Darragh Duffy

NAP1 switches from an activator to a limiter of interferon induction by trapping TBK1 in condensates

This study shows NAP1 switches from enhancing to limiting TBK1 activity through condensate formation, affecting IFN induction and linking to interferonopathies.

Temperature-Dependent Replication and Sensitivity to Innate Immunity of Human Coronavirus HKU1

This study shows human coronavirus HKU1 replicates more efficiently at nasal temperature (33°C) than at body temperature (37°C), with differences in innate immune response and viral stability.

Humans homozygous for rare or common hypomorphic IL23R variants are prone to tuberculosis

Homozygosity for hypomorphic IL23R variants (G149R, G300V, R381Q) partly impairs IL-23-dependent IFN-γ production in patient cells; with L372F (effect inferred), they are enriched in tuberculosis, not MSMD or CMC patients.

Identification and Functional Characterization of Regulatory Variants in DPP9 Associated with COVID-19 Severity

The paper identifies and functionally characterizes regulatory variants in DPP9 associated with severe COVID-19 by analyzing genetic risk factors and their impact on gene expression and immune cell function.

Dysregulated dsRNA sensor signaling and viral infection during onset of pediatric autoimmune interferonopathy

The paper identifies dysregulated dsRNA sensing and RNA viral exposure as potential triggers of type I interferon dysregulation in juvenile dermatomyositis onset.

Integration of immunomonitoring assays with PET/CT in TB patients identifies on-treatment biomarkers

The paper identifies on-treatment biomarkers in TB patients by integrating immunomonitoring assays with PET/CT scans, showing significant cytokine changes and machine learning-based biomarkers for treatment response.

Human macrophages secrete both interferon α and interferon β protein during infection with Mycobacterium tuberculosis.

This study shows human macrophages secrete both interferon α and β during Mtb infection, challenging previous assumptions about their kinetics and timing.

Strain-level translocation and enrichment mechanisms of oral bacteria in the lower gastrointestinal tract of stunted children

The paper investigates strain translocation and enrichment of oral bacteria in the lower gastrointestinal tract of stunted children, finding increased oral bacteria in the duodenum and colon linked to biomass changes.

Stealth replication of SARS-CoV-2 Omicron in the nasal epithelium at physiological temperature

This study shows that the SARS-CoV-2 Omicron variant replicates more efficiently and evades innate immune responses in a nasal epithelium model at physiological temperature.

AXL mediates mast cell survival and resistance to tyrosine kinase inhibitors in mastocytosis

This study identifies AXL as a driver of mast cell survival and TKI resistance in mastocytosis and shows that dual KIT/AXL inhibition restores TKI sensitivity.

Modeling viral and bacterial infections in human lung organotypic systems reveals strain specific host responses

This study uses human lung organoid-on-chip models to compare host responses to Streptococcus pneumoniae and SARS-CoV-2 variants, showing strain-specific infection and immune responses.

A multivariate outcome test of covariance

The paper introduces MANOCCA, a method to test the effect of predictors on the covariance matrix of multivariate outcomes, showing it outperforms existing methods in simulations and identifies significant associations in real data.

Environmental and genetic drivers of population differences in SARS-CoV-2 immune responses

The paper identifies environmental and genetic factors influencing population differences in SARS-CoV-2 immune responses using single-cell RNA-sequencing data.

The Immune Factors Driving DNA Methylation Variation in Human Blood

This study identifies factors influencing DNA methylation variation in human blood, showing that cytomegalovirus infection and aging drive methylation changes, with cellular composition and DNA sequence as key predictors.

Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes

The paper identifies novel genetic and non-genetic factors associated with plasma protein levels in healthy donors, highlighting their impact on immune response variability.

A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals

This study identifies non-genetic factors associated with gut microbiome diversity in a cohort of healthy individuals, finding no genome-wide significant genetic associations.

Accurate prediction of cell composition, age, smoking consumption and infection serostatus based on blood DNA methylation profiles

The paper develops a method to predict blood cell composition, age, smoking, and infection status using DNA methylation profiles, achieving high accuracy with fewer methylation sites than existing methods.

Genetic factors and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

This study identifies age, sex, and genetic variants as key predictors of variability in humoral immune responses to pathogens and vaccines.