A multi-omics recovery factor predicts long COVID in the IMPACC study.

Background: Following SARS-CoV-2 infection, ~10-35% of COVID-19 patients experience long COVID (LC), in which debilitating symptoms persist for at least three months. Elucidating biologic underpinnings of LC could identify therapeutic opportunities.

Methods: We utilized machine learning methods on biologic analytes provided over 12-months after hospital discharge from >500 COVID-19 patients in the IMPACC cohort to identify a multi-omics "recovery factor", trained on patient-reported physical function survey scores.

Multiomics approach to evaluating personalized biomarkers of allergen immunotherapy.

Recent advancements in genomics and "omic" technologies have ushered in a transformative era referred to as personalized or precision medicine. This innovative approach considers the unique genetic profiles of individuals, along with a range of variability factors, to devise tailored disease treatments and prevention strategies that cater to the distinct needs of each patient. Although the terms personalized medicine and precision medicine are frequently utilized interchangeably, it is essential to delineate the subtle distinctions between them.

Mepolizumab alters gene regulatory networks of nasal airway type-2 and epithelial inflammation in urban children with asthma.

Mepolizumab (anti-IL5 therapy) reduces asthma exacerbations in urban children with exacerbation-prone eosinophilic asthma. We previously utilized nasal transcriptomics to identify inflammatory pathways (gene co-expression modules) associated with asthma exacerbations despite this therapy. In this study, we applied differential gene correlation analysis on these targeted gene co-expression modules to gain better insight into the treatment effects on correlation structure within gene networks.

Loss of the actin remodeling protein Flightless-1 impairs CD8 and regulatory T cell function.

T cell immunity depends on the precise coordination of signaling networks with actin cytoskeleton remodeling, yet the molecular regulators of these processes remain incompletely defined. Flightless-1 (FLII) is a gelsolin-family actin regulator with unique leucine-rich repeats that can couple cytoskeletal dynamics to diverse signaling pathways. Here, using conditional knockout mice, we identify essential roles for FLII in both CD8⁺ and regulatory T cells.

TSLP: contrasting roles in cancer.

Thymic stromal lymphopoietin (TSLP) is an alarmin cytokine possessing a plethora of pleiotropic properties. Human and mouse TSLP exerts their activity a heterodimeric complex composed of TSLP receptor (TSLPR) chain and IL-7Rα. TSLP is predominantly expressed by epithelial cells and keratinocytes but can also be produced by several immune cells and some cancers.

ScreeningLessons from Prediction and Prevention of Type 1 Diabetes.

Two major accomplishments in the field of prediction and prevention have had important implications for type 1 diabetes (T1D), as well as other immune-mediated diseases such as inflammatory bowel disease (IBD). First, individuals destined to develop T1D can now be identified by testing for the presence of autoantibodies, long before signs or symptoms of clinical disease. Second, there is now an FDA-approved therapy to delay disease progression.

Profiling associations of interactive ligand-receptors (HLA class I and KIR gene products) with the progression to type 1 diabetes among seroconverted participants.

Aims/hypothesis: The aim of this work was to explore associations between type 1 diabetes progression from stages 1 or 2 to stage 3 and interacting ligand-receptor complexes of HLA class I (HLA-I) and KIR gene products.

Methods: Applying next-generation sequencing technology to genotype HLA-I genes (HLA-A, -B, -C) and KIR genes (KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, KIR3DL1, KIR3DL3, KIR3DS1, KIR2DP1, KIR3DP1) from 1215 participants in the Diabetes Prevention Trial-Type 1 (DPT-1) and the Diabetes Prevention Trial (TN07), we systematically explored associations of HLA-I-KIR ligand-receptor interactions (LRIs) with disease progression via a Cox regression model. We investigated the structural properties of identified LRI complexes.

Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code.

Transcriptional regulatory sequences in metazoans contain intricate combinations of transcription factor (TF) motifs. Stereospecific arrangements of simple motifs constitute composite elements (CEs) that enhance DNA-protein interaction specificity and enable combinatorial regulatory logic. Despite their importance, CEs remain underexplored.

TCR2HLA: calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.

T cell receptors (TCRs) recognize peptides presented by polymorphic human leukocyte antigen (HLA) molecules, but HLA genotype data are often missing from TCR repertoire sequencing studies. To address this, we developed TCR2HLA, an open-source tool that infers HLA genotypes from TCRβ repertoires. Expanding on work linking public TRBV-CDR3 sequences to HLA genotypes, we incorporated "quasi-public" metaclonotypes - composed of rarer TCRβ sequences with shared amino acid features - enriched by HLA genotypes.

Blood samples collected under anesthesia can be used as a source of non-diseased controls for immune-based assays.

Recruiting very young, healthy children to serve as age-matched controls in research presents substantial ethical and practical challenges. One potential approach to address this issue is to recruit healthy children who are referred for elective procedures under general anesthesia. As infants are typically anesthetized using volatile anesthetics before cannula insertion for additional drug administration, blood samples become readily accessible after the onset of drug-induced coma.

Distinct Roles for Thymic Stromal Lymphopoietin (TSLP) and IL-33 in Experimental Eosinophilic Esophagitis.

Rationale: Thymic stromal lymphopoietin (TSLP) and IL-33 are alarmins implicated in eosinophilic esophagitis (EoE) pathogenesis by activating multiple cells, including mast cells (MCs). Whether TSLP or IL-33 have a role in EoE and whether their activities are distinct requires further investigation.

Methods: Experimental EoE was induced in wild type (WT) Il33 and Crlf2 mice.

The Palliation of Unresectable Pancreatic Cancer: Evolution from Surgery to Minimally Invasive Modalities.

Pancreatic cancer is an aggressive malignancy, with a current 5-year survival rate in the United States of approximately 13.3%. Although the current standard for resectable pancreatic cancer most commonly includes neoadjuvant chemotherapy prior to a curative resection, surgery, in the majority of patients, has historically been palliative.

Cockroach immunotherapy modulates dominant T-cell responses independent of allergen extract content.

Background: T-cell responses to the individual components of allergen extracts have not been fully elucidated in subcutaneous allergen immunotherapy (SCIT). Specifically, it is unknown whether T-cell responses to immunodominant allergens are more or less sensitive to modulation, and whether allergen abundance in the immunotherapy extract influences T-cell response modulation.

Objective: To fill these gaps, we evaluated CD4 T-cell reactivity specific to each of the main cockroach allergens in the double-blinded, placebo controlled, multicenter CRITICAL (NCT03541187) SCIT trial.

Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort.

Background: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly after its identification in December 2019 to cause a global pandemic. The respiratory tract is the primary site of infection, and there is a large range in the severity of respiratory illnesses caused by the virus. Defining molecular and cellular factors for protection from severe disease and death has been a goal to better understand and to predict and mitigate the effects of SARS-CoV-2 and future coronaviruses.

Contrasting Adult and Pediatric Populations in a Cohort of At-Risk Relatives in The T1D TrialNet Pathway to Prevention Study.

Objective: More than half of incident type 1 diabetes (T1D) occurs in adults, yet research on disease progression predominantly focuses on at-risk children. We compared autoantibody screening outcomes and T1D progression in adults versus children.

Research Design And Methods: We studied 135,914 children (aged <18 years) and 99,795 adult relatives of individuals with T1D screened in the TrialNet Pathway to Prevention study.

Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study.

Introduction: The coronavirus disease 2019 (COVID-19) pandemic threatened public health and placed a significant burden on medical resources. The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study collected clinical, demographic, blood cytometry, serum receptor-binding domain (RBD) antibody titers, metabolomics, targeted proteomics, nasal metagenomics, Olink, nasal viral load, autoantibody, SARS-CoV-2 antibody titers, and nasal and peripheral blood mononuclear cell (PBMC) transcriptomics data from patients hospitalized with COVID-19. The aim of this study is to select baseline biomarkers and build predictive models for 28-day in-hospital COVID-19 severity and mortality with most predictive variables while prioritizing routinely collected variables.

Single-cell transcriptomic profiling of eosinophils and airway immune cells in childhood asthma.

Background: Single-cell RNA sequencing has transformed our understanding of cellular heterogeneity but remains inadequate in capturing granulocytes, particularly in tissue compartments, owing to technical limitations.

Objective: To enhance granulocyte recovery in single-cell RNA sequencing, we used nasal lavage samples from children with asthma, leveraging the 10× Genomics Flex platform combined with a customized data processing pipeline.

Methods: Nasal lavage samples were processed without prior manipulation to avoid technical artifacts such as lysis or stimulation.

Population risk predictors of major adverse kidney events attributed to focal segmental glomerulosclerosis from the CURE-CKD registry.

Background: Predictors of major adverse kidney events (MAKE) in focal segmental glomerulosclerosis (FSGS) have not been previously explored within large, real-world populations. The study aim was to evaluate population-level predictors of MAKE attributed to FSGS from health system data.

Methods: The study population was derived from electronic health records from Providence and University of California Los Angeles Health Systems.

cytoKernel: robust kernel embeddings for assessing differential expression of single-cell data.

Motivation: High-throughput sequencing of single-cell data can be used to rigorously evaluate cell specification and enable intricate variations between groups or conditions to be identified. Many popular existing methods for differential expression target differences in aggregate measurement (mean, median, sum) and limit their approaches to detect only global differential changes.

Results: We present a robust method for differential expression of single-cell data using a kernel-based score test, cytoKernel.

Inflammatory Pathways in Residual Asthma Exacerbations Among Mepolizumab-Treated Urban Children: A Secondary Analysis of a Randomized Clinical Trial.

Importance: While biologic therapies targeting type 2 (T2) inflammation reduce acute exacerbation rates in children with asthma and T2 inflammation, exacerbations still occur, and the underlying molecular mechanisms are poorly defined.

Objective: To identify multiple distinct molecular mechanisms implicated in asthma exacerbations by characterizing respiratory illnesses among urban children with eosinophilic asthma enrolled in a clinical trial comparing treatment with mepolizumab vs placebo.

Design, Setting, And Participants: This is a secondary analysis of the Mechanisms Underlying Asthma Exacerbations Prevented and Persistent With Immune-Based Therapy: A Systems Approach Phase 2 (MUPPITS-2) double-blind, placebo-controlled, parallel-group, randomized clinical trial comparing treatment with mepolizumab vs placebo among children with exacerbation-prone asthma in low-income urban centers in 9 US cities.

Hypoxia-inducible factor 2α promotes protective Th2 cell responses during intestinal helminth infection.

Th2 cells must sense and adapt to the tissue milieu to provide protective host immunity and tissue repair. Here, we examined the mechanisms promoting Th2 cell differentiation and function within the small intestinal lamina propria. Single cell RNA-seq analyses of CD4+ T cells from the small intestinal lamina propria of helminth infected mice revealed high expression of the gene Epas1, encoding the transcription factor hypoxia-inducible factor 2a (HIF2α).

Genetic contributions to epigenetic-defined endotypes of allergic phenotypes in children.

Asthma is a common respiratory disease, with contributions from both genes and the environment and significant heterogeneity in underlying endotypes; yet, little is known about the relative contributions of each to these endotypes. To address this gap, we used nasal mucosal cell DNA methylation (DNAm) and gene expression and genotypes for 284 children in the Urban Environment and Childhood Asthma (URECA) birth cohort. Using an unbiased data-reduction approach and 37,256 CpGs on a custom-content Asthma&Allergy array, empirical Bayesian factorization was implemented to identify three DNAm signatures that were associated with phenotypes reflecting allergic diseases (allergic asthma and allergic rhinitis), allergic sensitization (atopy) (specific and total immunoglobulin E), and/or type 2 inflammation (eosinophil count and fractional exhaled nitric oxide [FeNO]).

Kinetics of early peanut allergy development and resolution in the EAT, LEAP, and PAS cohorts.

Background: Little is known about the development and resolution of early peanut allergy (PA).

Objective: We examined the natural history and biomarkers of PA longitudinally in 3 cohorts.

Methods: PA development was examined in the Enquiring About Tolerance (EAT), Learning Early About Peanut (LEAP), and Peanut Allergy Sensitization (PAS) cohorts.

MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury.

MHC class I polypeptide-related sequence B (MICB) is a ligand for NKG2D. We have shown NK cells are central to lung transplant acute lung injury (ALI) via NKG2D activation, and increased MICB in bronchoalveolar lavage predicts ALI severity. Separately, we found a MICB polymorphism (MICBG406A) is associated with decreased ALI risk.

Transcriptional fingerprinting of regulatory T cells: ensuring quality in cell therapy applications.

Introduction: The success of regulatory T cell (Treg) therapies depends on the source of Treg and the quality of the Treg manufacturing product that maintains Treg identity. Commonly used methods to identify Treg, including assessment of FOXP3 expression and demethylation of the Treg-specific demethylated region (TSDR), may not be sufficient on their own to ensure that Treg cell therapy drug products have an optimal identity and phenotype prior to infusion into patients.

Methods: To address this critical need, we developed a robust framework to molecularly characterize Treg products using next-generation sequencing.