Protein Translation Rates Research Articles

Endoplasmic Reticulum Stress Delays Choroid Development in the HCAR1 Knockout Mouse

The subretina, composed of the choroid and the retinal pigment epithelium (RPE), bears a critical role in proper vision. In addition to phagocytosis of photoreceptor debris, the RPE shuttles oxygen and nutrients to the neuroretina. For their own energy production, RPE cells mainly rely on lactate, a major by-product of glycolysis. Lactate, in turn, is believed to convey most of its biological effects via the hydroxycarboxylic acid receptor 1 (HCAR1). Here, the lactate-specific receptor, HCAR1, is found to be exclusively expressed in the RPE cells within the subretina, and Hcar1-/- mice exhibit a substantially thinner choroidal vasculature during development. Notably, the angiogenic properties of lactate on the choroid are impacted by the absence of Hcar1. HCAR1-deficient mice exhibit elevated endoplasmic reticulum stress along with eukaryotic initiation factor 2α phosphorylation, a significant decrease in the global protein translation rate, and a lower proliferation rate of choroidal vasculature. Strikingly, inhibition of the integrated stress response using an inhibitor that reverses the effect of eukaryotic initiation factor 2α phosphorylation restores protein translation and rescues choroidal thinning. These results provide evidence that lactate signalling via HCAR1 is important for choroidal development/angiogenesis and highlight the importance of this receptor in establishing mature vision.

Mutational analyses of mitochondrial ATP6 gene reveal a possible association with abnormal levels of lactic acid and ammonia in Bangladeshi children with autism spectrum disorder: A case-control study

Autism spectrum disorder (ASD) is a multifactorial and highly heterogeneous neurodevelopmental disorder. Mitochondrial dysfunction, caused by the genetic variations in the electron transport chain (ETC) complexes and marked by higher lactic acid and ammonia levels, can play a crucial role in the development of autism. This study focused on identifying genetic variants in the mitochondrial ATP6 gene of children with ASD and their association with autism disease outcome, disease severity, lactic acid and ammonia levels. Ninety children were recruited of which 53 were with autism and the remaining 37 were healthy controls. The ATP6 gene was amplified by PCR, purified, and sequenced by Sanger sequencing. In total forty-two genetic variants were identified within the gene. Among them 8886G > A and 8911 T > C were found to be associated with higher lactic acid levels and 8748C > T, 8886G > A, and 8964C > T were associated with higher ammonia levels after the adjustment with age, gender, and disease response. Additionally, all the synonymous variants were found to alter the relative synonymous codon usage (RSCU) values, potentially affecting the protein's structure and translation rate. Although there was no significant association between any ATP6 variants and disease outcomes, the variants associated with mitochondrial dysfunction as reflected by abnormal levels of lactic acid and ammonia may provide an improved understanding of the pathophysiology of ASD. Therefore they need to be explored further along with other components of the electron transport complex.

TRNA m1A modification regulate HSC maintenance and self-renewal via mTORC1 signaling

Haematopoietic stem cells (HSCs) possess unique physiological adaptations to sustain blood cell production and cope with stress responses throughout life. To maintain these adaptations, HSCs rely on maintaining a tightly controlled protein translation rate. However, the mechanism of how HSCs regulate protein translation remains to be fully elucidated. In this study, we investigate the role of transfer RNA (tRNA) m1A58 ‘writer’ proteins TRMT6 and TRMT61A in regulating HSCs function. Trmt6 deletion promoted HSC proliferation through aberrant activation of mTORC1 signaling. TRMT6-deficient HSCs exhibited an impaired self-renewal ability in competitive transplantation assay. Mechanistically, single cell RNA-seq analysis reveals that the mTORC1 signaling pathway is highly upregulated in HSC-enriched cell populations after Trmt6 deletion. m1A-tRNA-seq and Western blot analysis suggest that TRMT6 promotes methylation modification of specific tRNA and expression of TSC1, fine-tuning mTORC1 signaling levels. Furthermore, Pharmacological inhibition of the mTORC1 pathway rescued functional defect in TRMT6-deficient HSCs. To our knowledge, this study is the first to elucidate a mechanism by which TRMT6-TRMT61A complex-mediated tRNA-m1A58 modification regulates HSC homeostasis.

Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.

Model-guided DNA sequence design can accelerate the reprogramming of living cells. It allows us to engineer more complex biological systems by removing the need to physically assemble and test each potential design. While mechanistic models of gene expression have seen some success in supporting this goal, data-centric, deep learning-based approaches often provide more accurate predictions. This accuracy, however, comes at a cost - a lack of generalization across genetic and experimental contexts that has limited their wider use outside the context in which they were trained. Here, we address this issue by demonstrating how a simple transfer learning procedure can effectively tune a pre-trained deep learning model to predict protein translation rate from 5' untranslated region (5'UTR) sequence for diverse contexts in Escherichia coli using a small number of new measurements. This allows for important model features learnt from expensive massively parallel reporter assays to be easily transferred to new settings. By releasing our trained deep learning model and complementary calibration procedure, this study acts as a starting point for continually refined model-based sequence design that builds on previous knowledge and future experimental efforts.

The long noncoding RNA CARDINAL attenuates cardiac hypertrophy by modulating protein translation.

One of the features of pathological cardiac hypertrophy is enhanced translation and protein synthesis. Translational inhibition has been shown to be an effective means of treating cardiac hypertrophy, although system-wide side effects are common. Regulators of translation, such as cardiac-specific long noncoding RNAs (lncRNAs), could provide new, more targeted therapeutic approaches to inhibit cardiac hypertrophy. Therefore, we generated mice lacking a previously identified lncRNA named CARDINAL to examine its cardiac function. We demonstrate that CARDINAL is a cardiac-specific, ribosome-associated lncRNA and show that its expression was induced in the heart upon pathological cardiac hypertrophy and that its deletion in mice exacerbated stress-induced cardiac hypertrophy and augmented protein translation. In contrast, overexpression of CARDINAL attenuated cardiac hypertrophy in vivo and in vitro and suppressed hypertrophy-induced protein translation. Mechanistically, CARDINAL interacted with developmentally regulated GTP-binding protein 1 (DRG1) and blocked its interaction with DRG family regulatory protein 1 (DFRP1); as a result, DRG1 was downregulated, thereby modulating the rate of protein translation in the heart in response to stress. This study provides evidence for the therapeutic potential of targeting cardiac-specific lncRNAs to suppress disease-induced translational changes and to treat cardiac hypertrophy and heart failure.

Abstract A145: CBFβ supports global protein translation in osteosarcoma and may provide a new therapeutic target

Abstract Background: Core binding factor beta (CBFβ) is a binding partner to the RUNX family of DNA binding transcription factors (RUNX1-3) and acts as a transcriptional co-activator by allosterically increasing their affinity for DNA. RUNX2 is the master regulator of bone growth and differentiation, and its binding to CBFβ is of particular interest to osteosarcoma (OS) research. Notably, increased expression of each is correlated with poor disease-free and overall survival in numerous sarcomas. CBFβ’s transcriptional role is well-understood but recent research in breast cancer cells proposes a non-canonical role in the regulation of protein translation, influencing translation of hundreds of mRNA transcripts via binding with heterogenous nuclear ribonucleoprotein K (hnRNPK). The binding of CBFβ to hnRNPK or RUNX1 is reportedly mutually exclusive, suggesting possible interplay between the two roles. We hypothesize that CBFβ regulates protein translation in OS, participating in the translation of RUNX2 and other oncoproteins, promoting a malignant phenotype. Furthermore, we propose that disrupting its translational role may result in an antitumor effect. While CBFβ’s transcriptional activities are well-characterized, we endeavored to isolate its translational role and investigate its contribution to OS. Methods: CRISPR/Cas9 was used to generate a CBFβ knockout (KO) U2OS cell line, while site-directed mutagenesis of CBFβ and lentiviral transduction of U2OS CBFβ KO cells was used to generate cell lines expressing FLAG-tagged wild type (WT) mutant CBFβ. Western Blotting (WB) was used to assess changes in protein expression and subcellular localization while RUNX2 mRNA expression was measured via qPCR and RNAseq. CBFβ’s interacting partners were identified by Immunoprecipitation Mass Spectrometry (IP-MS). Cellular electro-thermal shift assay was used to evaluate influences of CBFβ mutations on RUNX2 and hnRNPK binding. The Click-IT system followed by WB and IP-MS were used to assess global protein translation and synthesis rates of specific proteins, respectively. Results: CBFβ and hnRNPK interact in U2OS cells and loss of CBFβ leads to a decrease in global protein translation. This results in decreased RUNX2 protein, but not mRNA, expression. Re-introduction of WT CBFβ caused RUNX2 protein levels to recover while expression of CBFβ with key mutations in the binding interface abrogated this effect. Importantly, we observed this was not due to direct protection of RUNX2 from proteasomal degradation by WT CBFβ. We identified a cohort of proteins that appear to be translationally regulated by CBFβ and investigated the impact of CBFβ mutations on its translational activities and RUNX2 binding. We also identified a list of putative CBFβ protein-protein interactions in human OS cells that are altered by these mutations. Conclusions: CBFβ appears to participate in protein translation in OS, regulating the expression of numerous oncoproteins including RUNX2. Key mutations in CBFβ designed to interrupt RUNX2 binding also affect this non-canonical activity of CBFβ. Citation Format: Nicholas A Oldberg, Dayn R Godinez, Luke A Wittenburg. CBFβ supports global protein translation in osteosarcoma and may provide a new therapeutic target [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A145.

Rps19 and Rpl5 Play Distinct Roles in hematopoietic Stem Cell maintenance and Erythroid Differentiation

Mutations in ribosomal proteins (RPs) lead to ribosomopathies. Mechanistic basis underlying the failure of erythropoiesis due to mutations in various RPs is yet to be fully defined. Lack of relevant murine models of ribosomapathies has hindered significant progress. To fill this gap, we generated Rps19 and Rpl5 floxed mice using CRISPR/Cas9 technologies and characterized their hematologic phenotype following crossing them to a Vav-iCremice. Vav-iCre;Rps19 fl/+mice are born at expected Mendelian rates with severe macrocytic anemia and reticulocytopenia. These mice die by post-natal day 10 (P10), due to bone marrow failure and absence of splenic stress erythropoiesis. Analysis of fetal erythropoiesis revealed a 40% reduction in the total number of erythroid cells in Vav-iCre;Rps19 fl/+, however erythroblasts at all stages of terminal erythroid differentiation were found. Intriguingly, studies of hematopoietic stem and progenitor cell s demonstrated a progressive exhaustion of the stem cell compartment. scRNAseq studies of Vav-iCre;Rps19 fl/+ fetal livers demonstrated increased expression of RUNX1, a transcription factor implicated in the regulation of ribosome biogenesis. Accordingly, we observed that hematopoietic progenitors of Vav-iCre,Rps19 fl/+had enhanced global protein synthesis along with increased RUNX1 protein, despite ribosomal protein haploinsufficiency demonstrated by polysome profiling. In marked contrast, Vav-iCre;Rpl5 fl/+ mice presented with a more severe phenotype and died perinatally from anemia. Further analysis revealed a failure of erythropoiesis at erythroid progenitor stages in Vav-iCre;Rpl5 fl/+. In striking contrast with the Rps19 model, Vav-iCre;Rpl5 fl/+ mice had an expansion of the hematopoietic stem and progenitor cell compartment that also had an increased protein translation rate . This increased translation occurred in the context of normal expression levels of RUNX1. Interestingly Vav-iCre;Rpl5 fl/+ micehad reduced mTORC1 activity and a dramatic reduction in the expression of other ribosomal proteins. Consistent with previous studies about the pivotal role of mTORC1 in erythropoiesis Vav-iCre,Raptor fl/fl(mTORC1 conditional knockout) had reduced expressions of RPs in fetal liver. In summary, we report different requirements for Rps19 and Rpl5 during fetal hematopoiesis in regulating erythroid progenitor biology. While Rps19 plays an essential role at the HSC level to maintain the generation of erythroid progenitors, Rpl5 is critical once progenitors are committed towards an erythroid fate. Along with the findings that translation is increased in RP haploinsufficient models, our study unravels potential compensatory mechanisms during fetal hematopoiesis.

One-carbon metabolism and microbial pathogenicity.

One-carbon metabolism (OCM) pathways are responsible for several functions, producing a number of one-carbon unit intermediates (formyl, methylene, methenyl, methyl) that are required for the synthesis of various amino acids and other biomolecules such as purines, thymidylate, redox regulators, and, in most microbes, folate. As humans must acquire folate from the diet, folate production is a target for antimicrobials such as sulfonamides. OCM impacts the regulation of microbial virulence such that in a number of instances, limiting the availability of para-aminobenzoic acid (pABA), an essential OCM precursor, causes a reduction in pathogenicity. Porphyromonas gingivalis, however, displays increased pathogenicity in response to lower pABA levels, and exogenous pABA exerts a calming influence on heterotypic communities of P. gingivalis with pABA-producing partner species. Differential responses to pABA may reflect both the physiology of the organisms and their host microenvironment. OCM plays an integral role in regulating the global rate of protein translation, where the alarmones ZMP and ZTP sense insufficient stores of intracellular folate and coordinate adaptive responses to compensate and restore folate to sufficient levels. The emerging interconnections between OCM, protein synthesis, and context-dependent pathogenicity provide novel insights into the dynamic host-microbe interface.

The cellular response to ocean warming in Emiliania huxleyi.

Marine phytoplankton contribute substantially to the global flux of carbon from the atmosphere to the deep ocean. Sea surface temperatures will inevitably increase in line with global climate change, altering the performance of marine phytoplankton. Differing sensitivities of photosynthesis and respiration to temperature, will likely shift the strength of the future oceanic carbon sink. To further clarify the molecular mechanisms driving these alterations in phytoplankton function, shotgun proteomic analysis was carried out on the globally-occurring coccolithophore Emiliania huxleyi exposed to moderate- (23°C) and elevated- (28°C) warming. Compared to the control (17°C), growth of E. huxleyi increased under elevated temperatures, with higher rates recorded under moderate- relative to elevated- warming. Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.

CNPY2-orchestrated unfolded protein responses play redundant roles in regulating anti-tumor immunity of CD8 +T cells

Abstract Tumors evade immune surveillance by creating a hostile environment that impairs the functions of immune cells. Persistent perturbations including chronic antigen stimulation and metabolic challenges cause endoplasmic reticulum (ER) stress and unfolded protein responses (UPR) in T cells. CNPY2 is one of the key initiators of UPR in the ER, but its roles in T cell activation and persistence have not been reported. Herein, we found that the expressions of CNPY2 and other molecules in UPR pathways were upregulated in both activated and exhausted T cells, indicating UPR activation. However, genetic deletion of Cnpy2 in CD8 +T cells did not result in changes in viability, proliferation, mitochondrial functions, and protein translation rate under acute or chronic antigen stimulation in vitro. Furthermore, no differences were seen between wild-type and CD8-specific Cnpy2 knockout mice in protection against multiple syngeneic tumor models including colon (MC38 and CT26), bladder (MB49), melanoma (YUMM1.7 and B16-F10) and breast tumors (4T1). Although CD8 +T cells from tumors were moderately more activated in the absence of CNPY2, no apparent impact was observed on CD8 +infiltration and effector differentiation. Finally, by mRNA profiling and proteomic analysis, we found that the downstream UPR signaling pathways remained intact in T cells despite loss of CNPY2. In summary, we concluded that persistent TCR stimulation and the tumor microenvironment induce CNPY2 expression and UPR in CD8 +T cells. However, ablating CNPY2 alone failed to overcome UPR-mediated T cell dysfunction, suggesting that targeting multiple initiators of UPRs in CD8 +T cells need to be considered to improve cancer immunotherapy.

Abstract 6233: Omacetaxine reduces c-MYC expression and demonstrates antitumor effects in osteosarcoma

Abstract Omacetaxine mepesuccinate (OMX), also known as homoharringtonine, is a protein translation inhibitor approved for use in chronic myeloid leukemia. Recent studies suggest OMX may be effective against other cancer types with high rates of protein translation, and may be successful against protein targets that are difficult to inhibit by reducing their translation rates. Using both canine and human osteosarcoma (OS) cell lines, we have investigated the efficacy of OMX against osteosarcoma and expression of c-MYC. OMX provides significant growth inhibition of OS cells with IC50 values in the low nanomolar range. OMX also reduces migration and invasion capabilities of OS cells. Strikingly, we observed reduction in levels of c-MYC protein in most canine and human OS cell lines after OMX exposure. This reduction was both dose and time dependent. We also investigated the efficacy of OMX against OS in an orthotopic mouse OS model. OMX is a promising candidate for treatment of OS in both dogs and humans, and potentially additional cancers dependent on c-MYC. Citation Format: Kristen B. Farrell, Douglas H. Thamm. Omacetaxine reduces c-MYC expression and demonstrates antitumor effects in osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6233.

SARS-CoV-2 viral protein Nsp2 stimulates translation under normal and hypoxic conditions

When viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.

Multiple Copies of microRNA Binding Sites in Long 3'UTR Variants Regulate Axonal Translation.

Rapid responses to changes within subcellular compartments of highly polarized cells, such as neuron axons, depend on local translation and post-transcriptional regulation. The mechanism by which microRNAs (miRNAs) regulate this process is not fully understood. Here, using live cell imaging and RNA sequencing analysis, we demonstrated how miRNAs can differentially control hundreds of transcripts at the subcellular level. We demonstrated that the seed match length of the miRNA target-sequence regulates both mRNA stability and protein translation rates. While longer seed matches have an increased inhibitory effect, transcriptome analysis did not reveal differences in seed match length between axonal and somata mRNAs of motor neurons. However, mRNA variants with longer 3'UTR are enriched in axons and contain multiple repeats of specific miRNA target sequences. Finally, we demonstrated that the long 3'UTR mRNA variant of the motor protein Kif5b is enriched explicitly in motor neuron axons and contains multiple sequence repeats for binding miR-129-5p. This subsequently results in the differential post-transcriptional regulation of kif5b and its synthesis in axons. Thus, we suggest that the number of miRNA binding sites at the 3'UTR of the mRNA, rather than the miRNA seed match length, regulates the axonal transcriptome.

Safety and Efficacy of the Addition of the Protein Translation Inhibitor Omacetaxine to Induction with Cytarabine and Idarubicin in Newly Diagnosed AML

Background: Omacetaxine mepesuccinate (OM), a semi-synthetic form of homoharringtonine (HHT), mechanistically inhibits aminoacyl-tRNA binding to ribosomal acceptor "A” sites, preventing mRNA translation (Wetzler,Curr Pharm Des 2011, 17:59-64), and causing a rapid decline of short-lived proteins e.g., c-myc, cyclin D, the anti-apoptotic proteins cFLIP, survivin and Mcl-1, an important anti-apoptotic regulator in AML.While HHT added to cytarabine and an anthracycline improved CR and 3-yr EFS in de novo AML patients (pts; Jin et al, Lancet Oncology 2013, 7:599-608), meta-analysis of Chinese studies in elderly pts indicated a CR of 47.5%. Aims: Early analysis of AML-02, a phase Ib trial of escalating doses of OM (an FDA-approved drug) added to a standard 7 + 3 induction regimen was described (NCT02440568; Christian et al., Blood, 2018, 132:5218). Here we report long-term pt outcomes and studies of their correlation with in vitro OM effects on protein translation and apoptosis sensitivity. Methods: From June 2015 to June 2018, 22 pts aged 18-70 yrs with newly diagnosed AML entered AML-02, receiving escalating doses of OM administered SQ q12h d1-7 with cytarabine (100mg/m2 CIV) d1-7 and Idarubicin 12mg/m2 IV d1-3. Four OM dose levels were tested starting with cohort #1 at 0.625mg/m2 sc q12h (also 1.25, 2.0, and 3.0mg/m2 q12h cohorts). The primary endpoint, the optimally safe and active dose (OD) was determined using a Bayesian adaptive design, EFFTOX, which considers trade-offs between efficacy and toxicity to establish the OD (Shah et al, Leukemia, 2015; 29:1945). Secondary endpoints included OS, RFS and EFS. Residual disease at d14 was deemed a study failure and pts were taken off study. Hematological toxicity (HT) was defined as incomplete hematologic recovery at d49 with the BM free of leukemia. Post-induction therapy consisted of standard high dose cytarabine consolidation chemotherapy or allogeneic HSCT, based on cytogenetic risk (ELN 2010). Potential correlations of the effects of OM on protein translation rates, measured using the OP-Puro technique, and apoptosis sensitivity, measured using BH3 profiling techniques, on pretreatment AML samples and subsequent patient outcomes were also examined. Follow-up is complete to August 1st, 2022. Results: Median age was 58 yrs, 12 pts had adverse cytogenetics, 6 intermediate and 3 favorable risk (1 unknown due to fibrosis); overall 73% (16) had adverse cytogenetics or secondary AML. Earlier results (Christian et al) indicated no HTs in 21 evaluable pts, and OD was established as 2.0mg/m2. CR was 45.5%, median OS 22.7 months (OS at 4 yrs 45%), and EFS 80 days. The median OS is now 24.2 months (95% CI 18.3-39.7), median EFS is 80 days (95% CI 280-964), and OS at 6 years remains at 45%. There were no new TEAEs. Notably, of 10 pts achieving CR, 1 pt relapsed at D60, 1 was lost to follow-up and 1 died of opiate overdose (in CR). Five of the remaining 7 underwent HSCT and all 7 remain in remission. In pts achieving CR, median RFS is 62.4 months (95% CI 42.6-82.2; Fig.1), suggesting potential LSC impact. Common adverse effects included neutropenia (82%), nausea (64%), vomiting (59%), diarrhea (45%), hyperglycemia (41%), and a transient desquamating skin reaction (27%) that is dose-related and may be due to OM-mediated downregulation of cFLIP levels in sweat glands (Hwang et al, British Journal of Haematology, 2021; 195:e138-e146). In in vitro studies, 3 pretreatment AML pt BM samples were analyzed after a short-term (non-cytotoxic) OM treatment for 4 hours at a dose (75 nM) equivalent to calculated systemic OM levels achieved in cohort#3 (2mg/m2). Responding pt samples (CR;n=2) had a greater reduction in protein translation than the non-responder (NR). With exposure to OM, CR pts also had greater reductions of proteins with a short T1/2, such as anti-apoptotic protein MCL-1, with a marked increase in cytochrome C loss, indicating high mitochondrial priming and sensitivity to apoptosis (Fig.2). Conclusion: This small phase Ib study of the addition of OM to a standard 7 + 3 regimen in a diverse population with predominantly high-risk AML and frequent co-morbidities demonstrates a manageable safety profile, acceptable efficacy and resulted in a prolonged DoR. Studies of pretreatment pt samples suggest that analysis of blast protein translation inhibition and especially BH3 profiling responses to OM may predict susceptibility of LSC to Omacetaxine, and potentially patient outcomes. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

211 (PB091) - A novel class of Ribosome Modulating Agents (RMAs) target MYC driven SCLC and synergize with DNA intercalating agents

Background: SCLC has a very poor prognosis and limited treatment options. Genomic studies in SCLC show that MYC isoforms are key oncogenic drivers in a majority of SCLC tumors. As a result, these tumors tend to have high proliferation and protein translation rates. We hypothesized that ribosome modulating agents (RMAs) that selectively inhibit protein translation may show activity in these MYC driven cancers prompting us to test these novel RMAs and understand their effects in SCLC models.

CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors.

Tools for synthetically controlling gene expression are a cornerstone of genetic engineering. CRISPRi and CRISPRa technologies have been applied extensively for programmable modulation of gene transcription, but there are few such tools for targeted modulation of protein translation rates. Here, we employ CRISPR-Cas13 as a programmable activator of translation. We develop a novel variant of the catalytically-deactivated Cas13d enzyme dCasRx by fusing it to translation initiation factor IF3. We demonstrate dCasRx-IF3’s ability to enhance expression 21.3-fold above dCasRx when both are targeted to the start of the 5′ untranslated region of mRNA encoding red fluorescent protein in Escherichia coli. Activation of translation is location-dependent, and we show dCasRx-IF3 represses translation when targeted to the ribosomal binding site, rather than enhancing it. We provide evidence that dCasRx-IF3 targeting enhances mRNA stability relative to dCasRx, providing mechanistic insights into how this new tool functions to enhance gene expression. We also demonstrate targeted upregulation of native LacZ 2.6-fold, showing dCasRx-IF3’s ability to enhance expression of endogenous genes. dCasRx-IF3 requires no additional host modification to influence gene expression. This work outlines a novel approach, CRISPR-RNAa, for post-transcriptional control of translation to activate gene expression.

Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification.

Until recently, post-transcriptional modifications of RNA were largely restricted to noncoding RNA species. However, this belief seems to have quickly dissipated with the growing number of new modifications found in mRNA that were originally thought to be primarily tRNA-specific, such as dihydrouridine. Recently, transcriptomic profiling, metabolic labeling, and proteomics have identified unexpected dihydrouridylation of mRNAs, greatly expanding the catalog of novel mRNA modifications. These data also implicated dihydrouridylation in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridylation of tRNAs and mRNAs are introduced by flavin-dependent dihydrouridine synthases. In this review, we will briefly outline the current knowledge on the distribution of dihydrouridines in the transcriptome, their chemical labeling, and highlight structural and mechanistic aspects regarding the dihydrouridine synthases enzyme family. A special emphasis on important research directions to be addressed will also be discussed. This new entry of dihydrouridine into mRNA modifications has definitely added a new layer of information that controls protein synthesis.

Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance

SignificanceProteins are the machinery which execute essential cellular functions. However, measuring their abundance within an organism can be difficult and resource-intensive. Cells use a variety of mechanisms to control protein synthesis from mRNA, including short open reading frames (uORFs) that lie upstream of the main coding sequence. Ribosomes can preferentially translate uORFs instead of the main coding sequence, leading to reduced translation of the main protein. In this study, we show that uORF sequence variation between individuals can lead to different rates of protein translation and thus variable protein abundances. We also demonstrate that natural variation in uORFs occurs frequently and can be linked to whole-plant phenotypes, indicating that uORF sequence variation likely contributes to plant adaptation.

PUS7 deficiency in human patients causes profound neurodevelopmental phenotype by dysregulating protein translation.

Protein translation is a highly regulated process involving the interaction of numerous genes on every component of the protein translation machinery. Upregulated protein translation is a hallmark of cancer and is implicated in autism spectrum disorder, but the risks of developing each disease do not appear to be correlated with one another. In this study we identified two siblings from the NIH Undiagnosed Diseases Program with loss of function variants in PUS7, a gene previously implicated in the regulation of total protein translation. These patients exhibited a neurodevelopmental phenotype including autism spectrum disorder in the proband. Both patients also had features of Lesch-Nyhan syndrome, including hyperuricemia and self-injurious behavior, but without pathogenic variants in HPRT1. Patient fibroblasts demonstrated upregulation of protein synthesis, including elevated MYC protein, but did not exhibit increased rates of cell proliferation. Interestingly, the dysregulation of protein translation also resulted in mildly decreased levels of HPRT1 protein suggesting an association between dysregulated protein translation and the LNS-like phenotypic findings. These findings strengthen the correlation between neurodevelopmental disease, particularly autism spectrum disorders, and the rate of protein translation.

Spatial discordances between mRNAs and proteins in the intestinal epithelium.

The use of transcriptomes as reliable proxies for cellular proteomes is controversial. In the small intestine, enterocytes operate for 4 days as they migrate along villi, which are highly graded microenvironments. Spatial transcriptomics have demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here we show that enterocyte proteins and messenger RNAs along the villus axis are zonated, yet often spatially discordant. Using spatial sorting with zonated surface markers, together with a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, we find that, while many genes exhibit proteins zonated toward the villus tip, mRNA is zonated toward the villus bottom. Finally, we demonstrate that space-independent protein synthesis delays can explain many of the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium, highlighting the importance of protein measurements for inferring cell states in tissues that operate outside of steady state.