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Bondoc et al perform single-cell RNA-Seq profiling of Hepatoblastoma, background liver, and patient-derived xenografts to investigate cell-type heterogeneity and characterise the driver malignant cell cluster.

Summary: Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, morphometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in synaptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.

Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease. We show that TRSs based on genes regulated by variants linked to inflammatory bowel disease (IBD) not only outperform genetic risk scores (GRSs) in distinguishing Crohn's disease from healthy samples, but also serve to identify patients who in time will progress to complicated disease. Our dissection of eQTL effects may be used to distinguish genes whose association with disease is through promotion versus protection, thereby linking statistical association to biological mechanism. The TRS approach constitutes a potential strategy for personalized medicine that enhances inference from static genotypic risk assessment.

BackgroundA lower heart rate is associated with better outcomes in patients with heart failure (HF) with reduced ejection fraction (EF). Less is known about this association in patients with HF with preserved ejection fraction (HFpEF).ObjectivesThe aims of this study were to examine associations of discharge heart rate with outcomes in hospitalized patients with HFpEF.MethodsOf the 8,873 hospitalized patients with HFpEF (EF ≥50%) in the Medicare-linked OPTIMIZE-HF (Organized Program to Initiate Lifesaving Treatment in Hospitalized Patients with Heart Failure) registry, 6,286 had a stable heart rate, defined as ≤20 beats/min variation between admission and discharge. Of these, 2,369 (38%) had a discharge heart rate of

BackgroundDigoxin use has been shown to be associated with a lower risk of 30-day all-cause hospital readmissions in older patients with heart failure (HF). In the current study, we examined this association among long-term care (LTC) residents hospitalized for HF.MethodsOf the 8049 Medicare beneficiaries discharged alive after hospitalization for HF from 106 Alabama hospitals, 545 (7%) were LTC residents, of which 227 (42%) received discharge prescriptions for digoxin. Propensity scores for digoxin use, estimated for each of the 545 patients, were used to assemble a matched cohort of 158 pairs of patients receiving and not receiving digoxin who were balanced on 29 baseline characteristics. Hazard ratios (HRs) and 95% confidence intervals (CIs) for outcomes associated with digoxin among matched patients were estimated using Cox regression models.ResultsMatched patients (n = 316) had a mean age of 83 years, 74% were women, and 18% African American. Thirty-day all-cause readmission occurred in 21% and 20% of patients receiving and not receiving digoxin, respectively (HR, 1.02; 95% CI, 0.63-1.66). Digoxin had no association with all-cause mortality (HR, 0.90; 95% CI, 0.48-1.70), HF readmission (HR, 0.90; 95% CI, 0.38-2.12), or a combined endpoint of all-cause readmission or all-cause mortality (HR, 0.97; 95% CI, 0.65-1.45) at 30 days. These associations remained unchanged at 1 year postdischarge.ConclusionsThe lack of an association between digoxin and 30-day all-cause readmission in older nursing home residents hospitalized for HF is intriguing and needs to be interpreted with caution given the small sample size.

BackgroundIsolated systolic hypertension and isolated diastolic hypotension are common in older adults and associated with a higher risk of incident heart failure (HF). However, little is known about the prevalence and impact of isolated diastolic hypertension in this population.MethodsIn the Cardiovascular Health Study (CHS), of the 5776 community-dwelling older adults ≥65years who had data on baseline systolic and diastolic blood pressure (SBP and DBP), 28 had isolated diastolic hypertension (DBP ≥90mmHg and SBP

BackgroundIsolated systolic hypertension (ISH) is common in older adults and is a risk factor for incident heart failure (HF). We examined the association of systolic-diastolic hypertension (SDH) with incident HF and other outcomes in older adults.MethodsIn the Cardiovascular Health Study (CHS), 5776 community-dwelling adults≥65years had data on baseline systolic and diastolic blood pressure (SBP and DBP). We excluded those with DBP

BackgroundStricturing and penetrating complications account for substantial morbidity and health-care costs in paediatric and adult onset Crohn's disease. Validated models to predict risk for complications are not available, and the effect of treatment on risk is unknown.MethodsWe did a prospective inception cohort study of paediatric patients with newly diagnosed Crohn's disease at 28 sites in the USA and Canada. Genotypes, antimicrobial serologies, ileal gene expression, and ileal, rectal, and faecal microbiota were assessed. A competing-risk model for disease complications was derived and validated in independent groups. Propensity-score matching tested the effect of anti-tumour necrosis factor α (TNFα) therapy exposure within 90 days of diagnosis on complication risk.FindingsBetween Nov 1, 2008, and June 30, 2012, we enrolled 913 patients, 78 (9%) of whom experienced Crohn's disease complications. The validated competing-risk model included age, race, disease location, and antimicrobial serologies and provided a sensitivity of 66% (95% CI 51-82) and specificity of 63% (55-71), with a negative predictive value of 95% (94-97). Patients who received early anti-TNFα therapy were less likely to have penetrating complications (hazard ratio [HR] 0·30, 95% CI 0·10-0·89; p=0·0296) but not stricturing complication (1·13, 0·51-2·51; 0·76) than were those who did not receive early anti-TNFα therapy. Ruminococcus was implicated in stricturing complications and Veillonella in penetrating complications. Ileal genes controlling extracellular matrix production were upregulated at diagnosis, and this gene signature was associated with stricturing in the risk model (HR 1·70, 95% CI 1·12-2·57; p=0·0120). When this gene signature was included, the model's specificity improved to 71%.InterpretationOur findings support the usefulness of risk stratification of paediatric patients with Crohn's disease at diagnosis, and selection of anti-TNFα therapy.FundingCrohn's and Colitis Foundation of America, Cincinnati Children's Hospital Research Foundation Digestive Health Center.

BackgroundTherapy with evidence-based heart failure (HF) medications has been shown to be associated with lower risk of 30-day all-cause readmission in patients with HF and reduced ejection fraction (HFrEF).MethodsWe examined the association of aldosterone antagonist use with 30-day all-cause readmission in this population. Of the 2443 Medicare beneficiaries with HF and left ventricular EF ≤35% discharged home from 106 Alabama hospitals during 1998-2001, 2060 were eligible for spironolactone therapy (serum creatinine ≤2.5 for men and ≤2mg/dl for women, and serum potassium

Background We aimed to characterize the occurrence of major adverse cardiovascular and limb events (MACE and MALE) among patients with peripheral artery disease (PAD) undergoing peripheral vascular intervention (PVI), as well as associated factors in patients with chronic limb threatening ischemia (CLTI). Methods and Results Patients undergoing PVI in the American College of Cardiology’s (ACC) National Cardiovascular Data Registry’s PVI Registry who could be linked to Centers for Medicare and Medicaid Services data were included. The primary outcomes were MACE, MALE, and readmission within 1 month and 1 year following index CLTI‐PVI or non‐CLTI‐PVI. Cox proportional hazards regression was used to identify factors associated with the development of the primary outcomes among patients undergoing CLTI‐PVI. There were 1758 (49.7%) patients undergoing CLTI‐PVI and 1779 (50.3%) undergoing non‐CLTI‐PVI. By 1 year, MACE occurred in 29.5% of patients with CLTI (n=519), and MALE occurred in 34.0% of patients with CLTI (n=598). By 1 year, MACE occurred in 8.2% of patients with non‐CLTI (n=146), and MALE occurred in 26.1% of patients with non‐CLTI (n=465). Predictors of MACE at 1 year in CLTI‐PVI included end‐stage renal disease on hemodialysis, congestive heart failure, prior CABG, and severe lung disease. Predictors of MALE at 1 year in CLTI‐PVI included treatment of a prior bypass graft, profunda femoral artery treatment, end‐stage renal disease on hemodialysis, and treatment of a previously treated lesion. Conclusions Patients ≥65 years old undergoing PVI experience high rates of MACE and MALE. A range of modifiable and non‐modifiable patient factors, procedural characteristics, and medications are associated with the occurrence of MACE and MALE following CLTI‐PVI.

There are many experimental methods for characterizing immune profiles of tumors, such as flow and mass cytometry. However, these approaches are time and resource intensive. Thus, several “digital cytometry” methods have been developed to extract cell frequencies from RNA-seq data. Here, we introduce TumorDecon, named for its potential to deconvolve the distribution of cells from the gene expression levels of a bulk of cells, such as a tumor. The Python package provides an accessible way of applying these methods. It includes four deconvolution methods as well as several gene sets, signature matrices, and functions for generating custom signature matrices.

Abstract The COVID-19 pandemic has affected African American populations disproportionately with respect to prevalence, and mortality. Expression profiles represent snapshots of combined genetic, socio-environmental (including socioeconomic and environmental factors), and physiological effects on the molecular phenotype. As such, they have potential to improve biological understanding of differences among populations, and provide therapeutic biomarkers and environmental mitigation strategies. Here, we undertook a large-scale assessment of patterns of gene expression between African Americans and European Americans, mining RNA-Seq data from 25 non-diseased and diseased (tumor) tissue-types. We observed the widespread enrichment of pathways implicated in COVID-19 and integral to inflammation and reactive oxygen stress. Chemokine CCL3L3 expression is up-regulated in African Americans. GSTM1, encoding a glutathione S-transferase that metabolizes reactive oxygen species and xenobiotics, is upregulated. The little-studied F8A2 gene is up to 40-fold more highly expressed in African Americans; F8A2 encodes HAP40 protein, which mediates endosome movement, potentially altering the cellular response to SARS-CoV-2. African American expression signatures, superimposed on single cell-RNA reference data, reveal increased number or activity of esophageal glandular cells and lung ACE2-positive basal keratinocytes. Our findings establish basal prognostic signatures that can be used to refine approaches to minimize risk of severe infection and improve precision treatment of COVID-19 for African Americans. To enable dissection of causes of divergent molecular phenotypes, we advocate routine inclusion of metadata on genomic and socio-environmental factors for human RNA-sequencing studies.

Introduction Aortic stenosis (AS) is considered severe when the aortic valve area (AVA) is < 1.0 cm 2 and the mean aortic valve gradient (mAVG) exceeds 40 mm Hg. Since many patients with AVA < 1.0 cm 2 do not manifest an mAVG > 40 mm Hg, we sought to determine the AVA at which mAVG tends to exceed 40 mm Hg in a sample of subjects with varied transvalvular flow rates. Material and methods Our echocardiography database was queried for subjects with native valve AS. We selected 200 subjects with an AVA < 1.0 cm 2 . The sample was selected to include subjects with varied mean systolic flow (MSF) rates. Linear regression was performed to determine the relationship between MSF and mAVG. Since this relationship varied by AVA, the regression was stratified by AVA (critical < 0.6 cm 2 , severe 0.6–0.79 cm 2 , moderately severe 0.8–0.99 cm 2 ). Results The study sample was 79 ±12 years old and was 60% female. The MSF rate at which mAVG tended to exceed 40 mm Hg was 120 ml/s for critical AVA, 183 ml/s for severe AVA and 257 ml/s for moderately severe AVA. Those with moderately severe AVA rarely (8%) had an mAVG > 40 mm Hg at a wide range of MSF. In contrast, those with severe AVA typically (75%) had mAVG > 40 mm Hg when MSF was normal (> 200 ml/s). Those with critical AVA frequently (44%) had mAVG > 40 mm Hg, even when MSF was reduced. Conclusions Subjects with AVA of 0.8 and 0.9 cm 2 rarely had mAVG > 40 mm Hg, even when the transvalvular flow rate was normal. Using current guidelines, it is not clear if such cases should be classified as severe.

Recurrent and acute bleeding from intestinal tract angioectasia (AEC) presents a major challenge for clinical intervention. Current treatments are empiric, with frequent poor clinical outcomes. Improvements in understanding the pathophysiology of these lesions will help guide treatment. Using data from the US Food and Drug Administration (FDA)’s Adverse Event Reporting System (FAERS), we analyzed 12 million patient reports to identify drugs inversely correlated with gastrointestinal bleeding and potentially limiting AEC severity. FAERS analysis revealed that drugs used in patients with diabetes and those targeting PPARγ‐related mechanisms were associated with decreased AEC phenotypes (P