Efficient, specific, and combinatorial control of endogenous exon splicing with dCasRx-RBM25.

Efficient targeted control of splicing is a major goal of functional genomics and therapeutic applications. Guide (g)RNA-directed, deactivated (d)Cas CRISPR enzymes fused to splicing effectors represent a promising strategy due to the flexibility of these systems. However, efficient, specific, and generalizable activation of endogenous exons using this approach has not been previously reported. By screening over 300 dCasRx-splicing factor fusion proteins tethered to splicing reporters, we identify dCasRx-RBM25 as a potent activator of exons. Moreover, dCasRx-RBM25 efficiently activates the splicing of ∼90% of targeted endogenous alternative exons and displays high on-target specificity. Using gRNA arrays for combinatorial targeting, we demonstrate that dCasRx-RBM25 enables multiplexed activation and repression of exons. Using this feature, the targeting of neural-regulated exons in Ptpb1 and Puf60 in embryonic stem cells reveals combinatorial effects on downstream alternative splicing events controlled by these factors. Collectively, our results enable versatile, combinatorial exon-resolution functional assays and splicing-directed therapeutic applications.

Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors.

Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.

Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis.

Alternative splicing (AS) is a critical regulatory layer; yet, factors controlling functionally coordinated splicing programs during developmental transitions are poorly understood. Here, we employ a screening strategy to identify factors controlling dynamic splicing events important for mammalian neurogenesis. Among previously unknown regulators, Rbm38 acts widely to negatively control neural AS, in part through interactions mediated by the established repressor of splicing, Ptbp1. Puf60, a ubiquitous factor, is surprisingly found to promote neural splicing patterns. This activity requires a conserved, neural-differential exon that remodels Puf60 co-factor interactions. Ablation of this exon rewires distinct AS networks in embryonic stem cells and at different stages of mouse neurogenesis. Single-cell transcriptome analyses further reveal distinct roles for Rbm38 and Puf60 isoforms in establishing neuronal identity. Our results describe important roles for previously unknown regulators of neurogenesis and establish how an alternative exon in a widely expressed splicing factor orchestrates temporal control over cell differentiation.

Automating sedation state assessments using natural language processing.

INTRODUCTION: Common goals for procedural sedation are to control pain and ensure the patient is not moving to an extent that is impeding safe progress or completion of the procedure. Clinicians perform regular assessments of the adequacy of procedural sedation in accordance with these goals to inform their decision-making around sedation titration and also for documentation of the care provided. Natural language processing could be applied to real-time transcriptions of audio recordings made during procedures in order to classify sedation states that involve movement and pain, which could then be integrated into clinical documentation systems. The aim of this study was to determine whether natural language processing algorithms will work with sufficient accuracy to detect sedation states during procedural sedation. DESIGN: A prospective observational study was conducted. METHODS: Audio recordings from consenting participants undergoing elective procedures performed in the interventional radiology suite at a large academic hospital were transcribed using an automated speech recognition model. Sentences of transcribed text were used to train and evaluate several different NLP pipelines for a text classification task. The NLP pipelines we evaluated included a simple Bag-of-Words (BOW) model, an ensemble architecture combining a linear BOW model and a "token-to-vector" (Tok2Vec) component, and a transformer-based architecture using the RoBERTa pre-trained model. RESULTS: A total of 15,936 sentences from transcriptions of 82 procedures was included in the analysis. The RoBERTa model achieved the highest performance among the three models with an area under the ROC curve (AUC-ROC) of 0.97, an F1 score of 0.87, a precision of 0.86, and a recall of 0.89. The Ensemble model showed a similarly high AUC-ROC of 0.96, but lower F1 score of 0.79, precision of 0.83, and recall of 0.77. The BOW approach achieved an AUC-ROC of 0.97 and the F1 score was 0.7, precision was 0.83 and recall was 0.66. CONCLUSION: The transformer-based architecture using the RoBERTa pre-trained model achieved the best classification performance. Further research is required to confirm the that this natural language processing pipeline can accurately perform text classifications with real-time audio data to allow for automated sedation state assessments. CLINICAL RELEVANCE: Automating sedation state assessments using natural language processing pipelines would allow for more timely documentation of the care received by sedated patients, and, at the same time, decrease documentation burden for clinicians. Downstream applications can also be generated from the classifications, including for example real-time visualizations of sedation state, which may facilitate improved communication of the adequacy of the sedation between clinicians, who may be performing supervision remotely. Also, accumulation of sedation state assessments from multiple procedures may reveal insights into the efficacy of particular sedative medications or identify procedures where the current approach for sedation and analgesia is not optimal (i.e. a significant amount of time spent in "pain" or "movement" sedation states).

Mechanisms underlying linear ubiquitination and implications in tumorigenesis and drug discovery.

Linear ubiquitination is a distinct type of ubiquitination that involves attaching a head-to-tail polyubiquitin chain to a substrate protein. Early studies found that linear ubiquitin chains are essential for the TNFα- and IL-1-mediated NF-κB signaling pathways. However, recent studies have discovered at least sixteen linear ubiquitination substrates, which exhibit a broader activity than expected and mediate many other signaling pathways beyond NF-κB signaling. Dysregulation of linear ubiquitination in these pathways has been linked to many types of cancers, such as lymphoma, liver cancer, and breast cancer. Since the discovery of linear ubiquitin, extensive effort has been made to delineate the molecular mechanisms of how dysregulation of linear ubiquitination causes tumorigenesis and cancer development. In this review, we highlight newly discovered linear ubiquitination-mediated signaling pathways, recent advances in the role of linear ubiquitin in different types of cancers, and the development of linear ubiquitin inhibitors. Video Abstract.

Opioid prescribing among new users for non-cancer pain in the USA, Canada, UK, and Taiwan: A population-based cohort study.

BACKGROUND: The opioid epidemic in North America has been driven by an increase in the use and potency of prescription opioids, with ensuing excessive opioid-related deaths. Internationally, there are lower rates of opioid-related mortality, possibly because of differences in prescribing and health system policies. Our aim was to compare opioid prescribing rates in patients without cancer, across 5 centers in 4 countries. In addition, we evaluated differences in the type, strength, and starting dose of medication and whether these characteristics changed over time. METHODS AND FINDINGS: We conducted a retrospective multicenter cohort study of adults who are new users of opioids without prior cancer. Electronic health records and administrative health records from Boston (United States), Quebec and Alberta (Canada), United Kingdom, and Taiwan were used to identify patients between 2006 and 2015. Standard dosages in morphine milligram equivalents (MMEs) were calculated according to The Centers for Disease Control and Prevention. Age- and sex-standardized opioid prescribing rates were calculated for each jurisdiction. Of the 2,542,890 patients included, 44,690 were from Boston (US), 1,420,136 Alberta, 26,871 Quebec (Canada), 1,012,939 UK, and 38,254 Taiwan. The highest standardized opioid prescribing rates in 2014 were observed in Alberta at 66/1,000 persons compared to 52, 51, and 18/1,000 in the UK, US, and Quebec, respectively. The median MME/day (IQR) at initiation was highest in Boston at 38 (20 to 45); followed by Quebec, 27 (18 to 43); Alberta, 23 (9 to 38); UK, 12 (7 to 20); and Taiwan, 8 (4 to 11). Oxycodone was the first prescribed opioid in 65% of patients in the US cohort compared to 14% in Quebec, 4% in Alberta, 0.1% in the UK, and none in Taiwan. One of the limitations was that data were not available from all centers for the entirety of the 10-year period. CONCLUSIONS: In this study, we observed substantial differences in opioid prescribing practices for non-cancer pain between jurisdictions. The preference to start patients on higher MME/day and more potent opioids in North America may be a contributing cause to the opioid epidemic.

Maternal focal atrial tachycardia during pregnancy: A systematic review.

INTRODUCTION: The presentation and optimal management of maternal focal atrial tachycardia (AT) during pregnancy are unknown. The objective of this study is to conduct a comprehensive summary of the existing evidence. METHODS AND RESULTS: A systematic review of all reported cases of maternal focal AT during pregnancy was performed. The primary search queried PubMed using the MeSH terms "supraventricular tachycardia" and "pregnancy." A stepwise ancillary search included article bibliographies, citations listed by the Google internet search engine, and PubMed using the MeSH terms "atrial tachycardia" and "pregnancy." In total, 28 citations that described 32 patients were retrieved. A case from our institution was added. Detailed information was available for 30 patients. Clinical characteristics at presentation included a mean ± standard deviation of 28.3 ± 5.7 years for maternal age and 24.6 ± 7.7 weeks for gestation age. Suspected tachycardia-induced cardiomyopathy was present in 20 of 30 (67%) patients and left ventricular ejection fraction improved in 15 of 15 (100%) patients with follow-up measurements. Medication failure was common. Focal AT resolved spontaneously after delivery in eight of nine (89%) patients treated with only medications. Automaticity was suggested by discrete electrograms at sites of origin and lack of reported inducibility and termination with programmed stimulation in all patients who underwent electrophysiology studies. There were nine cases of successful catheter ablation with zero fluoroscopy since 2010. CONCLUSIONS: Automaticity is the dominant mechanism for patients with maternal focal AT during pregnancy. Catheter ablation with zero fluoroscopy is an emerging therapy for medically refractory cases.

Toward a Synthetic Yeast Endosymbiont with a Minimal Genome.

Based on the endosymbiotic theory, one of the key events that occurred during mitochondrial evolution was an extensive loss of nonessential genes from the protomitochondrial endosymbiont genome and transfer of some of the essential endosymbiont genes to the host nucleus. We have developed an approach to recapitulate various aspects of endosymbiont genome minimization using a synthetic system consisting of Escherichia coli endosymbionts within host yeast cells. As a first step, we identified a number of E. coli auxotrophs of central metabolites that can form viable endosymbionts within yeast cells. These studies provide a platform to identify nonessential biosynthetic pathways that can be deleted in the E. coli endosymbionts to investigate the evolutionary adaptations in the host and endosymbiont during the evolution of mitochondria.

Enhancing protein stability with extended disulfide bonds.

Disulfide bonds play an important role in protein folding and stability. However, the cross-linking of sites within proteins by cysteine disulfides has significant distance and dihedral angle constraints. Here we report the genetic encoding of noncanonical amino acids containing long side-chain thiols that are readily incorporated into both bacterial and mammalian proteins in good yields and with excellent fidelity. These amino acids can pair with cysteines to afford extended disulfide bonds and allow cross-linking of more distant sites and distinct domains of proteins. To demonstrate this notion, we preformed growth-based selection experiments at nonpermissive temperatures using a library of random ß-lactamase mutants containing these noncanonical amino acids. A mutant enzyme that is cross-linked by one such extended disulfide bond and is stabilized by ∼9 °C was identified. This result indicates that an expanded set of building blocks beyond the canonical 20 amino acids can lead to proteins with improved properties by unique mechanisms, distinct from those possible through conventional mutagenesis schemes.

Enhancing Protein Stability with Genetically Encoded Noncanonical Amino Acids.

The ability to add noncanonical amino acids to the genetic code may allow one to evolve proteins with new or enhanced properties using a larger set of building blocks. To this end, we have been able to select mutant proteins with enhanced thermal properties from a library of E. coli homoserine O-succinyltransferase ( metA) mutants containing randomly incorporated noncanonical amino acids. Here, we show that substitution of Phe 21 with ( p-benzoylphenyl)alanine (pBzF), increases the melting temperature of E. coli metA by 21 °C. This dramatic increase in thermal stability, arising from a single mutation, likely results from a covalent adduct between Cys 90 and the keto group of pBzF that stabilizes the dimeric form of the enzyme. These experiments show that an expanded genetic code can provide unique solutions to the evolution of proteins with enhanced properties.

New-onset left bundle branch block-associated idiopathic nonischemic cardiomyopathy and time from diagnosis to cardiac resynchronization therapy: The NEOLITH II study.

BACKGROUND: The optimal timing for cardiac resynchronization therapy (CRT) after diagnosis of new-onset left bundle branch block (LBBB)-associated idiopathic nonischemic cardiomyopathy (NICM) and treatment with guideline-directed medical therapy (GDMT) is unknown. The purpose of this study was to describe relationships between time from diagnosis to CRT and outcomes in new-onset LBBB-associated idiopathic NICM with left ventricular ejection fraction (LVEF) ≤35%. METHODS: A retrospective cohort study examined associations between time from diagnosis to CRT (≤9 months vs >9 months) and clinical and echocardiographic outcomes. RESULTS: In 123 subjects with LBBB-associated idiopathic NICM, time from diagnosis to CRT was ≤9 months in 60 (49%) subjects and 9 months in 63 (51%) subjects. Clinical outcomes were similar for those implanted ≤9 months versus >9 months for adverse clinical events (hazard ratio [HR], 0.85; 95% confidence interval [CI], 0.41-1.78; P = 0.67) and all-cause mortality (HR, 0.57; 95% CI, 0.19-1.70; P = 0.31). Multivariable analyses demonstrated similar results. In 105 subjects with post-CRT echocardiograms, LVEF improvement to >35% was more likely in those implanted ≤9 months when compared to >9 months (odds ratio [OR], 3.53; 95% CI, 1.32-9.46; P = 0.01). This association persisted in the final multivariable model adjusted for age at diagnosis, sex, QRS duration, post-GDMT LVEF, and time from CRT to post-CRT echocardiogram (OR, 5.10; 95% CI, 1.71-15.22; P = 0.004). CONCLUSION: In LBBB-associated idiopathic NICM, earlier CRT implantation was associated with more favorable cardiac remodeling. Delaying CRT may miss a critical period to halt and reverse progressive myocardial damage.

Second-line therapy after nab-paclitaxel plus gemcitabine or after gemcitabine for patients with metastatic pancreatic cancer.

BACKGROUND: This exploratory analysis evaluated second-line (2L) therapy for metastatic pancreatic cancer in a large phase 3 trial (MPACT). METHODS: Patients who received first-line (1L) nab-paclitaxel+gemcitabine (nab-P+Gem) or Gem were assessed for survival based on 2L treatment received. Multivariate analyses tested influence of treatment effect and prognostic factors on survival. RESULTS: The majority of 2L treatments (267 out of 347, 77%) contained a fluoropyrimidine (5-fluorouracil or capecitabine). Median total survival (1L randomisation to death) for patients who received 2L treatment after 1L nab-P+Gem vs Gem alone was 12.8 vs 9.9 months (P=0.015). Median total survival for patients with a fluoropyrimidine-containing 2L therapy after nab-P+Gem vs Gem was 13.5 vs 9.5 months (P=0.012). Median 2L survival (duration from start of 2L therapy to death) was 5.3 vs 4.5 months for nab-P+Gem vs Gem, respectively (P=0.886). Factors significantly associated with longer post-1L survival by multivariate analyses included 1L nab-P+Gem, receiving 2L treatment, longer 1L progression-free survival, and Karnofsky performance status⩾70 and neutrophil-to-lymphocyte ratio⩽5 at the end of 1L treatment. CONCLUSIONS: These findings support the use of 2L therapy for patients with metastatic pancreatic cancer. Fluoropyrimidine-containing treatment after 1L nab-P+Gem is an active regimen with significant clinical effect.

Efficacy and safety profile of nab-paclitaxel plus gemcitabine in patients with metastatic pancreatic cancer treated to disease progression: a subanalysis from a phase 3 trial (MPACT).

BACKGROUND: The phase 3 MPACT trial in patients with metastatic pancreatic cancer demonstrated superior efficacy of nab-paclitaxel (nab-P) + gemcitabine (Gem) vs Gem monotherapy for all endpoints examined including overall survival, the primary endpoint. In the MPACT trial, patients were treated until progressive disease (PD) or unacceptable toxicity. The current exploratory analysis investigated outcomes of patients from the MPACT trial who were treated until PD, in order to understand how to maximize treatment benefit from nab-P + Gem. METHODS: The trial design has been described in detail previously. Progressive disease was determined by the investigator on the basis of radiological imaging. RESULTS: Among patients who were treated until PD, overall survival was significantly longer for those who received nab-P + Gem vs Gem (median, 9.8 vs 7.5 months; P < 0.001). Independently assessed progression-free survival and overall response rate were significantly greater among patients in the treatment-to-PD cohort who received nab-P + Gem compared with Gem (P < 0.001 for each). Although not compared statistically, patients who were treated until PD received greater treatment exposure and experienced more favourable efficacy than the intent-to-treat population of the MPACT trial. Among patients who were treated with nab-P + Gem until PD, > 50 % went on to receive a subsequent therapy. The safety profile for patients treated until PD was similar to what was reported in the overall MPACT trial. CONCLUSION: The nab-P + Gem regimen is an active first-line treatment option; most patients were treated until PD, and this exposure was associated with improved efficacy outcomes. Prolonged first-line treatment exposure and ability to receive subsequent therapies likely contributed to the improved survival among these patients. Our data highlight the importance of managing adverse events and indicate that patients should be treated until PD when possible. TRIAL REGISTRATION: ClinicalTrials.gov NCT00844649 (MPACT trial); Registration date of this prospective phase III trial: February 13, 2009; current exploratory subanalysis was conducted retrospectively.

Genetic Incorporation of a Reactive Isothiocyanate Group into Proteins.

Methods for the site-specific modification of proteins are useful for introducing biological probes into proteins and engineering proteins with novel activities. Herein, we genetically encode a novel noncanonical amino acid (ncAA) that contains an aryl isothiocyanate group which can form stable thiourea crosslinks with amines under mild conditions. We show that this ncAA (pNCSF) allows the selective conjugation of proteins to amine-containing molecular probes through formation of a thiourea bridge. pNCSF was also used to replace a native salt bridge in myoglobin with an intramolecular crosslink to a proximal Lys residue, leading to increased thermal stability. Finally, we show that pNCSF can form stable intermolecular crosslinks between two interacting proteins.

Implementation of a Blended-Learning Perioperative Nursing Education Program in Canada.

Governmental COVID-19 mandates in Ontario, Canada, resulted in a backlog of perioperative procedures. Organization leaders were required to expand services after the pandemic; however, the ongoing nursing shortage and college-based structure of perioperative education programs complicated their response. In 2021, we developed an in-house perioperative education program using a blended-learning theory comprising online modules and videos, skills laboratory sessions, and clinical placement experiences. Nurses were required to apply for the program and remain employed at the facility for two years. Program evaluations showed that the novice nurses felt confident when beginning clinical experiences and preceptors believed the nurses were prepared for practice. Sixteen of 19 participants successfully completed the program, which helped resolve the staffing shortage. Novice nurses may benefit from a shadowing experience before applying for this type of program. Leaders in nonperioperative specialties should consider an in-house education program to help meet staffing needs in their areas.

Pamrevlumab, a Fully Human Monoclonal Antibody Targeting Connective Tissue Growth Factor, for Non-Ambulatory Patients with Duchenne Muscular Dystrophy.

BACKGROUND: Duchenne muscular dystrophy (DMD) is a neuromuscular disease stemming from dystrophin gene mutations. Lack of dystrophin leads to progressive muscle damage and replacement of muscle with fibrotic and adipose tissue. Pamrevlumab (FG-3019), a fully human monoclonal antibody that binds to connective tissue growth factor (CTGF), is in Phase III development for treatment of DMD and other diseases. METHODS: MISSION (Study 079; NCT02606136) was an open-label, Phase II, single-arm trial of pamrevlumab in 21 non-ambulatory patients with DMD (aged≥12 years, receiving corticosteroids) who received 35-mg/kg intravenous infusions every 2 weeks for 2 years. The primary endpoint was change from baseline in percent predicted forced vital capacity (ppFVC). Secondary endpoints included other pulmonary function tests, upper limb function and strength assessments, and changes in upper arm fat and fibrosis scores on magnetic resonance imaging. RESULTS: Fifteen patients completed the trial. Annual change from baseline (SE) in ppFVC was -4.2 (0.7) (95% CI -5.5, -2.8). Rate of decline in ppFVC in pamrevlumab-treated patients was slower than observed in historical published trials of non-ambulatory patients. MISSION participants experienced slower-than-anticipated muscle function declines compared with natural history and historical published trials of non-ambulatory patients with DMD. Pamrevlumab was well-tolerated. Treatment-emergent adverse events were mild to moderate, and none led to study discontinuation. CONCLUSIONS: nti-CTGF therapy with pamrevlumab represents a potential treatment for DMD. The lack of internal control group limits the results.

Excitation Intensity-Dependent Quantum Yield of Semiconductor Nanocrystals.

One of the key phenomena that determine the fluorescence of nanocrystals is the nonradiative Auger-Meitner recombination of excitons. This nonradiative rate affects the nanocrystals' fluorescence intensity, excited state lifetime, and quantum yield. Whereas most of the above properties can be directly measured, the quantum yield is the most difficult to assess. Here we place semiconductor nanocrystals inside a tunable plasmonic nanocavity with subwavelength spacing and modulate their radiative de-excitation rate by changing the cavity size. This allows us to determine absolute values of their fluorescence quantum yield under specific excitation conditions. Moreover, as expected considering the enhanced Auger-Meitner rate for higher multiple excited states, increasing the excitation rate reduces the quantum yield of the nanocrystals.

Metabolome-wide Mendelian randomization characterizes heterogeneous and shared causal effects of metabolites on human health.

Metabolites are small molecules that are useful for estimating disease risk and elucidating disease biology. Nevertheless, their causal effects on human diseases have not been evaluated comprehensively. We performed two-sample Mendelian randomization to systematically infer the causal effects of 1,099 plasma metabolites measured in 6,136 Finnish men from the METSIM study on risk of 2,099 binary disease endpoints measured in 309,154 Finnish individuals from FinnGen. We identified evidence for 282 causal effects of 70 metabolites on 183 disease endpoints (FDR<1%). We found 25 metabolites with potential causal effects across multiple disease domains, including ascorbic acid 2-sulfate affecting 26 disease endpoints in 12 disease domains. Our study suggests that N-acetyl-2-aminooctanoate and glycocholenate sulfate affect risk of atrial fibrillation through two distinct metabolic pathways and that N-methylpipecolate may mediate the causal effect of N6, N6-dimethyllysine on anxious personality disorder. This study highlights the broad causal impact of plasma metabolites and widespread metabolic connections across diseases.

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.

Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.