Translational Profiling Research Articles

„Przyjaciele polskich książek” i „słudzy doskonałości”

“FRIENDS OF POLISH BOOKS” AND “SERVANTS OF EXCELLENCE”: TRANSLATORS’ PROFILES IN THE MONTHLY POLAND (1970-1981)
 The paper deals with the image of translators in the monthly Poland in the years 1970-1981. Forty articles are analysed with the intention of testing the hypothesis that the promotion of the profiles of translators in the journal was part of a broader campaign launched by the authorities of the Polish People’s Republic to promote the country abroad. The publications in which translators were called “friends of Polish books” and “servants of excellence” were to build a positive image of Poland as a country with an exemplary foreign cultural policy in which translation played an important role. The question to what extent the image-oriented efforts of translators convinced readers about the cultural policy of the Polish People’s Republic remains open.

Variance in translational fidelity of different bacterial species is affected by pseudouridines in the tRNA anticodon stem-loop

ABSTRACT Delicate variances in the translational machinery affect how efficiently different organisms approach protein synthesis. Determining the scale of this effect, however, requires knowledge on the differences of mistranslation levels. Here, we used a dual-luciferase reporter assay cloned into a broad host range plasmid to reveal the translational fidelity profiles of Pseudomonas putida, Pseudomonas aeruginosa and Escherichia coli. We observed that these profiles are surprisingly different, whereas species more prone to translational frameshifting are not necessarily more prone to stop codon readthrough. As tRNA modifications are among the factors that have been implicated to affect translation accuracy, we also show that translational fidelity is context-specifically influenced by pseudouridines in the anticodon stem-loop of tRNA, but the effect is not uniform between species.

A high-resolution map of human RNA translation

Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.

Kinematics and shear-induced alignment in confined granular flows of elongated particles

The kinematics and the shear-induced alignment of elongated particles in confined, heterogeneous flow conditions are investigated experimentally. Experiments are conducted in an annular shear cell with a rotating bottom wall and a top wall permitting confinement of the flow. Flow kinematics and particle orientation statistics are computed by particle tracking using optical imaging. Translational velocity profiles show an exponential decay, and surprisingly, only the slip velocity at the bottom is influenced by the particle shape. Rotations are highly frustrated by particle shape, more elongated particles showing, on average, a lower angular velocity. In addition, a clear shear-rate dependency of the proneness of a particle to rotate is observed, with a stronger inhibition in low shear zones. The average orientation of the particles does not correspond to the main flow direction, they are slightly tilted downwards. The corresponding angle decreases with the particles’ elongation. Orientational order was observed to increase with particles’ elongation, and surprisingly was not affected by the applied confinement. A weak but systematic decrease of the orientational order was observed in regions of higher shear rate. At the particle-scale, angular velocity fluctuations show a strong correlation with local particle orientation, particles being strongly misaligned with the preferential particles’ orientation rotating faster. This correlation becomes stronger for more elongated particles, while is almost unaffected by the applied confinement.

Alison G. Salvesen and Timothy Michael Law, eds. The Oxford Handbook of the Septuagint

Alison G. Salvesen and Timothy Michael Law, eds. <i>The Oxford Handbook of the Septuagint</i>

Estrogen distinctly regulates transcription and translation of lncRNAs and pseudogenes in breast cancer cells

Estrogen drives key transcriptional changes in breast cancer and stimulates breast cancer cells' growth with multiple mechanisms to coordinate transcription and translation. In addition to protein-coding transcripts, estrogen can regulate long non-coding RNA (lncRNA) transcripts, plus diverse non-coding RNAs including antisense, enhancer, and intergenic. LncRNA genes comprise the majority of human genes. The accidental, or regulated, translation of their short open reading frames by ribosomes remains a controversial topic. Here we report for the first time an integrated analysis of RNA abundance and ribosome occupancy level, using Ribo-seq combined with RNA-Seq, in the estrogen-responsive, estrogen receptor α positive, human breast cancer cell model MCF7, before and after hormone treatment. Translational profiling can determine, in an unbiased manner, which fraction of the genome is actually translated into proteins, as well as resolving whether transcription and translation respond concurrently, or differentially, to estrogen treatment. Our data showed specific transcripts more robustly detected in RNA-Seq than in the ribosome-profiling data, and vice versa, suggesting distinct gene-specific estrogen responses at the transcriptional and the translational level, respectively. Here, we showed that estrogen stimulation affects the expression levels of numerous lncRNAs, but not their association with ribosomes, and that most lncRNAs are not ribosome-bound. For the first time, we also demonstrated the transcriptional and translational response of expressed pseudogenes to estrogen, pointing to new perspectives for drug-target development in breast cancer in the future.

Molecular and Cellular Adaptations in Hippocampal Parvalbumin Neurons Mediate Behavioral Responses to Chronic Social Stress.

Parvalbumin-expressing interneurons (PV neurons) maintain inhibitory control of local circuits implicated in behavioral responses to environmental stressors. However, the roles of molecular and cellular adaptations in PV neurons in stress susceptibility or resilience have not been clearly established. Here, we show behavioral outcomes of chronic social defeat stress (CSDS) are mediated by differential neuronal activity and gene expression in hippocampal PV neurons in mice. Using in vivo electrophysiology and chemogenetics, we find increased PV neuronal activity in the ventral dentate gyrus is required and sufficient for behavioral susceptibility to CSDS. PV neuron-selective translational profiling indicates mitochondrial oxidative phosphorylation is the most significantly altered pathway in stress-susceptible versus resilient mice. Among differentially expressed genes associated with stress-susceptibility and resilience, we find Ahnak, an endogenous regulator of L-type calcium channels which are implicated in the regulation of mitochondrial function and gene expression. Notably, Ahnak deletion in PV neurons impedes behavioral susceptibility to CSDS. Altogether, these findings indicate behavioral effects of chronic stress can be controlled by selective modulation of PV neuronal activity or a regulator of L-type calcium signaling in PV neurons.

Initiation and elongation factor co-expression correlates with recurrence and survival in epithelial ovarian cancer

High grade epithelial ovarian cancer (EOC) represents a diagnostic and therapeutic challenge due to its aggressive features and short recurrence free survival (RFS) after primary treatment. Novel targets to inform our understanding of the EOC carcinogenesis in the translational machinery can provide us with independent prognostic markers and provide drugable targets. We have identified candidate eukaryotic initiation factors (eIF) and eukaryotic elongation factors (eEF) in the translational machinery for differential expression in EOC through in-silico analysis. We present the analysis of 150 ovarian tissue microarray (TMA) samples on the expression of the translational markers eIF2α, eIF2G, eIF5 (eIF5A and eIF5B), eIF6 and eEF1A1. All translational markers were differentially expressed among non-neoplastic ovarian samples and tumour samples (borderline tumours and EOC). In EOC, expression of eIF5A was found to be significantly correlated with recurrence free survival (RFS) and expression of eIF2G and eEF1A1 with overall survival (OS). Expression correlation among factor subunits showed that the correlation of eEF1A1, eIF2G, EIF2α and eIF5A were significantly interconnected. eIF5A was also correlated with eIF5B and eIF6. Our study demonstrates that EOCs have different translational profile compared to benign ovarian tissue and that eIF5A is a central dysregulated factor of the translation machinery.

Abstract 5441: Discovery of a novel RAD51 inhibitor SCR-6992 targeting homologous recombination pathways in cancer

Abstract Targeting DNA damage response (DDR) pathways has been proposed as an approach for amplifying tumor-specific replicative lesions. RAD51 plays a central role in the DDR pathway, and thus represents a promising anti-tumor target. We here report the discovery of a series of next generation RAD51 inhibitors that can prevent RAD51 foci formation and particularly, a pre-clinical candidate molecule SCR-6992 with potent anti-tumor efficacies and desirable pre-clinical development drug properties. SCR-6992 exhibits remarkable anti-proliferative potency in human lymphoma Daudi cells in vitro (IC50 = 12 nM) while has no inhibitory effect in normal human cells. The combination of SCR-6992 with chemotherapeutic agents or DDR-targeting drugs produces synergistical anti-cancer response in lymphoma and solid tumor cell lines. Furthermore, SCR-6992 significantly inhibits tumor growth in Daudi xenograft tumor model with the tumor regression observed when dosed orally at 80 mg/kg/day. SCR-6992 also shows acceptable translational drug properties and pharmacokinetic profiles in both rodents and dogs. SCR-6992 was well tolerated in rats and dogs in 14-day dose range finding studies without noted hematological or gastrointestinal toxicities, when dosed up to 200 mg/kg and 40 mg/kg, respectively. Taken together, SCR-6992 demonstrates as an effective RAD51 inhibitor with encouraging anti-tumor activities and favorable development drug properties. The clinical development plans of SCR-6992 have been formulated for hematologic malignancies and solid tumors. Citation Format: Peng Gu, Liting Xue, Ping Chen, Wenjing Li, Ya Geng, Feng Zhou, Guimei Yang, Xiaohong Hou, Chunyan Zhao, Wenqing Yang, Renhong Tang. Discovery of a novel RAD51 inhibitor SCR-6992 targeting homologous recombination pathways in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5441.

MiR-223 Exerts Translational Control of Proatherogenic Genes in Macrophages.

Background:A significant burden of atherosclerotic disease is driven by inflammation. Recently, microRNAs (miRNAs) have emerged as important factors driving and protecting from atherosclerosis. miR-223 regulates cholesterol metabolism and inflammation via targeting both cholesterol biosynthesis pathway and NFkB signaling pathways; however, its role in atherosclerosis has not been investigated. We hypothesize that miR-223 globally regulates core inflammatory pathways in macrophages in response to inflammatory and atherogenic stimuli thus limiting the progression of atherosclerosis.Methods and Results:Loss of miR-223 in macrophages decreases Abca1 gene and protein expression as well as cholesterol efflux to apoA1 (Apolipoprotein A1) and enhances proinflammatory gene expression. In contrast, overexpression of miR-223 promotes the efflux of cholesterol and macrophage polarization toward an anti-inflammatory phenotype. These beneficial effects of miR-223 are dependent on its target gene, the transcription factor Sp3. Consistent with the antiatherogenic effects of miR-223 in vitro, mice receiving miR223−/− bone marrow exhibit increased plaque size, lipid content, and circulating inflammatory cytokines (ie, IL-1β). Deficiency of miR-223 in bone marrow–derived cells also results in an increase in circulating pro-atherogenic cells (total monocytes and neutrophils) compared with control mice. Furthermore, the expression of miR-223 target gene (Sp3) and pro-inflammatory marker (Il-6) are enhanced whereas the expression of Abca1 and anti-inflammatory marker (Retnla) are reduced in aortic arches from mice lacking miR-223 in bone marrow–derived cells. In mice fed a high-cholesterol diet and in humans with unstable carotid atherosclerosis, the expression of miR-223 is increased. To further understand the molecular mechanisms underlying the effect of miR-223 on atherosclerosis in vivo, we characterized global RNA translation profile of macrophages isolated from mice receiving wild-type or miR223−/− bone marrow. Using ribosome profiling, we reveal a notable upregulation of inflammatory signaling and lipid metabolism at the translation level but less significant at the transcription level. Analysis of upregulated genes at the translation level reveal an enrichment of miR-223-binding sites, confirming that miR-223 exerts significant changes in target genes in atherogenic macrophages via altering their translation.Conclusions:Our study demonstrates that miR-223 can protect against atherosclerosis by acting as a global regulator of RNA translation of cholesterol efflux and inflammation pathways.

Translation and rotation of particles in different flow pattern areas of a silo

The present paper reports the results obtained for translational and rotational velocity profiles of spherical particles for the mixed flow in a conical silo. The discrete element method (DEM) based on Hertz-Mindlin (no slip) with RVD rolling friction contact model is used for simulations. Opposite correlations are found between translational and rotational velocities in different flow areas of the silo. In particular, the abrasion caused by rotation is dominant in the funnel flow area. In addition, increase of the mass flow rate of silo can effectively reduce the abrasion induced by rotation. This highlights that understanding of dynamic characteristics of particles is helpful for optimization of silos and reduction of granular material abrasion.

High-throughput translational profiling with riboPLATE-seq

Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages anti-rRNA ribosome immunoprecipitation on whole polysomes to measure ribosome association (RA). We compare RA to its analogue in ribosome profiling and RNA sequencing, translation efficiency, and demonstrate both the performance of riboPLATE-seq and its utility in detecting translational alterations induced by specific inhibitors of protein kinases.

Dynamics of Methyl Radical Formation Following 266 nm Dissociative Photoionization of Xylenes and Mesitylene.

The 266 nm dissociative photoionization of three xylene isomers and mesitylene leading to the formation of methyl radical was examined. The total translational energy distribution profiles [P(ET)] for the methyl radical were almost identical for all of the three isomers of xylene and mesitylene, while a substantial difference was observed for the corresponding P(ET) profile of the co-fragment produced by loss of one methyl group in m-xylene. This observation is attributed to the formation of the methyl radical from alternate channels induced by the probe. The P(ET) profiles were rationalized based on the dissociation of {sp2}C-C{sp3} bond in the cationic state, wherein the {sp2}C-C{sp3} bond dissociation energy is substantially lower relative to the neutral ground state. The dissociation in the cationic state follows a resonant three-photon absorption process, resulting in a maximum translational energy of about 1.6-1.8 eV for the photofragments in the center-of-mass frame. Fitting of the P(ET) profiles to empirical function reveals that the dynamics of {sp2}C-C{sp3} bond dissociation is insensitive to the position of substitution but marginally dependent on the number of methyl groups.

Master Training of Translation Specialists in the Context of the Postmodern Educational Paradigm

The article deals with the problems of inconsistency of Ukrainian translation education with the trends of the postmodern state of society and the advisability of introducing the achievements of the American system of training translators is substantiated. The article describes the organization of training masters in technical translation in the United States on the basis of a systematic analysis, in particular, the structure and content, forms and methods of teaching and learning masters in technical translation. Postmodern tendencies and peculiarities of master's education in the USA are revealed and substantiated. The principles of permanent improvement of translation competence, profile and general cultural orientation are described; ensuring the full formation of the readiness of graduates of master's programs in technical translation for highly qualified, productive and creative professional activities; learning in a multicultural environment; application of the latest means of automated translation during training; certification of technical translators. For the reform of translation education in Ukraine, these trends are identified as key. The results of the study were obtained by applying a comparative typological and systems analysis, the method of extrapolating educational trends in the United States and Ukraine in relation to the postmodern context of society and its practical requirements for translation education. The practical significance of the article lies in borrowing the American experience of postmodern aspects of translation education, which can be useful to the countries of the former socialist camp and post-Soviet society.

Aberrant translation regulated by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives head and neck squamous cell carcinoma progression.

BackgroundCancer cells selectively promote the translation of oncogenic transcripts to stimulate cancer progression. Although growing evidence has revealed that tRNA modifications and related genes participate in this process, their roles in head and neck squamous cell carcinoma (HNSCC) remain largely uncharacterized. Here, we sought to investigate the function and mechanisms of the transfer RNA (tRNA) N7‐methylguanosine (m7G) modification in regulating the occurrence and development of HNSCC.MethodsCell lost‐of‐function and gain‐of‐function assays, xenograft models, conditional knockout and knockin mouse models were used to study the physiological functions of tRNA m7G modification in HNSCC tumorigenesis. tRNA modification and expression profiling, mRNA translation profiling and rescue assays were performed to uncover the underlying molecular mechanisms. Single‐cell RNA sequencing (scRNA‐seq) was conducted to explore the tumor microenvironment changes.ResultsThe tRNA m7G methyltransferase complex components Methyltransferase‐like 1 (METTL1)/WD repeat domain 4 (WDR4) were upregulated in HNSCC and associated with a poor prognosis. Functionally, METTL1/WDR4 promoted HNSCC progression and metastasis in cell‐based and transgenic mouse models. Mechanistically, ablation of METTL1 reduced the m7G levels of 16 tRNAs, inhibiting the translation of a subset of oncogenic transcripts, including genes related to the phosphatidylinositol‐3‐kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway. In addition, chemical modulators of the PI3K/Akt/mTOR signaling pathway reversed the effects of Mettl1 in mouse HNSCC. Furthermore, scRNA‐seq results revealed that Mettl1 knockout in mouse tumor cells altered the immune landscape and cell‐cell interaction between the tumor and stromal compartment.ConclusionsThe tRNA m7G methyltransferase METTL1 was found to promote the development and malignancy of HNSCC through regulating global mRNA translation, including the PI3K/AKT/mTOR signaling pathway, and found to alter immune landscape. METTL1 could be a promising treatment target for HNSCC patients.

Glial activation in prion diseases is selectively triggered by neuronal PrPSc.

Although prion infections cause cognitive impairment and neuronal death, transcriptional and translational profiling shows progressive derangement within glia but surprisingly little changes within neurons. Here we expressed PrPC selectively in neurons and astrocytes of mice. After prion infection, both astrocyte and neuron‐restricted PrPC expression led to copious brain accumulation of PrPSc. As expected, neuron‐restricted expression was associated with typical prion disease. However, mice with astrocyte‐restricted PrPC expression experienced a normal life span, did not develop clinical disease, and did not show astro‐ or microgliosis. Besides confirming that PrPSc is innocuous to PrPC‐deficient neurons, these results show that astrocyte‐born PrPSc does not activate the extreme neuroinflammation that accompanies the onset of prion disease and precedes any molecular changes of neurons. This points to a nonautonomous mechanism by which prion‐infected neurons instruct astrocytes and microglia to acquire a specific cellular state that, in turn, drives neural dysfunction.

Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions.

Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum's response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.

Erratum: Megat et al., "Differences between Dorsal Root and Trigeminal Ganglion Nociceptors in Mice Revealed by Translational Profiling".

In the article, “Differences between Dorsal Root and Trigeminal Ganglion Nociceptors in Mice Revealed by Translational Profiling,” by Salim Megat, Pradipta R. Ray, Diana Tavares-Ferreira, Jamie K. Moy, Ishwarya Sankaranarayanan, Andi Wanghzou, Tzu Fang Lou, Paulino Barragan-Iglesias, Zachary T.

Transcriptional regulation of neural stem cell expansion in the adult hippocampus.

Experience governs neurogenesis from radial-glial neural stem cells (RGLs) in the adult hippocampus to support memory. Transcription factors (TFs) in RGLs integrate physiological signals to dictate self-renewal division mode. Whereas asymmetric RGL divisions drive neurogenesis during favorable conditions, symmetric divisions prevent premature neurogenesis while amplifying RGLs to anticipate future neurogenic demands. The identities of TFs regulating RGL symmetric self-renewal, unlike those that regulate RGL asymmetric self-renewal, are not known. Here, we show in mice that the TF Kruppel-like factor 9 (Klf9) is elevated in quiescent RGLs and inducible, deletion of Klf9 promotes RGL activation state. Clonal analysis and longitudinal intravital two-photon imaging directly demonstrate that Klf9 functions as a brake on RGL symmetric self-renewal. In vivo translational profiling of RGLs lacking Klf9 generated a molecular blueprint for RGL symmetric self-renewal that was characterized by upregulation of genetic programs underlying Notch and mitogen signaling, cell cycle, fatty acid oxidation, and lipogenesis. Together, these observations identify Klf9 as a transcriptional regulator of neural stem cell expansion in the adult hippocampus.

Au Family Short Retroposons Contribute to Transcriptional and Phenotypic Diversity in Tomato (Solanaceae)

Here we report the current gene impact of the Au family of SINEs in tomato. The genome of Solanum lycopersicum ‘Heinz 1706’ SL3.0 -NCBI annotation release 103- was reference searched and the Au profile was characterized in-depth. Tomato genome comprises ca. 670 Au copies, of entire length-18.5%- or truncated, randomly inserted and eroded, forming three well supported (>80%) super clusters which disperse along the 12 chromosomes mirroring the subtelomeric gene distribution bias of the species. In tomato, the Au clade is largely localized at protein coding genes-69.5% introns, 7.8% 3UTRs, 2.1% 5UTRs, 1.2% CDSs- followed by genomic copies-18.3%-, long non coding RNA genes-1.4%- and pseudogenes-0.8%-. The 419 tomato genes harboring intronic Au are diverse, weakly associated considering biological processes and molecular functions, but include important traits such as stress response, hormone response or phenotype plasticity. Au was found to be transcribed inside circular RNAs derived from 12 genic loci. Exonic Au affect the transcriptional and/or translational profiles of 67 tomato genes, including biological/agronomical important ones, contributing to UTR length and composition, UTR transcript variants, CDS boundary definitions, protein domains and variants. We propose that biased survival of Au in tomato genes is an adaptive feature.