PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells

Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.

Cytoplasmic pool of U1 spliceosome protein SNRNP70 shapes the axonal transcriptome and regulates motor connectivity

Regulation of pre-mRNA splicing and polyadenylation plays a profound role in neurons by diversifying the proteome and modulating gene expression in response to physiological cues. Although most of the pre-mRNA processing is thought to occur in the nucleus, numerous splicing regulators are also found in neurites. Here, we show that U1-70K/SNRNP70, a component of the major spliceosome, localizes in RNA-associated granules in zebrafish axons. We identify the extra-nuclear SNRNP70 as an important regulator of motor axonal growth, nerve-dependent acetylcholine receptor (AChR) clustering, and neuromuscular synaptogenesis. This cytoplasmic pool has a protective role for a limited number of transcripts regulating their abundance and trafficking inside axons. Moreover, non-nuclear SNRNP70 regulates splice variants of transcripts such as agrin, thereby controlling synapse formation. Our results point to an unexpected, yet essential, function of non-nuclear SNRNP70 in axonal development, indicating a role of spliceosome proteins in cytoplasmic RNA metabolism during neuronal connectivity.

Cortical wiring by synapse type-specific control of local protein synthesis

Neurons use local protein synthesis to support their morphological complexity, which requires independent control across multiple subcellular compartments up to the level of individual synapses. We identify a signaling pathway that regulates the local synthesis of proteins required to form excitatory synapses on parvalbumin-expressing (PV+) interneurons in the mouse cerebral cortex. This process involves regulation of the TSC subunit 2 (Tsc2) by the Erb-B2 receptor tyrosine kinase 4 (ErbB4), which enables local control of messenger RNA {mRNA} translation in a cell type-specific and synapse type-specific manner. Ribosome-associated mRNA profiling reveals a molecular program of synaptic proteins downstream of ErbB4 signaling required to form excitatory inputs on PV+ interneurons. Thus, specific connections use local protein synthesis to control synapse formation in the nervous system.

Prematurely terminated intron-retaining mRNAs invade axons in SFPQ null-driven neurodegeneration and are a hallmark of ALS

Loss of SFPQ is a hallmark of motor degeneration in ALS and prevents maturation of motor neurons when occurring during embryogenesis. Here, we show that in zebrafish, developing motor neurons lacking SFPQ exhibit axon extension, branching and synaptogenesis defects, prior to degeneration. Subcellular transcriptomics reveals that loss of SFPQ in neurons produces a complex set of aberrant intron-retaining (IR) transcripts coding for neuron-specific proteins that accumulate in neurites. Some of these local IR mRNAs are prematurely terminated within the retained intron (PreT-IR). PreT-IR mRNAs undergo intronic polyadenylation, nuclear export, and localise to neurites in vitro and in vivo. We find these IR and PreT-IR mRNAs enriched in RNAseq datasets of tissue from patients with familial and sporadic ALS. This shared signature, between SFPQ-depleted neurons and ALS, functionally implicates SFPQ with the disease and suggests that neurite-centred perturbation of alternatively spliced isoforms drives the neurodegenerative process.

Functional Annotation of Custom Transcriptomes

Many eukaryotic genes can give rise to different alternative transcripts depending on stage of development, cell type, and physiological cues. Current transcriptome-wide sequencing technologies highlight the remarkable extent of this regulation in metazoans and allow for RNA isoforms to be profiled in increasingly small biological samples and with a growing confidence. Understanding biological functions of sample-specific transcripts is a major challenge in genomics and RNA processing fields. Here we describe simple bioinformatics workflows that facilitate this task by streamlining reference-guided annotation of novel transcripts. A key part of our protocol is the R package factR that rapidly matches custom-assembled transcripts to their likely host genes, deduces the sequence and domain structure of novel protein products, and predicts sensitivity of newly identified RNA isoforms to nonsense-mediated decay.

A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons

The RNA-binding protein SFPQ plays an important role in neuronal development and has been associated with several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease. Here, we report that loss of sfpq leads to premature termination of multiple transcripts due to widespread activation of previously unannotated cryptic last exons (CLEs). These SFPQ-inhibited CLEs appear preferentially in long introns of genes with neuronal functions and can dampen gene expression outputs and/or give rise to short peptides interfering with the normal gene functions. We show that one such peptide encoded by the CLE-containing epha4b mRNA isoform is responsible for neurodevelopmental defects in the sfpq mutant. The uncovered CLE-repressive activity of SFPQ is conserved in mouse and human, and SFPQ-inhibited CLEs are found expressed across ALS iPSC-derived neurons. These results greatly expand our understanding of SFPQ function and uncover a gene regulation mechanism with wide relevance to human neuropathologies.

The prevalence of hypersensitivity reactions to snake antivenoms administered in sultanah nur zahirah hospital from 2013 to 2016

INTRODUCTION

Snakebite is an important medical emergency. Antivenoms remain the only proven treatment for snake envenoming. However, the use of antivenom is associated with hypersensitivity reactions. The aims of this study were to determine the prevalence and types of hypersensitivity reactions and types and outcomes of pharmacological and non-pharmacological treatments for antivenom reactions among snakebite patients that received antivenoms.

METHODS

This was a 4-year cross-sectional study of snakebite patients from January 2013 to December 2016 in Hospital Sultanah Nur Zahirah (HSNZ), Terengganu. Data was extracted from the Pharmacy Record on the usage of antivenom and patients of snakebites treated with antivenom were identified. Data of patients were then obtained from the electronic medical records.' Demographic details, clinical features and characteristics of antivenom reactions of patients were recorded in standardized data collection forms and analyzed using chi-square or Mann- Whitney U tests.

RESULTS

Of the 44 patients who received antivenom, 24 (54.5%) developed hypersensitivity reaction. All patients developed reaction early. No patient developed delayed (serum-sickness) reaction. Of the 24 patients, 14 (58.3%) had moderate to severe hypersensitivity reaction and 9 (37.5%) patients had mild reactions. Only one (4.2%) patient presented with bradycardia.

CONCLUSION

The prevalence of early hypersensitivity reaction to snake antivenom in HSNZ was relatively high. Healthcare providers should be aware of the appropriate method of preparing and administering antivenom, and the management for acute hypersensitivity reactions. This will optimize the management of snakebite and ensure patient safety.

The effect of three-monthly albendazole treatment on Th2 responses: Differential effects on IgE and IL-5

Helminth parasites induce a strong Th2 response, characterized by high levels of IgE and elevated signature cytokines such as IL-5. As many global deworming programmes are underway, there is concern that this might lead to emergence of Th1-mediated pathologies when the counterbalancing helminth-induced Th2 response is absent. Therefore, we assessed the effect of deworming on Th2-mediated responses in a household-clustered randomized controlled trial in Indonesia. Total plasma IgE and whole-blood IL-5 responses to mitogen phytohaemagglutinin (PHA) were measured in 1494 and 682 subjects, respectively, at baseline, 9 and 21 months after three-monthly single-dose treatment with albendazole or placebo. Anthelmintic treatment did not result in complete removal of helminth infections in the community. However, treatment significantly decreased IgE levels in albendazole- compared to placebo-treated subjects. IL-5 responses to PHA were not significantly affected by anthelmintic treatment and tended to increase in albendazole-treated subjects, indicating that intensive treatment of helminth parasites has different outcomes on B-cell (IgE levels) and T-cell (IL-5) responses. The data shows that 2 years of deworming can have differential effects on responses typified as Th2-mediated, which needs to be taken into account when examining the impact of helminths on noncommunicable diseases.

Investigation into the suitability and accessibility of catering practices to inpatients from minority ethnic groups in Brent

BACKGROUND

The Borough of Brent has one of the largest ethnic minority populations in England, with a growing number of refugee communities from Africa and Europe. Two important issues to be considered when developing culturally sensitive services in the hospital (including food provision) are that practices meet the religious and cultural requirements of the population that the hospital serves and that staff are equipped with the skills to understand cultural differences in illness and treatment.

AIMS

To review accessibility and suitability of multicultural meals to minority ethnic communities across five hospital sites in Brent and determine the level of nursing staff knowledge of multicultural dietary competencies.

METHODS

One survey was completed in each of the five hospital sites to gather information about current catering practices. Two separate questionnaires obtained information of the level of inpatient satisfaction with multicultural meals amongst Hindu, Muslim, Caribbean and Jewish patient groups and knowledge of nursing staff about multicultural competencies. Community groups representing minority ethnic populations participated in focus groups to establish feedback about dietary requirements in hospitals.

RESULTS

Access to multicultural meals varied across hospital sites. Of 98 patients in the inpatient satisfaction survey, 74% were aware of the availability of multicultural meals with 51% of these patients not ordering any of the Asian vegetarian, Asian halal, Caribbean or kosher meals, citing satisfaction with European food as the main reason. Those ordering multicultural meals reported satisfaction most of the time (42%), satisfied most of the time (38%) and never satisfied (19%). The African Muslim group was the least satisfied with current halal meal provision. Forty-seven per cent of nurses questioned could accurately answer questions about multicultural dietary competencies.

CONCLUSIONS

Improvements could be made to improve accessibility and improve suitability of meal choices to inpatients from minority ethnic groups.

Osteonecrosis in HIV: a case-control study

BACKGROUND

Osteonecrosis (avascular necrosis) has been infrequently reported in HIV-infected patients. It is not known whether HIV itself is an independent risk factor for osteonecrosis.

METHODS

We identified 25 patients with osteonecrosis from 1984 to 1999 from a large county teaching hospital and two large practices in Dallas County that specialize in HIV-disease related therapy. A retrospective chart review was performed to evaluate potential risk factors for osteonecrosis. Each case was matched with two controls for HIV positive status and date of osteonecrosis diagnosis.

RESULTS

In the study, 22 of 25 (88%) case patients had at least one osteonecrosis risk factor compared with 24 of 50 (48%) controls, p =.003. The most common osteonecrosis risk factors were hyperlipidemia (32%), alcoholism (28%), pancreatitis (16%), corticosteroids (12%), and hypercoaguability (12%). Of the cases, 12% were idiopathic. Multiple joints were involved in 72% of cases. Four of the case patients compared with none of the controls received megesterol acetate before the diagnosis of osteonecrosis, p =.01. No significant differences were found between cases and controls with respect to liver function tests, testosterone levels, triglyceride levels, cholesterol levels, or CD4 cell counts. Saquinavir was independently associated with osteonecrosis, p <.05. However, no differences in overall use of protease inhibitors among cases and controls were noted: 79% versus 76%, respectively.

CONCLUSIONS

The increased incidence of osteonecrosis in HIV/AIDS may be due to an increased frequency of risk factors previously associated with osteonecrosis such as hyperlipidemia, corticosteroid use, alcohol abuse, and hypercoaguability. Use of protease inhibitors was not independently associated with osteonecrosis.

Pharmacological effects of the leaf-nosed viper snake (Eristocophis macmahoni) venom and its HPLC fractions

Crude venom from Eristocophis macmahoni was demonstrated to exert a potent inhibition of human blood platelet aggregation mediated by adenosine diphosphate (ADP), platelet activating factor (PAF) and arachidonic acid (AA). The venom caused lysis of the platelets, however, the red blood cells were not lysed by the venom. Substantial oedema was produced upon injection of the venom into the rat hind paw. Contrarily, the intraperitoneal injection of the venom to the rats caused an inhibition of the carrageenin-induced rat paw oedema. However, an 100% lethality within 24 h was observed with a dose of 40 mg/kg body weight. The venom was fractionated by reverse phase high pressure liquid chromatography (HPLC) and the fractions were analyzed for their effect on ADP-induced platelet aggregation. The fraction eluted at 15.5 min (20% acetonitrile concentration) exhibited an inhibitory effect of several-fold greater potency than that of the crude venom. Fractions eluted at 18.5 min (25.4% acetonitrile concentration) and onward showed a proaggregatory but insignificant effect. It is suggested that although the venom contains pro aggregatory components, inhibition of platelet aggregation seems to be its predominant activity.

Effect of the crude extract of Cestrum parqui on carrageenin-induced rat paw oedema and aggregation of human blood platelets

An extract of Cestrum parqui aerial parts in methanol:water (1:1) showed inhibition of carrageenin-induced oedema. The aggregation of human blood platelets induced by adenosine diphosphate and platelet activating factor was also inhibited (IC(50)s were 3 and 2 mg/mL, respectively). On the contrary, the extract did not inhibit arachidonic acid-mediated platelet aggregation.

Lethal congenital muscular dystrophy in two sibs with arthrogryposis multiplex: new entity or variant of cobblestone lissencephaly syndrome?

We report on two sisters of first degree cousin parents who were born with severe hypotonia, arthrogryposis multiplex congenita (AMC) and dysmorphic features consistent with the fetal akinesia/hypokinesia sequence. They needed assisted ventilation and each died at the age of 5 months. Both had type II lissencephaly (cobblestone lissencephaly) which was visualized by magnetic resonance imaging (MRI) in the proband. Ophthalmic evaluation revealed no ocular malformations in either of them. Brain auditory evoked potentials (BAEP) revealed bilateral severe sensorineural hearing loss in the proband, whereas an MRI-guided open muscle biopsy of the sartorius muscle (the only remaining thigh muscle) showed features of muscular dystrophy. Immunohistochemistry revealed normal dystrophin, dystrophin-associated glycoproteins (DAG) and merosin. Certain clinical and pathological features distinguish the disease seen in these sisters from reported isolated cases where lethal AMC was associated with brain dysplasia and from the main syndromes of congenital muscular dystrophy/cobblestone lissencephaly. Differences from the Walker-Warburg syndrome, which simulates it in severity, included the absence of severe hydrocephalus, normal creatine kinase (for age) and minimal (mainly periventricular) white matter abnormalities. The findings suggest either an independent entity, in the studied family, or an allelic variation of the cobblestone lissencephaly (type II lissencephaly) syndrome.

Intracranial epidural tuberculoma presenting as a scalp swelling

The first case of an intracranial epidural tuberculoma with the absence of dural and brain involvement in a 27-year-old woman is presented. The possible pathogenesis of this unique lesion is discussed.

CT findings in paranasal aspergillosis

Computed tomographic (CT) scan of eight cases of paranasal sinus aspergillosis were reviewed. Different CT patterns were observed such as areas of high densities, linear interlacing network of high density, radiolucent thin rim periphery to the masses, calcification, expansion of involved sinuses and bone erosion. Two cases of invasive type showed extension beyond the sinuses into the orbit and intracranially simulating a malignant tumour. The findings are similar to those described by previous authors. The differential diagnosis is also discussed.