Mid-life anti-inflammatory metabolites are inversely associated with long-term cardiovascular disease events.

Background: Preclinical data have shown that low levels of metabolites with anti-inflammatory properties may impact metabolic disease processes. However, the association between mid-life levels of such metabolites and long-term ASCVD risk is not known.

Methods: We characterised the plasma metabolomic profile (1228 metabolites) of 1852 participants (58.

Oral Disease and Atherosclerosis May Be Associated with Overlapping Metabolic Pathways.

Objectives: Dental caries and periodontitis are among the most prevalent chronic diseases worldwide and have been associated with atherosclerotic cardiovascular diseases (ASCVD). This study aimed to determine (1) the independent associations between subclinical ASCVD markers (carotid intima media thickness [CIMT] and coronary artery calcification [CAC]) and quantitative indices of oral disease including the decayed, missing, and filled teeth (DMFT) index, gingivitis parameters, periodontal status, and number of teeth lost and (2) the extent to which metabolites altered in individuals with oral disease overlapped with those altered in individuals with ASCVD.

Methods: We used data from 552 participants recruited through the Dental Strategies Concentrating on Risk Evaluation project.

BLEND: Probabilistic Cellular Deconvolution with Automated Reference Selection.

Cellular deconvolution aims to estimate cell type fractions from bulk transcriptomic and other omics data. Most existing deconvolution methods fail to account for the heterogeneity in cell type-specific (CTS) expression across bulk samples, ignore discrepancies between CTS expression in bulk and cell type reference data, and provide no guidance on cell type reference selection or integration. To address these issues, we introduce BLEND, a hierarchical Bayesian method that leverages multiple reference datasets.

The association of infant urinary adrenal steroids with the risk of childhood asthma development.

Background: Adrenal steroids play important roles in early-life development. However, our understanding of the effects of perinatal adrenal steroids on the development of childhood asthma is incomplete.

Objective: To evaluate the associations between early-life adrenal steroid levels and childhood asthma.

scMD facilitates cell type deconvolution using single-cell DNA methylation references.

The proliferation of single-cell RNA-sequencing data has led to the widespread use of cellular deconvolution, aiding the extraction of cell-type-specific information from extensive bulk data. However, those advances have been mostly limited to transcriptomic data. With recent developments in single-cell DNA methylation (scDNAm), there are emerging opportunities for deconvolving bulk DNAm data, particularly for solid tissues like brain that lack cell-type references.

Clinical and economic impacts of a modified-observational screening approach to well-appearing infants born to mothers with chorioamnionitis.

Objective: Term infants born to mothers with chorioamnionitis are at risk for early-onset sepsis (EOS). We aimed to measure the impact of changing from a categorical to a modified-observational EOS screening approach on NICU admission, antibiotic utilization, and hospitalization costs.

Study Design: Single-center retrospective pre-post cohort study of full-term infants born to mothers with chorioamnionitis.

scMD: cell type deconvolution using single-cell DNA methylation references.

The proliferation of single-cell RNA sequencing data has led to the widespread use of cellular deconvolution, aiding the extraction of cell type-specific information from extensive bulk data. However, those advances have been mostly limited to transcriptomic data. With recent development in single-cell DNA methylation (scDNAm), new avenues have been opened for deconvolving bulk DNAm data, particularly for solid tissues like the brain that lack cell-type references.

Accurate estimation of rare cell type fractions from tissue omics data via hierarchical deconvolution.

Bulk transcriptomics in tissue samples reflects the average expression levels across different cell types and is highly influenced by cellular fractions. As such, it is critical to estimate cellular fractions to both deconfound differential expression analyses and infer cell type-specific differential expression. Since experimentally counting cells is infeasible in most tissues and studies, cellular deconvolution methods have been developed as an alternative.

Association of citrulline concentration at birth with lower respiratory tract infection in infancy: Findings from a multi-site birth cohort study.

Assessing the association of the newborn metabolic state with severity of subsequent respiratory tract infection may provide important insights on infection pathogenesis. In this multi-site birth cohort study, we identified newborn metabolites associated with lower respiratory tract infection (LRTI) in the first year of life in a discovery cohort and assessed for replication in two independent cohorts. Increased citrulline concentration was associated with decreased odds of LRTI (discovery cohort: aOR 0.

African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans.

Background: Asthma is the most common chronic disease in children, occurring at higher frequencies and with more severe disease in children with African ancestry.

Methods: We tested for association with haplotypes at the most replicated and significant childhood-onset asthma locus at 17q12-q21 and asthma in European American and African American children. Following this, we used whole-genome sequencing data from 1060 African American and 100 European American individuals to identify novel variants on a high-risk African American-specific haplotype.

Estimating and accounting for unobserved covariates in high-dimensional correlated data.

Many high dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput 'omic' data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation of and inference on the effects of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods to choose the number of and estimate latent confounding factors present in high dimensional data with correlated or nonexchangeable residuals.

Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution.

Motivation: Tissue-level omics data such as transcriptomics and epigenomics are an average across diverse cell types. To extract cell-type-specific (CTS) signals, dozens of cellular deconvolution methods have been proposed to infer cell-type fractions from tissue-level data. However, these methods produce vastly different results under various real data settings.

ESTIMATION AND INFERENCE IN METABOLOMICS WITH NON-RANDOM MISSING DATA AND LATENT FACTORS.

High throughput metabolomics data are fraught with both non-ignorable missing observations and unobserved factors that influence a metabolite's measured concentration, and it is well known that ignoring either of these complications can compromise estimators. However, current methods to analyze these data can only account for the missing data or unobserved factors, but not both. We therefore developed MetabMiss, a statistically rigorous method to account for both non-random missing data and latent factors in high throughput metabolomics data.

Unconjugated bilirubin is associated with protection from early-life wheeze and childhood asthma.

Background: Wheeze and allergic sensitization are the strongest early-life predictors of childhood asthma development; the molecular origins of these early-life phenotypes are poorly understood.

Objectives: We sought to identify metabolites associated with early-life wheeze, allergic sensitization, and childhood asthma.

Methods: We conducted a nested case-control study using Environmental influences on Child Health Outcomes Program cohorts for discovery and independent replication.

Longitudinal data reveal strong genetic and weak non-genetic components of ethnicity-dependent blood DNA methylation levels.

Epigenetic architecture is influenced by genetic and environmental factors, but little is known about their relative contributions or longitudinal dynamics. Here, we studied DNA methylation (DNAm) at over 750,000 CpG sites in mononuclear blood cells collected at birth and age 7 from 196 children of primarily self-reported Black and Hispanic ethnicities to study race-associated DNAm patterns. We developed a novel Bayesian method for high-dimensional longitudinal data and showed that race-associated DNAm patterns at birth and age 7 are nearly identical.

Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age.

Background: The upper airways present a barrier to inhaled allergens and microbes, which alter immune responses and subsequent risk for diseases, such as allergic rhinitis (AR).

Objective: We tested the hypothesis that early-life microbial exposures leave a lasting signature in DNA methylation that ultimately influences the development of AR in children.

Methods: We studied upper airway microbiota at 1 week, 1 month, and 3 months of life, and measured DNA methylation and gene expression profiles in upper airway mucosal cells and assessed AR at age 6 years in children in the Copenhagen Prospective Studies on Asthma in Childhood birth cohort.

ER-luminal [Ca] regulation of InsP receptor gating mediated by an ER-luminal peripheral Ca-binding protein.

Modulating cytoplasmic Ca concentration ([Ca]) by endoplasmic reticulum (ER)-localized inositol 1,4,5-trisphosphate receptor (InsPR) Ca-release channels is a universal signaling pathway that regulates numerous cell-physiological processes. Whereas much is known regarding regulation of InsPR activity by cytoplasmic ligands and processes, its regulation by ER-luminal Ca concentration ([Ca]) is poorly understood and controversial. We discovered that the InsPR is regulated by a peripheral membrane-associated ER-luminal protein that strongly inhibits the channel in the presence of high, physiological [Ca].

Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study.

Background: African ancestry is associated with a higher prevalence and greater severity of asthma than European ancestries, yet genetic studies of the most common locus associated with childhood-onset asthma, 17q12-21, in African Americans have been inconclusive. The aim of this study was to leverage both the phenotyping of the Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium, and the reduced linkage disequilibrium in African Americans, to fine map the 17q12-21 locus.

Methods: We first did a genetic association study and meta-analysis using 17q12-21 tag single-nucleotide polymorphisms (SNPs) for childhood-onset asthma in 1613 European American and 870 African American children from the CREW consortium.

Accounting for unobserved covariates with varying degrees of estimability in high-dimensional biological data.

An important phenomenon in high-throughput biological data is the presence of unobserved covariates that can have a significant impact on the measured response. When these covariates are also correlated with the covariate of interest, ignoring or improperly estimating them can lead to inaccurate estimates of and spurious inference on the corresponding coefficients of interest in a multivariate linear model. We first prove that existing methods to account for these unobserved covariates often inflate Type I error for the null hypothesis that a given coefficient of interest is zero.

Induction of the Immunoproteasome Subunit Lmp7 Links Proteostasis and Immunity in α-Synuclein Aggregation Disorders.

Accumulation of aggregated α-synuclein into Lewy bodies is thought to contribute to the onset and progression of dopaminergic neuron degeneration in Parkinson's disease (PD) and related disorders. Although protein aggregation is associated with perturbation of proteostasis, how α-synuclein aggregation affects the brain proteome and signaling remains uncertain. In a mouse model of α-synuclein aggregation, 6% of 6215 proteins and 1.