mM after 24 h of culture and was around 17 mM after 48 h of culture in the HG group. The concentration of lactate increased from 0 to approximately 9 mM at 24 h and then dropped slightly in the LG group, while it increased linearly to 21 mM in the HG group at 48 h. The phosphorylation of p70 S6 kinase, marker for the protein translation initiation was significantly lower and the ratio of LC3-II/LC3-I, marker for the induction of autophagy was significantly higher in the LG group. GLUT1 and hexokinase II expression were significantly higher in the LG group. Together, these changes in glucose and lactate concentrations in the culture media suggest that C2C12 myotubes depend on anaerobic glycolysis. Our findings also suggest that glucose depletion stimulates the expression of key molecules involved in glycolysis and that cellular autophagy is also activated in C2C12 myotubes.

The m6A reader YTHDF1 promotes ovarian cancer progression via augmenting EIF3C translation.

N 6-Methyladenosine (m6A) is the most abundant RNA modification in mammal mRNAs and increasing evidence suggests the key roles of m6A in human tumorigenesis. However, whether m6A, especially its ‘reader’ YTHDF1, targets a gene involving in protein translation and thus affects overall protein production in cancer cells is largely unexplored. Here, using multi-omics analysis for ovarian cancer, we identified a novel mechanism involving EIF3C, a subunit of the protein translation initiation factor EIF3, as the direct target of the YTHDF1. YTHDF1 augments the translation of EIF3C in an m6A-dependent manner by binding to m6A-modified EIF3C mRNA and concomitantly promotes the overall translational output, thereby facilitating tumorigenesis and metastasis of ovarian cancer. YTHDF1 is frequently amplified in ovarian cancer and up-regulation of YTHDF1 is associated with the adverse prognosis of ovarian cancer patients. Furthermore, the protein but not the RNA abundance of EIF3C is increased in ovarian cancer and positively correlates with the protein expression of YTHDF1 in ovarian cancer patients, suggesting modification of EIF3C mRNA is more relevant to its role in cancer. Collectively, we identify the novel YTHDF1-EIF3C axis critical for ovarian cancer progression which can serve as a target to develop therapeutics for cancer treatment.

Brightness-gated two-color coincidence detection unravels two distinct mechanisms in bacterial protein translation initiation

Life on the molecular scale is based on a complex interplay of biomolecules under which the ability of binding is crucial. Fluorescence based two-color coincidence detection (TCCD) is commonly used to characterize molecular binding, but suffers from an underestimation of coincident events. Here, we introduce a brightness-gated TCCD which overcomes this limitation and benchmark our approach with two custom-made calibration samples. Applied to a cell-free protein synthesis assay, brightness-gated TCCD unraveled a previously disregarded mode of translation initiation in bacteria.

A Novel Cereblon E3 Ligase Modulator Eradicates Acute Myeloid Leukemia Stem Cells through Degradation of Translation Termination Factor GSPT1

Acute myeloid leukemia (AML) is a clonal malignant disease initiated and propagated by leukemia stem cells (LSCs). Both LSCs and normal hematopoietic stem cells (HSCs) share many biological properties including self-renewal and quiescence. One such shared property that we have recently established involves the pro-survival features of proteostatic stress signaling. Stem cells have reduced protein translation initiation due to scarcity of the eIF2α translation initiation complex (van Galen et al Nature 2014; Cell Reports 2018). This in turn, increases the activity of activating transcription factor 4 (ATF4) uniquely in HSCs and LSCs. In homeostasis, this level of ATF4 facilitates stem cell persistence and survival, but upon stronger stress activation stem cell apoptosis ensues. This mechanism predicts that agonists of the integrated stress response (ISR) could provide a novel therapeutic approach to eradicate LSCs. Here we report that the novel cereblon E3 ligase modulator (CELMoD) CC-90009, which causes degradation of the translation termination factor G1 to S phase transition protein 1 (GSPT1) and downstream activation of ISR, is potent against primary AML both in vitro and in vivo, and reduces self-renewing LSCs in preclinical xenograft models for human AML. We first carried out in vitro assays to evaluate the effect of CC-90009 on primary AML samples. We found that CC-90009 degraded GSPT1 in primary AML cells and induced leukemic cell apoptosis in 24 hours. Leukemic colony forming progenitors were also reduced by CC-90009 in a dose-dependent manner. We next tested the efficacy of CC-90009 against primary AML samples in xenografts in NOD/SCID mice. Leukemia cells were transplanted intrafemorally 21 days prior to CC-90009 treatment. Mice were treated with vehicle or CC-90009 at 2.5mg/kg BID for 4 weeks. Heterogeneous responses to the CC-90009 treatment were observed. Of 35 AML samples tested, 16 were highly responsive to CC-90009 with &gt;75% reduction of AML engraftment, 10 showed moderate response between 45% and 75% reductions, and 9 showed reductions of &lt;25%. AML is clinically characterized by accumulation of blasts that are impaired for differentiation and maturation. We observed that, in addition to the reduction of total AML graft, CC-90009 also induced myeloid differentiation of AML blasts in the CC-90009 responders, as evidenced by increases in late myeloid cell surface markers (CD14, CD15 and CD11b) and reductions of the immature marker CD34. To determine the efficacy of CC-90009 against AML cases at high risk of relapse following standard induction chemotherapy, we assessed CC-90009 efficacy vs. the status of an expression-based 17-gene leukemia stem cell score (the LSC17 score) that was recently implemented for rapid risk stratification of AML patients (Ng et al, Nature 2016). LSC17-high patients are predicted to have poor treatment response and poor clinical outcome. We found that, while 8 out of 9 poor responders to CC-90009 had high LSC17 scores, 20 out of 28 samples that had high LSC17 scores responded well to CC-90009, indicating that the drug is able to target high risk cases. Serial transplantation utilizing limiting dilution analysis showed that CC-90009 targeted self-renewing LSCs. Our data established that a new CELMoD CC-90009 has anti-proliferative effects on human primary AML cells and self-renewing LSCs evaluated in xenograft assays. These observations provide important implications for CC-90009 in its clinical development as a new therapeutic agent to treat AML patients with high risk disease when treated with standard of care therapies. Currently, a phase I study evaluating CC-90009 in relapsed or refractory AML is ongoing (CC-90009-AML-001; NCT02848001). Disclosures Jin: Trillium Therapeutics: Other: licensing agreement. Ng:Celgene: Research Funding. Wang:Pfizer AG Switzerland: Honoraria, Other: Travel and accommodation; Trilium therapeutics: Other: licensing agreement, Research Funding; NanoString: Other: Travel and accommodation; Pfizer International: Honoraria, Other: Travel and accommodation. Minden:Trillium Therapetuics: Other: licensing agreement. Fan:Celgene Corporation: Employment, Equity Ownership. Pierce:Celgene Corporation: Employment, Equity Ownership. Pourdehnad:Celgene Corporation: Employment, Equity Ownership.

Upregulated expression of eIF3C is associated with malignant behavior in renal cell carcinoma.

Eukaryotic initiation factor 3c (eIF3C) is involved in the initiation of protein translation. Aberrant eIF3C expression has been reported in different types of human cancer. The present study aimed to assess the role of eIF3C in the malignant behavior of renal cell carcinoma invitro and invivo. eIF3C expression was assessed in 16 pairs of renal cell carcinoma (RCC) and matched distant normal tissues, and in RCC cell lines using immunohistochemistry. Subsequently, eIF3C was depleted using lentiviral short hairpin RNA and cell proliferation, cell cycle distribution and apoptosis of these eIF3C‑depleted cells were examined. Additionally, tumor cell xenograft assays in nude mice, Affymetrix microarrays and ingenuity pathway analyses were performed. eIF3C expression was upregulated in RCC tissues and cell lines. Depletion of eIF3C reduced tumor cell proliferation and arrested them at the G1 stage, thus promoting their apoptosis invitro. Depletion of eIF3C also inhibited the formation and growth of tumor cell xenografts in nude mice. In addition, depletion of eIF3C altered the expression levels of 994 differentially expressed genes in RCC cells (516 genes were upregulated and 478genes were downregulated). The expression levels of phosphorylated‑AKT, c‑JUN and NFKB inhibitor α were lower in the shorth hairpin RNA eIF3C‑transfected RCC cells compared with in the control group. In conclusion, the present study demonstrated that upregulated eIF3C expression contributed to the development and progression of RCC. Future studies should further evaluate whether eIF3C could be used as a potential strategy for RCC targeting therapy.

Pharmacokinetics-pharmacodynamics of sertraline as an antifungal in HIV-infected Ugandans with cryptococcal meningitis.

The ASTRO-CM dose-finding pilot study investigated the role of adjunctive sertraline for the treatment of HIV-associated cryptococcal meningitis in HIV-infected Ugandan patients. The present study is a post hoc pharmacokinetic-pharmacodynamic analysis of the ASTRO-CM pilot study to provide insight into sertraline exposure-response-outcome relationships. We performed a population pharmacokinetic analysis using sertraline plasma concentration data and correlated various predicted PK-PD indices with the percentage change in log10 CFU/mL from baseline. Sertraline clearance was 1.95-fold higher in patients receiving antiretroviral (ART), resulting in 49% lower drug exposure. To quantify the clinical benefit of sertraline, we estimated rates of fungal clearance from cerebrospinal fluid (CSF) of ASTRO-CM patients using Poisson model and compared the clearance rates to a historical control study (COAT) in which patients received standard Cryptococcus therapy of amphotericin B (0.7-1.0mg/kg per day) and fluconazole (800mg/day) without sertraline. Adjunctive sertraline significantly increased CSF fungal clearance rate compared to COAT trial and sertraline effect was dose-independent with no covariate found to affect fungal clearance including ART. Study findings suggest sertraline response could be mediated by different mechanisms than directly inhibiting the initiation of protein translation as previously suggested; this is supported by the prediction of unbound sertraline concentrations is unlikely to reach MIC concentrations in the brain. Study findings also recommend against the use of higher doses of sertraline, especially those greater than the maximum FDA-approved daily dose (200mg/day), since they unlikely provide any additional benefits and come with greater costs and risk of adverse events.

Polyamines and Aging: A CLEAR Connection?

A decline in polyamine levels with age has been implicated in the pathophysiology of aging, and nutritional supplementation of spermidine can reduce age-related pathology and increase lifespan in a number of different organisms. In this issue of Molecular Cell, Zhang and colleagues provide a mechanistic link between polyamines, autophagy, and aging.

Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling

DEAD-box ATP-dependent helicases (DEAH/D) are a family of conserved genes predominantly involved in gene expression regulation and RNA processing. As its prototype, eIF4AI is an essential component of the protein translation initiation complex. Utilizing a screening system based on wild-type eIF4AI and its L243G mutant with a changed linker domain, we discovered an eIF4AI inhibitor, sanguinarine (SAN) and used it to study the catalytic mechanism of eIF4AI. Herein, we describe the crystal structure of the eIF4AI-inhibitor complex and demonstrate that the binding site displays certain specificity, which can provide the basis for drug design to target eIF4AI. We report that except for competitive inhibition SAN's possible mechanism of action involves interference with eIF4AI catalytic cycling process by hindering the formation of the closed conformation of eIF4AI. In addition, our results highlight a new targetable site on eIF4AI and confirm eIF4AI as a viable pharmacological target.

Translational downregulation of Twist1 expression by antiproliferative gene, B-cell translocation gene 2, in the triple negative breast cancer cells

Twist1, a key transcription factor regulating epithelial–mesenchymal transition and cancer metastasis, is highly expressed in invasive cancers in contrast to the loss of BTG2/TIS21 expression. Based on our observation that forced expression of BTG2/TIS21 downregulated Twist1 protein expression without altering mRNA level, we investigated molecular mechanisms of the BTG2/TIS21-inhibited Twist1 translation in the triple negative breast cancer (TNBC) cells and in vivo BTG2/TIS21-knockout (KO) mice and human breast cancer tissues. (1) C-terminal domain of Twist1 and Box B of BTG2/TIS21 interacted with each other, which abrogated Twist1 activity. (2) BTG2/TIS21 inhibited translational initiation by depleting eIF4E availability via inhibiting 4EBP1 phosphorylation. (3) Expression of BTG2/TIS21 maintained p-eIF2α that downregulates initiation of protein translation, confirmed by eIF2α-AA mutant expression and BTG2/TIS21 knockdown in MEF cells. (4) cDNA microarray analysis revealed significantly higher expression of initiation factors-eIF2A, eIF3A, and eIF4G2-in the BTG2/TIS21-KO mouse than that in the wild type. (5) BTG2/TIS21-inhibited translation initiation lead to the collapse of polysome formation and the huge peak of 80s monomer in the BTG2/TIS21 expresser, but not in the control. (6) mRNAs and protein expressions of elongation factors were also downregulated by BTG2/TIS21 expression in TNBC cells, but much higher in both TIS21-KO mice and lymph node-positive human breast cancers. (7) BTG2/TIS21-mediated Twist1 loss was not due to the protein degradation by ubiquitination and autophagy activation. (8) Twist1 protein level was significantly higher in various organs of TIS21-KO mice compared with that in the control, indicating the in vivo role of BTG2/TIS21 gene in the regulation of Twist1 protein level. Altogether, the present study support our hypothesis that BTG2/TIS21 is a promising target to combat with metastatic cancers with high level of Twist1 without BTG2/TIS21 expression.

Profiling RNA‐Associated Proteins for Vasopressin‐Mediated Translation in Kidney Collecting Duct Cells

Vasopressin‐mediated gene expression changes in the renal collecting duct has been intensively studied over the last decade. Prior studies were focused on transcriptional regulation as a mechanism of regulation of transport by vasopressin. However, post‐transcriptional regulation at the RNA level has not been studied. To identify vasopressin‐mediated RNA modulators, 1) a comprehensive list of RNA‐associated proteins was curated, and 2) vasopressin‐regulated genes from this list were identified using RNA‐seq in mouse mpkCCD cells exposed to vasopressin for various times.The curated database of RNA‐associated proteins was generated by mining information from multiple databases as follows. RNA processing‐related proteins were identified from Gene Ontology (GO) ‘Molecular Function’ and ‘Biological Process’, KEGG pathway, RNA modification database and Reactome. In addition, proteins that have RNA‐binding domains were identified from five different databases (RBPDB, ATtRACT, RBPmap, InterPro and UniProt). A total of 1369 proteins are listed in the current database of RNA‐associated proteins (https://hpcwebapps.cit.nih.gov/ESBL/Database/RNAprocessing_Proteins/). Among these proteins, 646 proteins have known RNA‐binding domain structures and 723 proteins were identified with annotated molecular functions related to RNA processing. 371 proteins were identified by both criteria.RNA‐seq was carried out in mpkCCD cells treated with the vasopressin analog dDAVP (10−10 M) for 3, 6 and 12 h. Relative transcript abundance was estimated using transcripts per million (TPM) and change of transcript abundance was presented as Log2 of the dDAVP:vehicle TPM ratio at each time point. Interestingly, we found that transcript abundance of genes coding for ribosomal proteins (60S ribosomal proteins and 40S ribosomal proteins) and translation initiation proteins (eukaryotic translation initiation factors) were extensively changed by dDAVP at all time points. These results indicate that vasopressin‐mediated gene expression includes changes mediated by abundance changes of translation‐associated proteins. Beyond this, the current study provides new resources for further study of RNA‐associated processes in the kidney.Support or Funding InformationThe work was supported by the Division of Intramural Research, National Heart, Lung, and Blood Institute projects ZIA‐HL001285 (to MAK) and ZIA‐HL006129 (to MAK).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Pulsed SILAC-based proteomic analysis unveils hypoxia- and serum starvation-induced de novo protein synthesis with PHD finger protein 14 (PHF14) as a hypoxia sensitive epigenetic regulator in cell cycle progression.

Hypoxia is an environmental cue that is associated with multiple tumorigenic processes such as immunosuppression, angiogenesis, cancer invasion, metastasis, drug resistance, and poor clinical outcomes. When facing hypoxic stress, cells initiate several adaptive responses such as cell cycle arrest to reduce excessive oxygen consumption and co-activation of oncogenic factors. In order to identify the critical novel proteins for hypoxia responses, we used pulsed-SILAC method to trace the active cellular translation events in A431 cells. Proteomic discovery data and biochemical assays showed that cancer cells selectively activate key glycolytic enzymes and novel ER-stress markers, while protein synthesis is severely suppressed. Interestingly, deprivation of oxygen affected the expression of various epigenetic regulators such as histone demethylases and NuRD (nucleosome remodeling and deacetylase) complex in A431 cells. In addition, we identified PHF14 (the plant homeodomain finger-14) as a novel hypoxia-sensitive epigenetic regulator that plays a key role in cell cycle progress and protein synthesis. Hypoxia-mediated inhibition of PHF14 was associated with increase of key cell cycle inhibitors, p14ARF, p15INK4b, and p16INK4a, which are responsible for G1-S phase transition and decrease of AKT-mTOR-4E-BP1/pS6K signaling pathway, a master regulator of protein synthesis, in response to environmental cues. Analysis of TCGA colon cancer (n=461) and skin cancer (n=470) datasets revealed a positive correlation between PHF14 expression and protein translation initiation factors, eIF4E, eIF4B, and RPS6. Significance of PHF14 gene was further demonstrated by in vivo mouse xenograft model using PHF14 KD cell lines.

Hepatic IFN-Induced Protein with Tetratricopeptide Repeats Regulation of HCV Infection.

Interferons (IFNs) suppress viral infection through the induction of >400 interferon-stimulated genes (ISGs). Among ISGs, IFN-induced protein with tetratricopeptide repeats (IFITs) is one of the most potent and well-characterized ISGs. IFIT family consists of 4 cluster genes. It has been suggested that the antiviral action of each IFIT employs distinct mechanisms. In addition, it has been shown that each IFIT exhibits its antiviral properties partially in a pathogen-specific manner. To date, the expression profile of IFITs in the liver, as well as the antiviral potency of the individual IFITs in the regulation of hepatitis C virus (HCV) infection, is not yet fully defined. Our previous study found that the expression of hepatic IFITs is well correlated with the outcome of IFN-based antiviral therapy. This study explored the significance of each IFIT in the suppression of HCV. Our in vitro and in vivo studies with humanized liver chimeric mouse system revealed that IFIT1, 2, and 3/4 play an important role in the suppression of HCV. In addition, our in vitro experiment found that all IFITs possess a comparable anti-HCV potency. Follow-up studies collectively indicated that IFITs suppress HCV likely through 2 distinct mechanisms: (1) inhibition of internal ribosome entry site-dependent viral protein translation initiation complex according to experiments with bicistronic reporter assay as well as confocal microscopic analyses and (2) sequestration of viral genome based on an experiment using replication defective viral genome. In conclusion, our study defined the importance of IFITs in the regulation of HCV and also suggested the multifaceted antiviral actions.

Biosensor-guided improvements in salicylate production by recombinant Escherichia coli

BackgroundSalicylate can be biosynthesized from the common metabolic intermediate shikimate and has found applications in pharmaceuticals and in the bioplastics industry. While much metabolic engineering work focused on the shikimate pathway has led to the biosynthesis of a variety of aromatic compounds, little is known about how the relative expression levels of pathway components influence salicylate biosynthesis. Furthermore, some host strain gene deletions that improve salicylate production may be impossible to predict. Here, a salicylate-responsive transcription factor was used to optimize the expression levels of shikimate/salicylate pathway genes in recombinant E. coli, and to screen a chromosomal transposon insertion library for improved salicylate production.ResultsA high-throughput colony screen was first developed based on a previously designed salicylate-responsive variant of the E. coli AraC regulatory protein (“AraC-SA”). Next, a combinatorial library was constructed comprising a series of ribosome binding site sequences corresponding to a range of predicted protein translation initiation rates, for each of six pathway genes (> 38,000 strain candidates). Screening for improved salicylate production allowed for the rapid identification of optimal gene expression patterns, conferring up to 123% improved production of salicylate in shake-flask culture. Finally, transposon mutagenesis and screening revealed that deletion of rnd (encoding RNase D) from the host chromosome further improved salicylate production by 27%.ConclusionsThese results demonstrate the effectiveness of the salicylate sensor-based screening platform to rapidly identify beneficial gene expression patterns and gene knockout targets for improving production. Such customized high-throughput tools complement other cell factory engineering strategies. This approach can be generalized for the production of other shikimate-derived compounds.

HnRNP K: A Regulator of Global Transcription and Translation That Drives Lymphomagenesis

hnRNP K is an RNA binding protein that controls a multitude of cellular processes and is aberrantly expressed in cancers. We have previously shown that hnRNP K functions as a haploinsufficient tumor suppressor in AML patients with 9q deletions. However, overexpression of hnRNP K is the more commonly observed clinical phenomenon. We have recently discovered that hnRNP K overexpression in patients with diffuse large B-cell lymphoma correlates with dismal outcomes and directly resulted in the development of lymphomas in transgenic mice.To understand the mechanistic basis for the oncogenicity of hnRNP K overexpression and to identify therapeutic vulnerabilities, we performed RNA-sequencing, RNA immunoprecipitation following by sequencing (RIP-Seq), mass spectrometry, and polysome assays. We observed that hnRNP K regulates both global transcription and translational processes within the cell via modulation of 7SK and translation initiation proteins (such as the eIFs and PABP), respectively. Consequently, we hypothesized that aberrant hnRNP K expression primarily perturbs oncogenes with short half-lives. Mechanistically, we identified that hnRNP K binds to the RNA and regulates the expression of a plethora of critical oncogenes and tumor suppressors involved in hematologic malignancies such as c-Myc, RUNX1, and Cyclin D1. As proof of concept for clinical applications, we have demonstrated that hnRNP K-driven c-Myc overexpression renders tumors susceptible to bromodomain inhibition.Given that hnRNP K directs global transcription and translation, it is likely that hnRNP K overexpressing tumors will also be sensitive to transcriptional and translational inhibitors such as CDK9 inhibitors and omacetaxine mepesuccinate, respectively. However, since hnRNP K also regulates a plethora of additional cellular processes that extend far beyond mRNA and protein synthesis, there is a need to develop hnRNP K-specific inhibitors that will only target these activities. Thus, we have recently begun to identify small molecule compounds that can directly inhibit hnRNP K-RNA binding function on specific targets using an in vitro fluorescent binding assay. Using this assay, we are currently screening a library of 70,000 small molecule compounds to identify agents that can prevent hnRNP K-RNA interactions.In summary, we have established that hnRNP K is a bona fide oncogene that drives lymphomagenesis. Global analyses have revealed therapeutic vulnerabilities of hnRNP K overexpressing tumors. Furthermore, using our in vitro RNA binding assays, we anticipate identification of novel hnRNP K-specific inhibitors. DisclosuresNo relevant conflicts of interest to declare.

Targeting Oncoprotein Translation with Rocaglates in MYC-Driven Lymphoma

Background: c-MYC (MYC) is commonly dysregulated in aggressive B cell lymphomas. MYC associated lymphoma, especially Double Hit lymphoma (DHL) and Double-Expression Lymphoma (DEL) which are characterized by MYC and BCL2 dual overexpression usually present with the inferior outcome as rapid disease progression and poor response to standard chemotherapy regimen. Nevertheless, MYC is considered as an “undruggable” target and targeting strategies such as suppressing MYC transcription by bromodomain (BRD)-4 inhibitors have been widely investigated in both preclinical models and clinical trials. However, increasing evidence has shown that lymphoma cells displayed a wide range of resistance to BRD-4 inhibition, due to transcription adaptation or kinome reprogramming. Hence, alternative approaches for suppressing MYC or its function are urgently needed. Strategies directed against oncoprotein translation may efficiently repress key oncoproteins regardless of the abundant MYC mRNA due to genetic aberrations and secondary transcription up-regulated by MYC. Rocaglate is a class of natural products derived from plants of the Aglaia genus that have been demonstrated to potently inhibit protein translation initiation via eIF4A. The use of rocaglates for anti-cancer treatment was limited due to the scarcity and instability of these natural products e.g. Silvestrol. Recent chemical modification and screening studies have unveiled a few synthetic rocaglates that are more potent than Silvestrol such as SDS-1-021-(−), which unlocked the potential use of rocaglates for clinical applications.Methods and Results: To probe effective reagents for MYC-driven lymphoma, a screening of 50 drugs targeting common oncogenic pathways and tumorigenic machinery was performed in two isogenic B-lymphoma lines. Several protein translation inhibitors, such as mTOR kinase inhibitors (TORKi), and eIF4A inhibitor Silvestrol were identified as the most potent drugs in all of the tested cells. Further, we found that Silvestrol but not TORKi efficiently repressed MYC protein translation in MYC-driven B lymphoma cells, whereas neither of them inhibited BCL2 expression. Moreover, we demonstrated that eIF4E knockdown or eIF4E/eIF4G disruptor Briciclib did not significantly affect MYC expression, whereas eIF4A inhibitor hippuristanol and rocaglates derivate SDS-1-021-(−) diminished MYC expression similar to that observed in Silvestrol treated cells. By using dual luciferase assay, we demonstrated that rocaglates had stronger cap-dependent and IRES translation inhibition than TORKi in lymphoma cells. Next, by native RNA immunoprecipitation and siRNA knocking down, we found that rocaglates repressed MYC translation not only via eIF4A1 but also via eIF4A2, however, with different underlying mechanisms. Furthermore, to explore the molecular targets of rocaglates treatment in B cell lymphoma, we performed TMT-Mass Spectrometry which identified multiple oncoproteins including NEK2, MYC, MCL1, TCF3, BCL6, PLK1, AURKA, and WEE1 were significantly down-regulated by SDS-1-021-(−) treatment. Finally, we demonstrated that SDS-1-021-(−) is highly potent as a single agent and synergized with ABT199 at a low dose (0.2mg/kg) in PDX models with DHL/DEL.Brief summary: Our pre-clinical study provided strong evidence that rocaglates but not TORKi efficiently suppress MYC protein translation because 1). Rocaglates exhibit strong inhibition on both Cap- and IRES-dependent translation, 2). Rocaglates decrease PLK1 and AURKA/B thus destabilizing MYC protein. The synthetic rocaglate SDS-1-021-(−) is a potent agent that exhibits significant synergistic killing effect with ABT199 on DHL/DEL cells in the pre-clinical animal study. [Display omitted] DisclosuresLunning:TG Therapeutics: Consultancy; AbbVie: Consultancy; Genentech: Consultancy; Astra-Zeneca: Consultancy; Genzyme: Consultancy; Celgene: Consultancy; Bayer: Consultancy; Gilead: Consultancy; Spectrum: Consultancy; Genentech: Consultancy; Seattle Genetics: Consultancy; Portola: Consultancy; Kite: Consultancy; Juno: Consultancy; Janssen: Consultancy; Verastem: Consultancy. Vose:Novartis: Honoraria, Research Funding; Epizyme: Honoraria; Incyte Corp.: Research Funding; Bristol Myers Squibb: Research Funding; Kite Pharma: Research Funding; Merck Sharp & Dohme Corp.: Research Funding; Abbvie: Honoraria; Legend Pharmaceuticals: Honoraria; Seattle Genetics, Inc.: Research Funding; Acerta Pharma: Research Funding; Celgene: Research Funding; Roche: Honoraria.