Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function.

Stress granules and P bodies are conserved cytoplasmic aggregates of nontranslating messenger ribonucleoprotein complexes (mRNPs) implicated in the regulation of mRNA translation and decay and are related to RNP granules in embryos, neurons, and pathological inclusions in some degenerative diseases. Using baker's yeast, 125 genes were identified in a genetic screen that affected the dynamics of P bodies and/or stress granules. Analyses of such mutants, including CDC48 alleles, provide evidence that stress granules can be targeted to the vacuole by autophagy, in a process termed granulophagy. Moreover, stress granule clearance in mammalian cells is reduced by inhibition of autophagy or by depletion or pathogenic mutations in valosin-containing protein (VCP), the human ortholog of CDC48. Because mutations in VCP predispose humans to amyotrophic lateral sclerosis, frontotemporal lobar degeneration, inclusion body myopathy, and multisystem proteinopathy, this work suggests that autophagic clearance of stress granule related and pathogenic RNP granules that arise in degenerative diseases may be important in reducing their pathology.

Stress granule and P-body clearance: Seeking coherence in acts of disappearance.

Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.

EDC3 phosphorylation regulates growth and invasion through controlling P-body formation and dynamics.

Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P-bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P-body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P-body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P-bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin ß1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer-relevant functions and suggest that modulation of P-body activity may represent a new paradigm for cancer treatment.

Alterations of signaling pathways in response to chemical perturbations used to measure mRNA decay rates in yeast.

Assessing variations in mRNA stability typically involves inhibiting transcription either globally or in a gene-specific manner. Alternatively, mRNA pulse-labeling strategies offer a means to calculate mRNA stability without inhibiting transcription. However, key stress-responsive cell signaling pathways, which affect mRNA stability, may themselves be perturbed by the approaches used to measure mRNA stability, leading to artifactual results. Here, we have focused on common strategies to measure mRNA half-lives in yeast and determined that commonly used transcription inhibitors thiolutin and 1,10 phenanthroline inhibit TORC1 signaling, PKC signaling, and partially activate HOG signaling. Additionally, 4-thiouracil (4tU), a uracil analog used in mRNA pulse-labeling approaches, modestly induces P-bodies, mRNA-protein granules implicated in storage and decay of nontranslating mRNA. Thiolutin also induces P-bodies, whereas phenanthroline has no effect. Doxycycline, which controls "Tet On/Tet Off" regulatable promoters, shows no impact on the above signaling pathways or P-bodies. In summary, our data argues that broad-acting transcriptional inhibitors are problematic for determining mRNA half-life, particularly if studying the impacts of the TORC1, HOG, or PKC pathway on mRNA stability. Regulatable promoter systems are a preferred approach for individual mRNA half-life studies, with 4tU labeling representing a good approach to global mRNA half-life analysis, despite modestly inducing P-bodies.

RPS28B mRNA acts as a scaffold promoting cis-translational interaction of proteins driving P-body assembly.

P-bodies (PBs) are cytoplasmic mRNA-protein (mRNP) granules conserved throughout eukaryotes which are implicated in the repression, storage and degradation of mRNAs. PB assembly is driven by proteins with self-interacting and low-complexity domains. Non-translating mRNA also stimulates PB assembly, however no studies to date have explored whether particular mRNA transcripts are more critical than others in facilitating PB assembly. Previous work revealed that rps28bΔ (small ribosomal subunit-28B) mutants do not form PBs under normal growth conditions. Here, we demonstrate that the RPS28B 3'UTR is important for PB assembly, consistent with it harboring a binding site for the PB assembly protein Edc3. However, expression of the RPS28B 3'UTR alone is insufficient to drive PB assembly. Intriguingly, chimeric mRNA studies revealed that Rps28 protein, translated in cis from an mRNA bearing the RPS28B 3'UTR, physically interacts more strongly with Edc3 than Rps28 protein synthesized in trans. This Edc3-Rps28 interaction in turn facilitates PB assembly. Our work indicates that PB assembly may be nucleated by specific RNA 'scaffolds'. Furthermore, this is the first description in yeast to our knowledge of a cis-translated protein interacting with another protein in the 3'UTR of the mRNA which encoded it, which in turn stimulates assembly of cellular structures.

Visual outcome following posterior capsule rupture during manual small incision cataract surgery.

BACKGROUND: The quality of cataract surgery can be measured by visual outcome, which is sometimes limited by intraoperative complications, most commonly posterior capsular rupture. AIMS: The aim of the study was to assess visual outcome at the last visit (≥8 weeks) following posterior capsule rupture (PCR) in patients who had manual small incision cataract surgery (MSICS) managed without access to an automated vitrector. METHODS: A review of medical records of all manual small incision cataract surgeries performed between January 2013 and December 2016 at the National Eye Centre, Kaduna, Nigeria was conducted. Descriptive statistics and logistic regression analysis were performed using STATA 14.0 to examine risk factors for the development of a poor visual outcome and to assess the impact of PCR on development of poor visual outcome. RESULTS: In total, 405 patients were operated on with MSICS (50.6% males). Mean age was 62.4 (SD 12.6) years. PCR was the most common complication (n = 19 (4.7%)). The proportion of good outcomes (≥6/18) rose from 12.4% non-PCR and 0.0% for those with PCR at day 1 postoperative review, to 71.5 and 26.3%, respectively, by final follow up (P = 0.001). Patients with PCR were 7.0 (P = 0.0001) times more likely to have borderline/poor visual outcome (<6/18) compared to those without PCR. Age >60 years increased the odds of borderline/poor by 1.4 times (P = 0.002). CONCLUSION: PCR significantly affects the visual outcome of cataract patients in settings with no facilities for automated vitrectomy. Minimizing complications will improve visual outcome of cataract patients and increase uptake of cataract surgical services.

TOR-tured yeast find a new way to stand the heat.

In this issue, Takahara and Maeda (2012) discover that together, Pbp1 and sequestration of the TORC1 complex in cytoplasmic mRNP stress granules provides a negative regulatory mechanism for TORC1 signaling during stress.

Defects in THO/TREX-2 function cause accumulation of novel cytoplasmic mRNP granules that can be cleared by autophagy.

The nuclear THO and TREX-2 complexes are implicated in several steps of nuclear mRNP biogenesis, including transcription, 3' end processing and export. In a recent genomic microscopy screen in Saccharomyces cerevisiae for mutants with constitutive stress granules, we identified that absence of THO and TREX-2 complex subunits leads to the accumulation of Pab1-GFP in cytoplasmic foci. We now show that these THO/TREX-2 mutant induced foci ("TT foci") are not stress granules but instead are a mRNP granule containing poly(A)(+) mRNA, some mRNP components also found in stress granules, as well several proteins involved in mRNA 3' end processing and export not normally seen in stress granules. In addition, TT foci are resistant to cycloheximide-induced disassembly, suggesting the presence of mRNPs impaired for entry into translation. THO mutants also exhibit defects in normal stress granule assembly. Finally, our data also suggest that TT foci are targeted by autophagy. These observations argue that defects in nuclear THO and TREX-2 complexes can affect cytoplasmic mRNP function by producing aberrant mRNPs that are exported to cytosol, where they accumulate in TT foci and ultimately can be cleared by autophagy. This identifies a novel mechanism of quality control for aberrant mRNPs assembled in the nucleus.

Canine MAS1: monoallelic expression is suggestive of an imprinted gene.

Imprinted genes are epigenetically modified in a parent-of-origin dependent manner and as a consequence are differentially expressed, with one allele typically expressed while the other is repressed. In canine, the insulin like growth factor 2 receptor gene (IGF2R) is imprinted with predominant expression of the maternally inherited allele. Because imprinted genes usually occur in clusters, we examined the allelic expression pattern of the gene encoding the canine Mas receptor (MAS1), which is located upstream of IGF2R on canine chromosome 1 and is highly conserved in mammals. In this report we describe monoallelic expression of canine MAS1 in the neonatal umbilical cord of several individuals and we identify the expressed allele as maternally inherited. These data suggest that canine MAS1 is an imprinted gene.

What are the priorities for improving cataract surgical outcomes in Africa? Results of a Delphi exercise.

PURPOSE: The quality of cataract surgery delivered in sub-Saharan Africa (SSA) is a significant constraint to achieving the elimination of avoidable blindness. No published reports from routine SSA cataract services attain the WHO benchmarks for visual outcomes; poor outcomes (<6/60) often comprise 20% in published case series. This Delphi exercise aimed to identify and prioritise potential interventions for improving the quality of cataract surgery in SSA to guide research and eye health programme development. METHODS: An initial email open-question survey created a ranked list of priorities for improving quality of surgical services. A second-round face-to-face discussion facilitated at a Vision 2020 Research Mentorship Workshop in Tanzania created a refined list for repeated ranking. RESULTS: Seventeen factors were agreed that might form target interventions to promote quality of cataract services. Improved training of surgeons was the top-ranked item, followed by utilisation of biometry, surgical equipment availability, effective monitoring of outcomes of cataract surgery by the surgeon, and well-trained support staff for the cataract pathway (including nurses seeing post-operative cases). CONCLUSION: Improving the quality of cataract surgery in SSA is a clinical, programmatic and public health priority. In the absence of other evidence, the collective expert opinion of those involved in ophthalmic services regarding the ranking of factors to promote quality improvement, refined through this Delphi exercise, provides us with candidate intervention areas to be evaluated.

Eukaryotic stress granules: the ins and outs of translation.

The stress response in eukaryotic cells often inhibits translation initiation and leads to the formation of cytoplasmic RNA-protein complexes referred to as stress granules. Stress granules contain nontranslating mRNAs, translation initiation components, and many additional proteins affecting mRNA function. Stress granules have been proposed to affect mRNA translation and stability and have been linked to apoptosis and nuclear processes. Stress granules also interact with P-bodies, another cytoplasmic RNP granule containing nontranslating mRNA, translation repressors, and some mRNA degradation machinery. Together, stress granules and P-bodies reveal a dynamic cycle of distinct biochemical and compartmentalized mRNPs in the cytosol, with implications for the control of mRNA function.

Role of Autophagy and Apoptosis in Non-Small-Cell Lung Cancer.

Non-small-cell lung cancer (NSCLC) constitutes 85% of all lung cancers, and is the leading cause of cancer-related death worldwide. The poor prognosis and resistance to both radiation and chemotherapy warrant further investigation into the molecular mechanisms of NSCLC and the development of new, more efficacious therapeutics. The processes of autophagy and apoptosis, which induce degradation of proteins and organelles or cell death upon cellular stress, are crucial in the pathophysiology of NSCLC. The close interplay between autophagy and apoptosis through shared signaling pathways complicates our understanding of how NSCLC pathophysiology is regulated. The apoptotic effect of autophagy is controversial as both inhibitory and stimulatory effects have been reported in NSCLC. In addition, crosstalk of proteins regulating both autophagy and apoptosis exists. Here, we review the recent advances of the relationship between autophagy and apoptosis in NSCLC, aiming to provide few insights into the discovery of novel pathogenic factors and the development of new cancer therapeutics.

Policies to sustain the nursing workforce: an international perspective.

AIM: Examine metrics and policies regarding nurse workforce across four countries. BACKGROUND: International comparisons inform health policy makers. METHODS: Data from the OECD were used to compare expenditure, workforce and health in: Australia, Portugal, the United Kingdom (UK) and the United States (US). Workforce policy context was explored. RESULTS: Public spending varied from less than 50% of gross domestic product in the US to over 80% in the UK. Australia had the highest life expectancy. Portugal has fewer nurses and more physicians. The Australian national health workforce planning agency has increased the scope for co-ordinated policy intervention. Portugal risks losing nurses through migration. In the UK, the economic crisis resulted in frozen pay, reduced employment, and reduced student nurses. In the US, there has been limited scope to develop a significant national nursing workforce policy approach, with a continuation of State based regulation adding to the complexity of the policy landscape. The US is the most developed in the use of nurses in advanced practice roles. Ageing of the workforce is likely to drive projected shortages in all countries. LIMITATIONS: There are differences as well as variation in the overall impact of the global financial crisis in these countries. CONCLUSION: Future supply of nurses in all four countries is vulnerable. IMPLICATIONS FOR NURSING AND HEALTH POLICY: Work force planning is absent or restricted in three of the countries. Scope for improved productivity through use of advanced nurse roles exists in all countries.

mRNP granules. Assembly, function, and connections with disease.

Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.

A multimodal physiotherapy programme plus deep water running for improving cancer-related fatigue and quality of life in breast cancer survivors.

The aim of the study was to assess the feasibility and effectiveness of aquatic-based exercise in the form of deep water running (DWR) as part of a multimodal physiotherapy programme (MMPP) for breast cancer survivors. A controlled clinical trial was conducted in 42 primary breast cancer survivors recruited from community-based Primary Care Centres. Patients in the experimental group received a MMPP incorporating DWR, 3 times a week, for an 8-week period. The control group received a leaflet containing instructions to continue with normal activities. Statistically significant improvements and intergroup effect size were found for the experimental group for Piper Fatigue Scale-Revised total score (d = 0.7, P = 0.001), as well as behavioural/severity (d = 0.6, P = 0.05), affective/meaning (d = 1.0, P = 0.001) and sensory (d = 0.3, P = 0.03) domains. Statistically significant differences between the experimental and control groups were also found for general health (d = 0.5, P < 0.05) and quality of life (d = 1.3, P < 0.05). All participants attended over 80% of sessions, with no major adverse events reported. The results of this study suggest MMPP incorporating DWR decreases cancer-related fatigue and improves general health and quality of life in breast cancer survivors. Further, the high level of adherence and lack of adverse events indicate such a programme is safe and feasible.

Stress-specific composition, assembly and kinetics of stress granules in Saccharomyces cerevisiae.

Eukaryotic cells respond to cellular stresses by the inhibition of translation and the accumulation of mRNAs in cytoplasmic RNA-protein (ribonucleoprotein) granules termed stress granules and P-bodies. An unresolved issue is how different stresses affect formation of messenger RNP (mRNP) granules. In the present study, we examine how sodium azide (NaN(3)), which inhibits mitochondrial respiration, affects formation of mRNP granules as compared with glucose deprivation in budding yeast. We observed that NaN(3) treatment inhibits translation and triggers formation of P-bodies and stress granules. The composition of stress granules induced by NaN(3) differs from that of glucose-deprived cells by containing eukaryotic initiation factor (eIF)3, eIF4A/B, eIF5B and eIF1A proteins, and by lacking the heterogeneous nuclear RNP (hnRNP) protein Hrp1. Moreover, in contrast with glucose-deprived stress granules, NaN(3)-triggered stress granules show different assembly rules, form faster and independently from P-bodies and dock or merge with P-bodies over time. Strikingly, addition of NaN(3) and glucose deprivation in combination, regardless of the order, always results in stress granules of a glucose deprivation nature, suggesting that both granules share an mRNP remodeling pathway. These results indicate that stress granule assembly, kinetics and composition in yeast can vary in a stress-specific manner, which we suggest reflects different rate-limiting steps in a common mRNP remodeling pathway.

HARLEY mitigates user bias and facilitates efficient quantification and co-localization analyses of foci in yeast fluorescence images.

Quantification of cellular structures in fluorescence microscopy data is a key means of understanding cellular function. Unfortunately, numerous cellular structures present unique challenges in their ability to be unbiasedly and accurately detected and quantified. In our studies on stress granules in yeast, users displayed a striking variation of up to 3.7-fold in foci calls and were only able to replicate their results with 62-78% accuracy, when re-quantifying the same images. To facilitate consistent results we developed HARLEY (Human Augmented Recognition of LLPS Ensembles in Yeast), a customizable software for detection and quantification of stress granules in S. cerevisiae. After a brief model training on ~ 20 cells the detection and quantification of foci is fully automated and based on closed loops in intensity contours, constrained only by the a priori known size of the features of interest. Since no shape is implied, this method is not limited to round features, as is often the case with other algorithms. Candidate features are annotated with a set of geometrical and intensity-based properties to train a kernel Support Vector Machine to recognize features of interest. The trained classifier is then used to create consistent results across datasets. For less ambiguous foci datasets, a parametric selection is available. HARLEY is an intuitive tool aimed at yeast microscopy users without much technical expertise. It allows batch processing of foci detection and quantification, and the ability to run various geometry-based and pixel-based colocalization analyses to uncover trends or correlations in foci-related data. HARLEY is open source and can be downloaded from https://github.com/lnilya/harley .

Self-efficacy to overcome exercise barriers in individuals with cancer-related lymphedema.

Although cancer survivors are recommended to exercise, they may lack confidence (self-efficacy) to be active. This research aimed to measure exercise barriers and related selfefficacy in individuals with cancer-related lymphedema as well as examine relationships between self-efficacy and participant characteristics. A cross-sectional survey was undertaken in individuals with cancer-related lymphedema using a validated 14-item Likert scale assessing self-efficacy to overcome general and lymphedema-specific exercise barriers (0%=not at all confident, 100%=extremely confident). Demographic, medical and lymphedema data were also collected. Of 109 participants (52% response), 79% (n=86) had breast cancer-related lymphedema. Participants were found to be moderately confident to exercise when facing general (48% [95% CI: 44, 52]) and lymphedema- specific exercise barriers (51% [95% CI: 47, 55]). Participants who were female, sedentary (p<0.05), had lymphedema for ≥2 years, and reported greater symptom burden (p<0.05) recorded lower general exercise barriers selfefficacy. Lower lymphedema-specific exercise barriers self-efficacy was reported by individuals who were sedentary, had cancers other than breast, and higher symptom burden. These findings suggest general and lymphedema- specific barriers challenge exercise confidence in those with cancer-related lymphedema, and strategies tailored to improve confidence in overcoming exercise barriers are warranted. Supporting individuals to be sufficiently active during and following cancer treatment should consider behavior change strategies tailored to the unique needs faced by individuals with lymphedema.

RNAs as Regulators of Cellular Matchmaking.

RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.