SMITten by the Speed of Splicing.

Splicing occurs co-transcriptionally, but relative rates of splicing and transcription that might reveal mechanisms of their coordinated control have remained mysterious. Now, Carrillo Oesterreich et al. show that the fastest introns are gone nearly as soon as the 3' splice site is transcribed and that introns have distinct splicing kinetics with respect to polymerase progression along the gene.

U1 snRNA rewrites the "script".

Expression of eukaryotic mRNAs requires the collaboration of a host of RNA processing factors acting upon the transcript. Berg et al. describe how a pre-mRNA splicing factor modulates the activity of the polyadenylation machinery to regulate mRNA length, with important implications for isoform expression in activated neuronal and immune cells.

The Exon Junction Complex: A Multitasking Guardian of the Transcriptome.

In a recent issue of Molecular Cell, Boehm et al. (2018), Blazquez et al. (2018), and Gonatopoulos-Pournatzis et al. (2018) uncover novel mechanisms by which the cell regulates splicing of cryptic splice sites and microexons.

The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae.

In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation. Here we show that splicing of intron-containing genes in cells lacking H2A.Z is impaired, particularly under suboptimal splicing conditions. Cells lacking H2A.Z are especially dependent on a functional U2 snRNP (small nuclear RNA [snRNA] plus associated proteins), as H2A.Z shows extensive genetic interactions with U2 snRNP-associated proteins, and RNA sequencing (RNA-seq) reveals that introns with nonconsensus branch points are particularly sensitive to H2A.Z loss. Consistently, H2A.Z promotes efficient spliceosomal rearrangements involving the U2 snRNP, as H2A.Z loss results in persistent U2 snRNP association and decreased recruitment of downstream snRNPs to nascent RNA. H2A.Z impairs transcription elongation, suggesting that spliceosome rearrangements are tied to H2A.Z's role in elongation. Depletion of disassembly factor Prp43 suppresses H2A.Z-mediated splice defects, indicating that, in the absence of H2A.Z, stalled spliceosomes are disassembled, and unspliced RNAs are released. Together, these data demonstrate that H2A.Z is required for efficient pre-mRNA splicing and indicate a role for H2A.Z in coordinating the kinetics of transcription elongation and splicing.

Posttranscriptional Regulation of Gcr1 Expression and Activity Is Crucial for Metabolic Adjustment in Response to Glucose Availability.

The transcription factor Gcr1 controls expression of over 75% of the genes in actively growing yeast. Yet despite its widespread effects, regulation of Gcr1 itself remains poorly understood. Here, we show that posttranscriptional Gcr1 regulation is nutrient dependent. Moreover, GCR1 RNA contains a long, highly conserved intron, which allows the cell to generate multiple RNA and protein isoforms whose levels change upon glucose depletion. Intriguingly, an isoform generated by intron retention is exported from the nucleus, and its translation is initiated from a conserved, intronic translation start site. Expression of gene products from both the spliced and unspliced RNAs is essential, as cells expressing only one isoform cannot adjust their metabolic program in response to environmental changes. Finally, we show that the Gcr1 proteins form dimers, providing an elegant mechanism by which this one gene, through its regulation, can perform the repertoire of transcriptional activities necessary for fine-tuned environmental response.

Mindfulness-Based Interdisciplinary Pain Management Program for Complex Polymorbid Pain in Veterans: A Randomized Controlled Trial.

OBJECTIVE: To evaluate the effects of interdisciplinary pain management on pain-related disability and opioid reduction in polymorbid pain patients with 2 or more comorbid psychiatric conditions. DESIGN: Two-arm randomized controlled trial testing a 3-week intervention with assessments at pre-treatment, post-treatment, 6-month, and 12-month follow-up. SETTING: Department of Veterans Affairs medical facility. PARTICIPANTS: 103 military veterans (N=103) with moderate (or worse) levels of pain-related disability, depression, anxiety, and/or posttraumatic stress disorder randomly assigned to usual care (n=53) and interdisciplinary pain management (n=50). All participants reported recent persistent opioid use. Trial participants had high levels of comorbid medical and mental health conditions. INTERVENTIONS: Experimental arm-a 3-week, interdisciplinary pain management program guided by a structured manual; comparison arm-usual care in a large Department of Veterans Affairs medical facility. MAIN OUTCOME MEASURES: Oswestry Disability Index (pain disability); Timeline Followback Interview and Medication Event Monitoring System (opioid use). Analysis used generalized linear mixed model with all posttreatment observations (posttreatment, 6-month follow-up, 12-month follow-up) entered simultaneously to create a single posttreatment effect. RESULTS: Veterans with polymorbid pain randomized to the interdisciplinary pain program reported significantly greater decreases in pain-related disability compared to veterans randomized to treatment as usual (TAU) at posttreatment, 6-month, and 12-month follow-up. Aggregated mean pain disability scores (ie, a summary effect of all posttreatment observations) for the interdisciplinary pain program were -9.1 (95% CI: -14.4, -3.7, P=.001) points lower than TAU. There was no difference between groups in the proportion of participants who resumed opioid use during trial participation (32% in both arms). CONCLUSION: These findings offer the first evidence of short- and long-term interdisciplinary pain management efficacy in polymorbid pain patients, but more work is needed to examine how to effectively decrease opioid use in this population.

How Were Wait Times for Priority Procedures in Canada Impacted during the First Six Months of the COVID-19 Pandemic?

In 2020, health systems across Canada responded to the COVID-19 pandemic by making rapid changes to reduce the risk of exposure for patients and staff and to allocate resources toward the treatment of COVID-19 patients. This included postponing surgical and diagnostic procedures. Data collected by the Canadian Institute for Health Information show that these interventions resulted in longer wait times across all provinces in April-September 2020 for scheduled surgical procedures, such as hip and knee replacements and cataract surgeries. The impact on wait times for cancer surgeries and diagnostic imaging varied by type of procedure and jurisdiction, while the wait times for hip fracture repair and radiation therapy were not impacted. Subsequent waves of the COVID-19 pandemic added to the initial backlog of procedures, and it will take time to assess the long-term impact of surgical and diagnostic imaging delays on patient outcomes and wait times.

The impact of care management for high-risk pediatric asthmatics on healthcare utilization.

INTRODUCTION: From 2011 to 2015, a series of quality improvement interventions were developed that targeted pediatric persistent asthmatics that included recalls for those overdue for care and access to specialist care. The objective of this study was to assess the impact on urgent care and emergency department visits and hospitalizations from enrollment into at least one intervention during the time period. METHODS: Persistent asthmatics were identified through electronic medical records, with patients having an asthma designation containing "persistent," asthma control containing "poor", and asthma risk being "high risk." Asthma utilization events were identified for these patients between January 1, 2011, and June 30, 2015 using ICD-9 diagnosis codes. Evaluation focused on differences in utilization for patients before and after receiving interventions through the use of logistic regression for each utilization outcome. RESULTS: The interventions were delivered to 1060 children out of a total of 2046 identified as having the persistent asthmatic criteria. The intervention group consisted of 389 (36.7%) moderate persistent asthmatics and 643 (60.7%) mild persistent asthmatics, with 976 (92.1%) identifying as a minority. Analysis of 60692 months of data showed patients who received the intervention were less likely to visit the urgent care (OR [0.80, 0.96]) or be hospitalized (OR [0.37, 0.75]) than those who did not receive any interventions. Adjustment for provider referral into the interventions resulted in slight changes for both hospitalizations (OR [0.38, 0.79]) and urgent care (OR [0.68, 0.94]). CONCLUSION: Children receiving interventions were less likely to be hospitalized or visit urgent care clinics.

The Experience of Primary Caregivers of Undocumented Immigrants with End-Stage Kidney Disease that Rely on Emergency-Only Hemodialysis.

BACKGROUND: Undocumented immigrants with end-stage kidney disease (ESKD) who rely on emergency-only hemodialysis (dialysis only after an emergency department evaluation) face psychosocial distress. Emergency-only hemodialysis (EOHD) is likely burdensome for primary caregivers as well. OBJECTIVE: To understand the experience of primary caregivers of undocumented immigrants with ESKD who rely on emergency-only hemodialysis. DESIGN, SETTING, AND PARTICIPANTS: A qualitative, semi-structured interview study to assess the experiences of primary caregivers of undocumented immigrants with ESKD at a safety-net hospital in Denver, Colorado from June 28 to November 15, 2018. Applied thematic analysis was used to analyze interviews. MAIN OUTCOMES AND MEASURES: Themes and subthemes. RESULTS: Twenty primary caregiver participants had a mean (SD) age of 46 (17), 13 (65%) were female, 7 (35%) were in an adult child caregiver role, and 13 (65%) were spouses. Five themes and 17 subthemes (in parentheses) were identified: (1) Caregiver role (providing emotional, physical, and economic support, advocacy and care navigation), (2) Caregiver burden (anxiety related to patient and personal death, emotional exhaustion and personal illness, struggle with finances, self-care and redefining relationship), (3) Unpredictable EOHD (acute episodes of illness that trigger emergency, stress when patient is denied dialysis, impact on work and sleep, and emotional relief after a session of EOHD), (4) Effect on children (dropping out or missing school, psychosocial distress, children assuming caregiver responsibilities, and juggling multi-generational caregiving of children), (5) Faith and appreciation (comfort in God and appreciation of healthcare). CONCLUSIONS AND RELEVANCE: Caregivers of undocumented immigrants with ESKD who rely upon EOHD experience caregiver burden and distress. The impact of EOHD on caregivers should be considered when assessing the consequences of excluding undocumented immigrants from public insurance programs.

Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing.

The spliceosome catalyzes the removal of introns from pre-messenger RNA (mRNA) and subsequent pairing of exons with remarkable fidelity. Some exons are known to be skipped or included in the mature mRNA in a cell type- or context-dependent manner (cassette exons), thereby contributing to the diversification of the human proteome. Interestingly, splicing is initiated (and sometimes completed) co-transcriptionally. Here, we develop a kinetic mathematical modeling framework to investigate alternative co-transcriptional splicing (CTS) and, specifically, the control of cassette exons' inclusion. We show that when splicing is co-transcriptional, default splice patterns of exon inclusion are more likely than when splicing is post-transcriptional, and that certain exons are more likely to be regulatable (i.e. cassette exons) than others, based on the exon-intron structure context. For such regulatable exons, transcriptional elongation rates may affect splicing outcomes. Within the CTS paradigm, we examine previously described hypotheses of co-operativity between splice sites of short introns (i.e. 'intron definition') or across short exons (i.e. 'exon definition'), and find that models encoding these faithfully recapitulate observations in the fly and human genomes, respectively.

Coordination of Care Could Improve: Canadian Results from the Commonwealth Fund International Health Policy Survey of Primary Care Physicians.

Care coordination is a critical component of a strong primary care system. The Commonwealth Fund (CMWF) 2019 International Health Policy Survey of Primary Care Physicians polled physicians in 11 countries, allowing international and pan-Canadian comparisons of physicians' perspectives in this area. Canadian physicians indicated that there was room for improvement in coordinating care with those outside their practice, particularly specialists, home-based care providers and social services. Opportunities may arise in learning from higher-performing CMWF countries and in adopting new information technologies that are growing methods of facilitating communication across care settings.

The chromatin remodeling complex Swi/Snf regulates splicing of meiotic transcripts in Saccharomyces cerevisiae.

Despite its relatively streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae, such as splicing of meiotic transcripts. Like other eukaryotes, S. cerevisiae undergoes a dramatic reprogramming of gene expression during meiosis, including regulated splicing of a number of crucial meiosis-specific RNAs. Splicing of a subset of these is dependent upon the splicing activator Mer1. Here we show a crucial role for the chromatin remodeler Swi/Snf in regulation of splicing of meiotic genes and find that the complex affects meiotic splicing in two ways. First, we show that Swi/Snf regulates nutrient-dependent downregulation of ribosomal protein encoding RNAs, leading to the redistribution of spliceosomes from this abundant class of intron-containing RNAs (the ribosomal protein genes) to Mer1-regulated transcripts. We also demonstrate that Mer1 expression is dependent on Snf2, its acetylation state and histone H3 lysine 9 acetylation at the MER1 locus. Hence, Snf2 exerts systems level control of meiotic gene expression through two temporally distinct mechanisms, demonstrating that it is a key regulator of meiotic splicing in S. cerevisiae. We also reveal an evolutionarily conserved mechanism whereby the cell redirects its energy from maintaining its translational capacity to the process of meiosis.

Chromatin-remodeling SWI/SNF complex regulates coenzyme Q6 synthesis and a metabolic shift to respiration in yeast.

Despite its relatively streamlined genome, there are many important examples of regulated RNA splicing in Saccharomyces cerevisiae Here, we report a role for the chromatin remodeler SWI/SNF in respiration, partially via the regulation of splicing. We find that a nutrient-dependent decrease in Snf2 leads to an increase in splicing of the PTC7 transcript. The spliced PTC7 transcript encodes a mitochondrial phosphatase regulator of biosynthesis of coenzyme Q6 (ubiquinone or CoQ6) and a mitochondrial redox-active lipid essential for electron and proton transport in respiration. Increased splicing of PTC7 increases CoQ6 levels. The increase in PTC7 splicing occurs at least in part due to down-regulation of ribosomal protein gene expression, leading to the redistribution of spliceosomes from this abundant class of intron-containing RNAs to otherwise poorly spliced transcripts. In contrast, a protein encoded by the nonspliced isoform of PTC7 represses CoQ6 biosynthesis. Taken together, these findings uncover a link between Snf2 expression and the splicing of PTC7 and establish a previously unknown role for the SWI/SNF complex in the transition of yeast cells from fermentative to respiratory modes of metabolism.

Identifying Subgroups of Adult Superutilizers in an Urban Safety-Net System Using Latent Class Analysis: Implications for Clinical Practice.

BACKGROUND: Patients with repeated hospitalizations represent a group with potentially avoidable utilization. Recent publications have begun to highlight the heterogeneity of this group. Latent class analysis provides a novel methodological approach to utilizing administrative data to identify clinically meaningful subgroups of patients to inform tailored intervention efforts. OBJECTIVE: The objective of the study was to identify clinically distinct subgroups of adult superutilizers. RESEARCH DESIGN: Retrospective cohort analysis. SUBJECTS: Adult patients who had an admission at an urban safety-net hospital in 2014 and 2 or more admissions within the preceding 12 months. MEASURES: Patient-level medical, mental health (MH) and substance use diagnoses, social characteristics, demographics, utilization and charges were obtained from administrative data. Latent class analyses were used to determine the number and characteristics of latent subgroups that best represented these data. RESULTS: In this cohort (N=1515), a 5-class model was preferred based on model fit indices, clinical interpretability and class size: class 1 (16%) characterized by alcohol use disorder and homelessness; class 2 (14%) characterized by medical conditions, MH/substance use disorders and homelessness; class 3 (25%) characterized primarily by medical conditions; class 4 (13%) characterized by more serious MH disorders, drug use disorder and homelessness; and class 5 (32%) characterized by medical conditions with some MH and substance use. Patient demographics, utilization, charges and mortality also varied by class. CONCLUSIONS: The overall cohort had high rates of multiple chronic medical conditions, MH, substance use disorders, and homelessness. However, the patterns of these conditions were different between subgroups, providing important information for tailoring interventions.

Safety and Quality of Care for Seniors Living with Dementia.

The number of Canadian seniors living with dementia is increasing because of the aging population and population growth. This article highlights various aspects of safety and quality of care for seniors with dementia as described in the Dementia in Canada digital report.

Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing.

When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based on transcription dynamics is widely recognized. Indeed, perturbation studies have reported that when transcription kinetics are perturbed genetically or pharmacologically splice patterns may change. However, whether kinetic control is contributing to the control of splicing within the normal range of physiological conditions remains unknown. We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in the structure and expression patterns of the genome and epigenome. To identify and then quantitatively relate multiple, simultaneous CTS determinants, we constructed a scalable mathematical model of the kinetic interplay of RNA synthesis and CTS and parameterized it with diverse next generation sequencing (NGS) data. We thus found a variety of CTS determinants encoded in vertebrate genomes and epigenomes, and that these combine variously for different groups of genes such as housekeeping versus regulated genes. Together, our findings indicate that the kinetic basis of splicing is functionally and physiologically relevant, and may meaningfully inform the analysis of genomic and epigenomic data to provide insights that are missed when relying on statistical approaches alone.

New Tools for Measuring and Improving Patient Safety in Canadian Hospitals.

The Canadian Institute for Health Information (CIHI) and the Canadian Patient Safety Institute (CPSI) have collaborated on a new measure of patient safety, along with a resource of evidence-informed practices. This measure captures four broad categories of harm in acute care hospitals, consisting of 31 clinical groups selected by clinicians. Analysis showed that harm was experienced in 1 of 18 hospital stays in Canada in 2014ߝ2015 and that no single category accounted for the majority of harmful events. Although CIHI and CPSI continue to work with hospitals and experts to further refine the methodology, the measure and associated Improvement Resource are useful new tools for monitoring and identifying harm, and have the potential to improve patient safety.

Aligning Strabismus Surgery with Duane Syndrome.

Initial consideration for surgical intervention tends to be resection and recession of affected muscles for strabismus. Resection of eye muscles in patients with Duane syndrome is often avoided because this increases retraction, thus decreasing eye movement and resulting binocular field of vision. Recession is the mainstay of surgical treatment in Duane syndrome to achieve straight eye alignment, increased binocular vision, and decreased head turn.