Subcytoplasmic location of translation controls protein output.

The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments.

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism.

The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences of this interplay. However, current transcriptome-wide experimental methods to chart these interactions are limited by their poor sensitivity. Here we extend the hiCLIP atlas of duplexes bound by Staufen1 (STAU1) ∼10-fold, through careful consideration of experimental assumptions, and the development of bespoke computational methods which we apply to existing data. We present Tosca, a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data generally. We use our extended duplex atlas to discover insights into the RNA selectivity of STAU1, revealing the importance of structural symmetry and duplex-span-dependent nucleotide composition. Furthermore, we identify heterogeneity in the relationship between transcripts with STAU1-bound 3' UTR duplexes and metabolism of the associated RNAs that we relate to RNA structure: transcripts with short-range proximal 3' UTR duplexes have high degradation rates, but those with long-range duplexes have low rates. Overall, our work enables the integrative analysis of proximity ligation data delivering insights into specific features and effects of RBP-RNA structure interactions.

Household Processing Methods and Their Impact on Bioactive Compounds and Antioxidant Activities of Sweetpotato Genotypes of Varying Storage Root Flesh Colours.

Sweetpotato storage roots, peeled and unpeeled, of varying flesh colours (white, cream, yellow, pale orange, deep orange, and purple) were spectrophotometrically evaluated for their bioactive compounds and antioxidant activities. Roots were boiled, steamed, baked, fried, or microwaved. The unpeeled roots had relatively higher (p < 0.001) bioactive compounds and antioxidant activities than the peeled ones. All cooking methods increased phenolic compounds, flavonoids, and tannins in all genotypes. Significant losses of total carotenoids occurred with all cooking methods (ranging from 24.18 to 172.76 µg/g in raw sweetpotatoes vs. 10.06 to 118.17 µg/g in cooked ones; p < 0.001), except the deep-orange-fleshed genotype, in which frying slightly increased carotenoids from 269.81 to 304.74 µg/g. Microwaving retained 69% vitamin C in the cream-fleshed one, the highest among the cooking methods. Anthocyanins decreased with baking and frying in the purple-fleshed one but increased with other methods; microwaving being highest at 13.9% (17.43 mg/g). While the 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid antioxidant activity decreased with all cooking techniques in some genotypes, ferricyanide-reducing antioxidant potential increased. The retention of bioactive compounds in sweetpotato storage roots depends on the processing method. Thus, to obtain the most health benefits, consumers should use different cooking methods but retain the peels.

TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A.

Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia1-3, two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-434,5. Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies.

Are Medical Devices Cost-Effective?

OBJECTIVE: Medical devices can offer important therapeutic advances but, as for any medical interventions, there are questions about their costs and benefits. We examined health benefits and costs for pre-market approved (PMA) devices approved by the US Food and Drug Administration (FDA) (1999-2015), grouping them by generic category (e.g., drug-eluting stents) and indication. METHODS: We searched PubMed for incremental health gain estimates [measured in quality-adjusted life-years (QALYs)] and incremental costs for each device category compared to previously available treatments. We calculated incremental cost-effectiveness ratios by dividing the average incremental costs by the average incremental QALY gains. In sensitivity analysis, we repeated the analysis when excluding industry-funded studies. RESULTS: We identified at least one relevant cost-utility or comparative-effectiveness study for 88 devices (15.9% of non-cosmetic devices approved from 1999 to 2015), and at least one device across 53 (26.2%) generic categories. The median (mean) incremental cost across generic device categories was $1701 ($13,320). The median (mean) incremental health gain across generic device categories was 0.13 (0.46) QALYs. We found that cost-effectiveness ratios for 36 of 53 (68%) and 43 of 53 (81%) device categories fell below (were more favorable than) $50,000 and $150,000 per QALY, respectively. Results were roughly similar when we excluded industry-funded studies. CONCLUSIONS: We found that roughly one-quarter of the major PMA medical device categories have published cost-effectiveness evidence accessible through a large, publicly available database. Available evidence suggests that devices generally offer good value, as judged relative to established cost-effectiveness benchmarks.

RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons.

RNA-binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long-ranged RNA hairpins in the 3'-untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2-dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and eventually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs.

TDP-43 condensation properties specify its RNA-binding and regulatory repertoire.

Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the specificity and function of protein-RNA complexes remains unclear. We created a series of TDP-43 C-terminal domain (CTD) variants that exhibited a gradient of low to high condensation propensity, as observed in vitro and by nuclear mobility and foci formation. Notably, a capacity for condensation was required for efficient TDP-43 assembly on subsets of RNA-binding regions, which contain unusually long clusters of motifs of characteristic types and density. These "binding-region condensates" are promoted by homomeric CTD-driven interactions and required for efficient regulation of a subset of bound transcripts, including autoregulation of TDP-43 mRNA. We establish that RBP condensation can occur in a binding-region-specific manner to selectively modulate transcriptome-wide RNA regulation, which has implications for remodeling RNA networks in the context of signaling, disease, and evolution.

The Potential of Sweetpotato as a Functional Food in Sub-Saharan Africa and Its Implications for Health: A Review.

Increasing urbanization in developing countries has resulted in busier lifestyles, accompanied by consumption of fast foods. The consequence is an increased prevalence in noncommunicable diseases (NCDs). Food-based approaches would be cheaper and more sustainable in reducing these NCDs compared to drugs, which may have side effects. Studies have suggested that consuming functional foods could potentially lower NCD risks. Sweetpotato is regarded as a functional food because it contains bioactive compounds. Recently, sweetpotato has gained attention in sub-Saharan Africa (SSA), but research has focused on its use in alleviating micronutrient deficiencies such as vitamin A deficiency, particularly the orange-fleshed variety of sweetpotato. Some studies conducted in other parts of the world have investigated sweetpotato as a functional food. There is a need to characterize the sweetpotato varieties in SSA and determine how processing affects their bioactive components. This review highlights some of the studies conducted in various parts of the world on the functionality of sweetpotato, its bioactive compounds, and how these are influenced by processing. In addition, the potential health benefits imparted by sweetpotato are expounded. The knowledge gaps that remain in these studies are also addressed, focusing on how they can direct sweetpotato research in SSA.

Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells.

Translation of ribosomal protein-coding mRNAs (RP-mRNAs) constitutes a key step in ribosome biogenesis, but the mechanisms that modulate RP-mRNA translation in coordination with other cellular processes are poorly defined. Here, we show that subcellular localization of RP-mRNAs acts as a key regulator of their translation during cell migration. As cells migrate into their surroundings, RP-mRNAs localize to the actin-rich cell protrusions. This localization is mediated by La-related protein 6 (LARP6), an RNA-binding protein that is enriched in protrusions. Protrusions act as hotspots of translation for RP-mRNAs, enhancing RP synthesis, ribosome biogenesis, and the overall protein synthesis in migratory cells. In human breast carcinomas, epithelial-to-mesenchymal transition (EMT) upregulates LARP6 expression to enhance protein synthesis and support invasive growth. Our findings reveal LARP6-mediated mRNA localization as a key regulator of ribosome biogenesis during cell migration and demonstrate a role for this process in cancer progression downstream of EMT.

Baseline Visual Acuity at Wet AMD Diagnosis Predicts Long-Term Vision Outcomes: An Analysis of the IRIS Registry.

BACKGROUND AND OBJECTIVE: Clinical trials in neovascular age-related macular degeneration (nAMD) demonstrate that high visual acuity (VA) can be maintained, and low VA can be improved with anti-vascular endothelial growth factor (VEGF) treatment. Few real-world data investigating the relationship between baseline VA and long-term outcomes exist. This study compares VA at diagnosis and after treatment using data from a large patient registry. PATIENTS AND METHODS: Retrospective study of IRIS Registry patients diagnosed with nAMD in one or both eyes between January 2013 and June 2017. Patients received at least two anti-VEGF injections in the study eye(s) less than 45 days apart during the study period. Primary outcomes were the percentage of eyes with 20/40 VA or better at diagnosis and association of VA at diagnosis with longer-term visual outcomes. RESULTS: The study included 162,902 eyes. Among all included eyes, 34.3% presented with 20/40 VA or better at diagnosis. Patients with 20/40 vision or better at baseline maintained a mean VA of 20/40 or better for 2 years after treatment initiation. CONCLUSIONS: Baseline VA at nAMD diagnosis predicts long-term VA outcomes. Early diagnosis before VA is adversely affected is a key factor in preserving vision in patients with nAMD. [Ophthalmic Surg Lasers Imaging Retina. 2020;51:633-639.].

Orphan Drugs Offer Larger Health Gains but Less Favorable Cost-effectiveness than Non-orphan Drugs.

BACKGROUND: Orphan drugs offer important therapeutic options to patients suffering from rare conditions, but are typically considerably more expensive than non-orphan drugs, leading to questions about their cost-effectiveness. OBJECTIVE: To compare the value of orphan and non-orphan drugs approved by the FDA from 1999 through 2015. DESIGN: We searched the PubMed database to identify estimates of incremental health gains (measured in quality-adjusted life-years, or QALYs) and incremental costs that were associated with orphan and non-orphan drugs compared with preexisting care. We excluded pharmaceutical industry-funded studies from the dataset. When a drug was approved for multiple indications, we considered each drug-indication pair separately. We then compared incremental QALY gains, incremental costs, and incremental cost-effectiveness ratios for orphan and non-orphan drugs using the Mann-Whitney U (MWU) test (to compare median values of the different distributions) and the Kolmogorov-Smirnov (KS) test (to compare the shape of different distributions). RESULTS: We identified estimates for 49 orphan drug-indication pairs, and for 169 non-orphan drug-indication pairs. We found that orphan drug-indication pairs offered larger median incremental health gains than non-orphan drug-indication pairs (0.25 vs. 0.05 QALYs; MWU p = 0.0093, KS p = 0.02), but were associated with substantially higher costs ($47,652 vs. $2870; MWU p < 0.001, KS p < 0.001) and less favorable cost-effectiveness ($276,288 vs. $100,360 per QALY gained; MWU p = 0.0068, KS p = 0.009). CONCLUSIONS: Our study suggests that orphan drugs often offer larger health gains than non-orphan drugs, but due to their substantially higher costs they tend to be less cost-effective than non-orphan drugs. Our findings highlight the challenge faced by health care payers to provide patients appropriate access to orphan drugs while achieving value from drug spending.

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.

RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.

Advances in CLIP Technologies for Studies of Protein-RNA Interactions.

RNA binding proteins (RBPs) regulate all aspects in the life cycle of RNA molecules. To elucidate the elements that guide RNA specificity, regulatory mechanisms, and functions of RBPs, methods that identify direct endogenous protein-RNA interactions are particularly valuable. UV crosslinking and immunoprecipitation (CLIP) purifies short RNA fragments that crosslink to a specific protein and then identifies these fragments by sequencing. When combined with high-throughput sequencing, CLIP can produce transcriptome-wide maps of RNA crosslink sites. The protocol is comprised of several dozen biochemical steps, and improvements made over the last 15 years have increased its resolution, sensitivity, and convenience. Adaptations of CLIP are also emerging in the epitranscriptomic field to map the positions of RNA modifications accurately. Here, we describe the rationale for each step in the protocol and discuss the impact of variations to help users determine the most suitable option.

miR-182 Regulates Slit2-Mediated Axon Guidance by Modulating the Local Translation of a Specific mRNA.

During brain wiring, cue-induced axon behaviors such as directional steering and branching are aided by localized mRNA translation. Different guidance cues elicit translation of subsets of mRNAs that differentially regulate the cytoskeleton, yet little is understood about how specific mRNAs are selected for translation. MicroRNAs (miRNAs) are critical translational regulators that act through a sequence-specific mechanism. Here, we investigate the local role of miRNAs in mRNA-specific translation during pathfinding of Xenopus laevis retinal ganglion cell (RGC) axons. Among a rich repertoire of axonal miRNAs, miR-182 is identified as the most abundant. Loss of miR-182 causes RGC axon targeting defects in vivo and impairs Slit2-induced growth cone (GC) repulsion. We find that miR-182 targets cofilin-1 mRNA, silencing its translation, and Slit2 rapidly relieves the repression without causing miR-182 degradation. Our data support a model whereby miR-182 reversibly gates the selection of transcripts for fast translation depending on the extrinsic cue.

Impact of treatment strategies for open angle glaucoma on intraocular pressure: the RiGOR study.

AIMS: The RiGOR study's primary outcome measure was a 15% reduction in intraocular pressure (IOP) for patients with open-angle glaucoma at 1 year. METHODS: Patients received treatment according to the ophthalmologist's usual practice. RESULTS: A higher proportion of patients in the incisional and other surgery group achieved a 15% reduction in IOP than in the laser surgery or additional medication groups (82, 57, and 57% respectively). In multivariate regression analyses, incisional surgery patients were 2.7-times as likely as patients treated with additional medication to achieve a 15% reduction in IOP (odds ratio: 2.67; 95% CI: 2.01-3.57). CONCLUSION: Incisional and other surgical procedures are effective treatments. There were no differences in treatment response by race or ethnicity.

Quality of life and visual acuity outcomes in the Registry in Glaucoma Outcomes Research study.

AIMS: The RiGOR study evaluated the association of treatment and patient-reported outcomes for open-angle glaucoma patients. METHODS: The Glaucoma Symptom Scale (National Eye Institute-Visual Function Questionnaire (NEI-VFQ) and visual acuity (VA) were collected as quality of life measures. RESULTS: The proportion of patients with improvement of at least two lines of vision was highest in the incisional surgery group (14.2% compared with 9.9% for laser surgery and 10.9% for additional medication). CONCLUSION: No clinically relevant differences were seen in benefit for the laser surgery or incisional surgery groups compared with additional medications for the Glaucoma Symptom Scale or NEI-VFQ measures or subscales. Differences in quality of life by race need to be explored in further studies.

RiGOR: a prospective observational study comparing the effectiveness of treatment strategies for open-angle glaucoma.

AIMS: The RigOR study was designed to assess comparative effectiveness of medications, laser trabeculoplasty and incisional surgery in patients with open-angle glaucoma (OAG) in the community initiating a new or additional course of therapy as judged necessary by their ophthalmologist. This paper focuses specifically on demographic and clinical characteristics of OAG patients at enrollment. PATIENTS & METHODS: A total of 2597 with OAG already on medical therapy were enrolled from 45 community and academic practices throughout the USA. RESULTS: Overall, 784 (30%) patients were treated with laser surgery, 436 with other surgical procedures (17%), and 1377 with additional medication (53%). Patients had mild (35%) or moderate (31%) glaucoma, with 28% with severe glaucoma. CONCLUSION: The RiGOR study enrolled a diverse population and will provide valuable information regarding visual function and treatment patterns among different racial/ethnic populations. African-American and Hispanic patients entered the study with poorer visual acuity and more severe glaucoma.

Practice patterns and treatment changes for open-angle glaucoma: the RiGOR study.

AIMS: The RiGOR study provides a current picture of the types of glaucoma treatment over 12 months. METHODS: Patients were identified and enrolled at the time of decision to proceed with laser surgery procedure or other procedure such as incisional surgery or drainage device implantation, or initiation of a new or additional course of therapy with medication for glaucoma treatment. RESULTS: The most frequent type of treatments were prostaglandin analogues (60%) among patients with additional medication, selective laser trabeculoplasty (87%) among patients with laser surgery and trabeculectomy (57%) among patients with incisional surgery. CONCLUSION: For 36% of patients, a treatment cascade involves two or more therapies over a year. This demonstrates the complex nature of open-angle glaucoma treatment.