Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity.

Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential for biological interpretation of cell processes. Here, we present TRIAGE-Cluster which uses genome-wide epigenetic data from diverse bio-samples to identify genes demarcating cell diversity in scRNA-seq data. By integrating patterns of repressive chromatin deposited across diverse cell types with weighted density estimation, TRIAGE-Cluster determines cell type clusters in a 2D UMAP space. We then present TRIAGE-ParseR, a machine learning method which evaluates gene expression rank lists to define gene groups governing the identity and function of cell types. We demonstrate the utility of this two-step approach using atlases of in vivo and in vitro cell diversification and organogenesis. We also provide a web accessible dashboard for analysis and download of data and software. Collectively, genome-wide epigenetic repression provides a versatile strategy to define cell diversity and study gene regulation of scRNA-seq data.

Comparative safety of biologic versus conventional synthetic DMARDs in rheumatoid arthritis with COPD: a real-world population study.

OBJECTIVES: Abatacept, a biologic DMARD, was associated with respiratory adverse events in a small subgroup of RA patients with chronic obstructive pulmonary disease (COPD) in a trial. Whether this potential risk is specific to abatacept or extends to all biologics and targeted synthetic DMARDs (tsDMARDs) is unclear. We assessed the risk of adverse respiratory events associated with biologic and tsDMARDs compared with conventional synthetic DMARDs (csDMARDs) among RA patients with concomitant COPD in a large, real-world cohort. METHODS: We used a prevalent new-user design to study RA patients with COPD in the US-based MarketScan databases. New users of biologic DMARDs and/or tsDMARDs were matched on time-conditional propensity scores to new users of csDMARDs. Adverse respiratory events were estimated using Cox models comparing current use of biologic/tsDMARDs with csDMARDs. RESULTS: The cohort included 7424 patients initiating biologic/tsDMARDs and 7424 matched patients initiating csDMARDs. The adjusted hazard ratio of hospitalized COPD exacerbation comparing biologic/tsDMARD vs csDMARD was 0.76 (95% CI: 0.55, 1.06), while it was 1.02 (95% CI: 0.82, 1.27) for bronchitis, 1.21 (95% CI: 0.92, 1.58) for hospitalized pneumonia or influenza and 0.99 (95% CI: 0.87, 1.12) for outpatient pneumonia or influenza. The hazard ratio of the combined end point of COPD exacerbation, bronchitis and hospitalized pneumonia or influenza was 1.04 (95% CI: 0.89, 1.21). CONCLUSION: In this large, real-world comparative safety study, biologic and tsDMARDs, including abatacept, were not associated with an increased risk of adverse respiratory events when compared with csDMARDs in patients with RA and COPD.

Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm.

Wnt signaling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single-cell RNA sequencing of hiPSCs responding to a dose escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified the small-molecule drug, tranilast. We found that tranilast synergistically activates Wnt signaling to promote cardiac lineage differentiation, which we validate by in vitro analysis of hiPSC differentiation and in vivo analysis of developing quail embryos. Our study provides an integrated workflow that links experimental datasets, prediction models, and small-molecule databases to identify drug-like compounds that control cell differentiation.

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function.

Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced pluripotent stem cell-derived cardiomyocytes to evaluate the genomic regulatory basis of the non-DNA-binding homeodomain protein HOPX. We show that HOPX interacts with and controls cardiac genes and enhancer networks associated with diverse aspects of heart development. Using perturbation studies in vitro, we define how upstream cell growth and proliferation control HOPX transcription to regulate cardiac gene programs. We then use cell, organoid, and zebrafish regeneration models to demonstrate that HOPX-regulated gene programs control cardiomyocyte function in development and disease. Collectively, this study mechanistically links cell signaling pathways as upstream regulators of HOPX transcription to control gene programs underpinning cardiomyocyte identity and function.

Trends in cardiac rehabilitation rates among patients admitted for acute heart failure in Japan, 2009-2020.

OBJECTIVES: To describe inpatient and outpatient cardiac rehabilitation (CR) utilization patterns over time and by subgroups among patients admitted for acute heart failure (AHF) in Japan. BACKGROUND: Cardiac rehabilitation (CR) is a crucial secondary prevention strategy for patients with heart failure. While the number of older patients with AHF continues to rise, trends in inpatient and outpatient CR participation following AHF in Japan have not been described to date. METHODS: We conducted a retrospective cohort study of adult patients hospitalized for AHF in Japan between April 2008 and December 2020. Using data from the Medical Data Vision database, we measured trends in inpatient and outpatient CR participation following AHF. Descriptive analyses and summary statistics for AHF patients by CR participation status were reported. RESULTS: The analytic cohort included 88,052 patients. Among these patients, 37,810 (42.9%) participated in inpatient and/or outpatient CR. Of those, 36,431 (96.4%) participated in inpatient CR only and 1,277 (3.4%) participated in both inpatient and outpatient CR. Rates of inpatient CR rose more than 6-fold over the study period, from 9% in 2009 to 55% in 2020, whereas rates of outpatient CR were consistently low. CONCLUSIONS: The rate of inpatient CR participation among AHF patients in Japan rose dramatically over a 12-year period, whereas outpatient CR following AHF was vastly underutilized. Further study is needed to assess the clinical effectiveness of inpatient CR and to create infrastructure and incentives to support and encourage outpatient CR.

A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification.

AIMS: The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The human lncRNA CARMEN, which is known to dictate specification toward the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced isoforms. METHODS AND RESULTS: The CARMEN locus can be manipulated to direct human primary cardiac precursor cells (CPCs) into specific cardiovascular fates. Investigating CARMEN isoform usage in differentiating CPCs represents therefore a unique opportunity to uncover isoform-specific functions in lncRNAs. Here, we identify one CARMEN isoform, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. CONCLUSIONS: These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA. They further demonstrated the crucial importance of the lncRNA isoform CARMEN-201 in SMC specification during heart development.

Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1-3 in mesendoderm cell differentiation.

Histone deacetylases (HDACs) are a class of enzymes that control chromatin state and influence cell fate. We evaluated the chromatin accessibility and transcriptome dynamics of zinc-containing HDACs during cell differentiation in vitro coupled with chemical perturbation to identify the role of HDACs in mesendoderm cell fate specification. Single-cell RNA sequencing analyses of HDAC expression during human pluripotent stem cell (hPSC) differentiation in vitro and mouse gastrulation in vivo reveal a unique association of HDAC1 and -3 with mesendoderm gene programs during exit from pluripotency. Functional perturbation with small molecules reveals that inhibition of HDAC1 and -3, but not HDAC2, induces mesoderm while impeding endoderm and early cardiac progenitor specification. These data identify unique biological functions of the structurally homologous enzymes HDAC1-3 in influencing hPSC differentiation from pluripotency toward mesendodermal and cardiac progenitor populations.

Charge transfer directed growth and morphology regulation of silver nanoparticles.

We demonstrate the control of silver nanoparticle growth in electroless deposition by utilizing surfaces of varying conductivity. Nanoscopic wires can be developed on non-conductive substrates, whereas nanoloops and microspheres are produced on surfaces of weak and high conductivity, respectively. Our observations reveal that the morphologies of electroless deposition can be regulated by the charge transfer through substrates, which indicates the important role of a redox reaction potential and a size-dependent chemical potential as the driving force behind this directed growth.

Evaluating the Effectiveness of Apixaban Additional Risk Minimisation Measures Using Surveys in Europe.

BACKGROUND: Apixaban (ELIQUIS®) is a direct oral anticoagulant authorised for multiple indications in the European Economic Area (EEA). Additional risk minimisation measures (aRMMs) to address the risk of bleeding include educational materials comprising a Prescriber Guide and Patient Alert Card. OBJECTIVES: This study evaluated effectiveness of the apixaban Prescriber Guide and Patient Alert Card in terms of healthcare professional (HCP) and patient knowledge of associated bleeding risk, as well as material distribution, utilisation and behaviour. METHODS: This non-interventional, cross-sectional study included online surveys in ten countries that represented a high proportion of apixaban usage in the EEA. The HCP source population was based on HCP lists used for communications about and distribution of the risk minimisation materials. Patient recruitment took place via HCPs. Study participants included HCPs involved in apixaban treatment and patients treated with apixaban (or their caregivers) for multiple indications. Data collection took place over an 18-month period between August 2015 and February 2017. RESULTS: Survey responses from 385 HCPs and 125 patients/caregivers were analysed. HCP knowledge of bleeding risk included early recognition of symptoms requiring immediate contact with an HCP (96.1%), appropriate dosing (83.6%), contraindications (76.1%) and subpopulations at increased risk of bleeding complications (ranging from 63.5 to 85.9%). Patient knowledge included abnormal bleeding as an important side effect (71.2%), communicating risk factors to HCPs (76.8%) and recognition of potential bleeding symptoms ('high' knowledge levels 22.4%, 'moderate' knowledge levels 49.6%). Of 226 (58.7%) HCPs who recalled receiving/obtaining the Prescriber Guide, 97.8% read at least part of it and 74.8% had used it to assist patient discussions. Of 74 (59.2%) patients who were aware of the Patient Alert Card, 89.2% recalled receiving/obtaining a copy. When received, 90.9% of patients read the card at least once and 93.9% kept it with them at least some of the time. CONCLUSIONS: HCP and patient respondent knowledge of bleeding risk was satisfactory. Although not optimal, reach of the aRMMs was consistent with other studies. No modifications to aRMM content were required. To increase reach, the Prescriber Guide has been provided in an additional format as a web-based platform whilst the Patient Alert Card was included within product packaging.

Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation.

Pluripotent stem cells underpin a growing sector that leverages their differentiation potential for research, industry, and clinical applications. This review evaluates the landscape of methods in single-cell transcriptomics that are enabling accelerated discovery in stem cell science. We focus on strategies for scaling stem cell differentiation through multiplexed single-cell analyses, for evaluating molecular regulation of cell differentiation using new analysis algorithms, and methods for integration and projection analysis to classify and benchmark stem cell derivatives against in vivo cell types. By discussing the available methods, comparing their strengths, and illustrating strategies for developing integrated analysis pipelines, we provide user considerations to inform their implementation and interpretation.

Congruence and Discrepancy of Interictal and Ictal EEG With MRI Lesions in Pediatric Epilepsies.

Purpose. To evaluate the congruence or discrepancy of the localization of magnetic resonance imaging (MRI) lesions with interictal epileptiform discharges (IEDs) or epileptic seizure patterns (ESPs) in surface EEG in lesional pediatric epilepsy patients. Methods. We retrospectively analyzed presurgical MRI and video-EEG monitoring findings of patients up to age 18 years. Localization of MRI lesions were compared with ictal and interictal noninvasive EEG findings of patients with frontal, temporal, parietal, or occipital lesions. Results. A total of 71 patients were included. Localization of ESPs showed better congruence with MRI in patients with frontal lesions (n = 21, 77.5%) than in patients with temporal lesions (n = 24; 40.7%) (P = .009). No significant IED distribution differences between MRI localizations could be found. Conclusions. MRI lesions and EEG findings are rarely fully congruent. Congruence of MRI lesions and ESPs was highest in children with frontal lesions. This is in contrast to adults, in whom temporal lesions showed the highest congruency with the EEG localization of ESP. Lesional pediatric patients should be acknowledged as surgical candidates despite incongruent findings of interictal and ictal surface EEG.

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity.

Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper's transparent peer review process is included in the Supplemental Information.

Comparative safety of abatacept in rheumatoid arthritis with COPD: A real-world population-based observational study.

OBJECTIVE: The ASSURE randomized trial of abatacept safety in rheumatoid arthritis (RA) reported more frequent respiratory adverse events with abatacept among the subgroup of 54 patients with chronic obstructive pulmonary disease (COPD), leading to a label warning. We assessed the risk of adverse respiratory events associated with abatacept, compared with other biologic DMARDs (bDMARDs), among patients with RA and COPD in a real-world observational setting. METHODS: We formed a prevalent new-user cohort of patients with RA and COPD treated with bDMARDs within the US-based MarketScan databases from 2007 to 2014. Abatacept users were matched on time-conditional propensity scores to users of other bDMARDs. Adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) of adverse respiratory events comparing abatacept with other bDMARDs were estimated using the Cox model. RESULTS: The cohort included 1807 patients initiating abatacept and 3547 matched patients initiating another bDMARD. The HR of the combined endpoint of hospitalized COPD exacerbation, bronchitis and hospitalized pneumonia or influenza with abatacept relative to other bDMARDs was 0.87 (95% CI: 0.68-1.12). For hospitalized COPD exacerbation it was 0.60 (95% CI: 0.32-1.11), 0.80 (95% CI: 0.56-1.14) for bronchitis, while for pneumonia or influenza it was 1.39 (95% CI: 0.91-2.13) if hospitalized and 1.05 (95% CI: 0.86-1.29) as outpatient. CONCLUSION: This large safety study from a real world setting finds no increased risk of adverse respiratory events with abatacept compared with other bDMARDs in patients with RA and COPD. This study does not substantiate the safety signal raised by the smaller ASSURE trial.

Decreased external home help use with improved clinical status in rheumatoid arthritis: an exploratory analysis of the Abatacept in Inadequate responders to Methotrexate (AIM) trial.

OBJECTIVES: The aims of this study were to examine the relationship between external home help (EHH) use (ie, help provided by someone other than family or friends) and clinical response and patient-reported outcomes in patients with rheumatoid arthritis (RA), and to determine whether abatacept treatment in addition to methotrexate reduces the need for EHH. METHODS: EHH use was recorded monthly in the Abatacept in Inadequate responders to Methotrexate (AIM) trial, a 12-month, randomized, double-blind, placebo-controlled trial of abatacept in patients with active RA also receiving methotrexate. Clinical response was defined using American College of Rheumatology (ACR) criteria, European League Against Rheumatism (EULAR) criteria, and Disease Activity Scale (DAS)-28 score. Patient-reported outcomes included the Health Assessment Questionnaire (HAQ), 100-mm visual analog scales (VASs) for pain and fatigue, and the Medical Outcomes Study 36-item Short Form Health Survey (SF-36) for health-related quality of life. Analysis of covariance and regression analysis were performed to investigate the relationship between change in EHH use and both clinical response and patient-reported outcomes. RESULTS: Of 590 patients enrolled in the study, 232 (39.3%) were receiving EHH at baseline (mean age, 50.2 years; 88% female; 85% white; mean duration of RA, 8.8 years; mean [SD] EHH use, 15.6 [11.3] days). The level of EHH use was consistently higher with poorer scores on the HAQ, pain and fatigue VASs, DAS28, and SF-36. At 12 months, the mean reduction from baseline in EHH use was significantly greater in patients with ACR-50 or ACR-70 clinical response, EULAR good or moderate response, DAS28 remission, and clinically meaningful improvements in patient-reported outcomes. On multiple regression analysis, change in SF-36 Physical Functioning subscale score was the most important contributor to change in EHH after adjustment for other variables. The mean reduction from baseline in EHH use was significantly greater with abatacept compared with placebo over the study period (all, P<0.001). CONCLUSIONS: In this exploratory analysis of data from patients with active RA from the AIM trial, EHH use was decreased significantly with improvements in clinical response, disease activity, and patient-reported outcomes. Treatment with abatacept in addition to methotrexate was associated with significantly decreased EHH use, suggesting that abatacept may have been associated with improved function and increased physical independence in these patients with RA.

How is Interprofessional Collaboration Applied by Radiation Therapists in the Radiation Therapy Department in British Columbia?

INTRODUCTION: Interprofessional collaboration (IPC) is the process when multiple health workers from different professional backgrounds work together with patients to deliver the highest quality of care. IPC can improve communication and knowledge sharing between collaborating professionals and can lead to an increase in efficient patient care. In the radiation therapy department, radiation oncologists, nurses, medical physicists, and radiation therapists are the key professionals involved in the multidisciplinary care team. METHODS: Although there is ample literature about interprofessional collaboration, very little of it is focused in radiation oncology. Using SurveyMonkey, an online survey was made available to radiation therapists in British Columbia, Canada, for a period of 3 months. In the six British Columbia Cancer Agency centres, champion disseminators assisted in distributing the survey link through e-mail. The questions pertained to the type of IPC, frequency, and modes of collaboration along with radiation therapists' level of satisfaction with collaboration. The number of respondents was 124. RESULTS: The results indicate that the top three professionals who radiation therapists collaborate with are radiation oncologists, nurses, and medical physicists, respectively. The frequency of IPC is mostly one to five times in 5 working days. The preferred method of communication with oncologists and physicists is face-to-face interactions or phone calls. The favoured method of communication with nurses is through tasking. E-mail is the least preferred method. CONCLUSIONS: British Columbia radiation therapists are generally satisfied with IPC. Some suggestions for improvements regarding communication efficiency and respect for others' roles, responsibilities, and professions are made. Overall, results of this study show that IPC generates positive attitudes, teamwork, and a patient-centred model.

Gold nanoparticle wires for sensing DNA and DNA/protein interactions.

The discontinuous Vertical Evaporation-driven Colloidal Deposition (dVECD) method has been used as a green technique for formatting nanoparticle wires by the direct deposition of nanoparticles from colloid suspensions onto hydrophilic substrates, without any lithographic procedures. Gold nanoparticles of different sizes are deposited into wire arrays for electronic detection of biological molecules. A sensitive detection of DNA molecules as low as ∼1 pM is achieved due to a high surface to volume ratio of the porous structures. The effects of the gold nanoparticles' size, DNA concentration, and DNA length on detection sensitivity of these gold nanoparticle wire sensors are discussed. Moreover, we can also detect the interaction between DNAs and proteins. Gold nanoparticle wires prepared by the nontoxic and simple dVECD are promising for detecting viruses involved in diseases.

Comparing variation in Medicare and private insurance spending in Texas.

OBJECTIVES: A great deal of research has documented the wide variation in Medicare spending across different geographic regions in the United States. However, little research has been done on spending variation in the commercial sector. The objectives of this paper are (1) to compare variations in spending and inpatient utilization in the Blue Cross Blue Shield of Texas (BCBSTX) population and the Medicare population across 32 Texas regions and (2) to investigate if the pattern of widely varying Medicare spending but similar BCBSTX spending found in a previous analysis of El Paso and Hidalgo/McAllen exists across the state. STUDY DESIGN: Retrospective study using 2008 BCBSTX and Medicare data. We used total spending per member/enrollee per month and inpatient admissions per 1000 members/enrollees. METHODS: After adjusting BCBSTX and Medicare spending for price and adjusting BCBSTX spending and utilization for age and gender, we computed coefficients of variation, standard deviations from the Texas means, and kernel density estimates for standard deviations from the mean to compare variation in BCBSTX and Medicare spending and inpatient utilization. RESULTS: Results indicated that variations across Texas in total spending and inpatient utilization are similar in BCBSTX and Medicare both in level and in direction, as the correlations between Medicare and commercial spending and inpatient utilization are positive after excluding the Hidalgo/McAllen regions. CONCLUSIONS: Over the state of Texas, regions of high Medicare spending also tend to be regions of high private insurance spending. McAllen appears to be an outlier for Medicare spending, but not for BCBSTX spending.