Biology subjects

Alcorn, J. F.

Publications and source records attributed to Alcorn, J. F..

5 recordsLinked to original sources

bioRxiv2026

Genome-Wide Transcriptomics Uncovers a Lung-to-Aorta Inflammatory Program Driving Influenza-Induced Atherosclerosis Exacerbation

Influenza infection increases cardiovascular risk in individuals with pre-existing atherosclerosis, yet the genome-wide transcriptional basis of this association remains undefined. We performed bulk RNA sequencing of aorta and lung tissues from high-fat diet-fed Apoe-/- mice infected with influenza A/PR/8/34 versus PBS-treated controls at day 15 post-infection, identifying 6,828 differentially expressed genes across both tissues (5,694 in the lung and 1,134 in the aorta; adjusted p < 0.05). In the lung, influenza sustained a CXCR3-driven chemokine storm, comprehensive Th1, Th17, and exhaustion T-cell activation programs, coordinated monocyte recruitment through Ccl2, Ccl7, Ccl8, and Ccl12, a broad acute phase response including Saa3 and A2m, alveolar identity collapse through loss of Nkx2-1 and surfactant proteins, and broad metabolic dysregulation involving suppression of fatty acid oxidation, mitochondrial function, and circadian metabolic regulators. In the aorta, influenza drove macrophage and DAMP activation through Trem1, Fpr2, and S100a8, cytotoxic T-cell engagement, smooth muscle cell dedifferentiation through Myocd loss, convergent bioenergetic failure, and an ectopic lung-identity gene signature representing a previously undescribed cross-organ communication mechanism. Circadian clock and Hippo/YAP pathway suppression were shared across both tissues, identifying systemic vulnerabilities connecting pulmonary infection to vascular structural compromise. Consistent with the in vivo findings, influenza-infected Apoe-/- bone marrow-derived macrophages exhibited inflammasome activation, DAMP amplification, M1 polarization, and suppression of prostaglandin-mediated inflammatory resolution. Together these findings define a lung-to-aorta inflammatory and metabolic axis driving atherosclerotic plaque destabilization during the post-infection recovery period and identify CCR2/CXCR3 antagonism, NLRP3 inhibition, and YAP pathway activation as candidate therapeutic interventions.

immunology↗

bioRxiv2022

Heterotypic Influenza Infections Mitigate Susceptibility to Secondary Bacterial Infection

Influenza associated bacterial super-infections have devastating impacts on the lung and can result in increased risk of mortality. New strains of influenza circulate throughout the population yearly promoting the establishment of immune memory. Nearly all individuals have some degree of influenza memory prior to adulthood. Due to this we sought to understand the role of immune memory during bacterial super-infections. An influenza heterotypic immunity model was established using influenza A/PR/8/34 and A/X31. We report here that influenza experienced mice are more resistant to secondary bacterial infection with methicillin-resistant Staphylococcus aureus as determined by wasting, bacterial burden, pulmonary inflammation, and lung leak, despite significant ongoing lung remodeling. Multidimensional flow cytometry and lung transcriptomics revealed significant alterations in the lung environment in influenza-experienced mice compared with naive animals. These include changes in the lung monocyte and T cell compartments, characterized by increased expansion of influenza tetramer specific CD8+ T cells. The protection that was seen in memory experienced mouse model is associated with the reduction in inflammatory mechanisms making the lung less susceptible to damage and subsequent bacterial colonization. These findings provide insight into how influenza heterotypic immunity re-shapes the lung environment and the immune response to a re-challenge event, which is highly relevant to the context of human infection.

immunology↗

bioRxiv2022

Novel Requirement for Staphylococcal Cell Wall-Anchored Protein SasD in Pulmonary Infection

Staphylococcus aureus can complicate preceding viral infections, including influenza virus. A bacterial infection combined with a preceeding viral infection, known as super-infection, leads to worse outcomes compared to single infection. Most of the super-infection literature focuses on the changes in immune responses to bacteria between homeostatic and virally infected lungs. However, it is unclear how much of an influence bacterial virulence factors have in super-infection. Staphylococcal species express a broad range of cell wall-anchored proteins (CWAs) that have roles in host adhesion, nutrient acquisition, and immune evasion. We screened the importance of these CWAs using mutants lacking individual CWAs in vivo in both bacterial pneumonia and influenza super-infection. In bacterial pneumonia, lacking individual CWAs led to varying decreases in bacterial burden, lung damage, and immune infiltration into the lung. However, the presence of a preceding influenza infection partially abrogated the requirement for CWAs. In the screen, we found that the uncharacterized CWA S. aureus surface protein D (SasD) induced changes in both inflammatory and homeostatic lung markers. We further characterized a SasD mutant (sasD A50.1) in the context of pneumonia. Mice infected with sasD A50.1 had decreased bacterial burden, inflammatory responses, and mortalty compared to wildtype S. aureus. Mice also had reduced levels of IL-1{beta} compared with wildtype, likely derived from macrophages. Reductions in IL-1{beta} transcript levels as well as increased macrophage viability implicate altered macrophage cell death pathways. These data identify a novel virulence factor for S. aureus that influences inflammatory signaling within the lung. ImportanceStaphylococcus aureus is a common commensal bacteria that can cause severe infections, such as pneumonia. In the lung, viral infections increase the risk of staphylococcal pneumonia, leading to combined infections known as super-infections. The most common virus associated with S. aureus pneumonia is influenza, and super-infections lead to worse patient outcomes compared to either infection alone. While there is much known about how the immune system differs between healthy and virally infected lungs, the role of bacterial virulence factors in super-infection is less understood. The significance of our research is identifying new bacterial virulence factors that play a role in the initiation of infection and lung injury, which could lead to future therapies to prevent pulmonary single or super-infection with S. aureus.

microbiology↗

bioRxiv2022

Low diversity and instability of the sinus microbiota over time in adults with cystic fibrosis

BackgroundChronic rhinosinusitis (CRS) is a common, yet underreported and understudied manifestation of upper respiratory disease in people with cystic fibrosis (CF). There are currently no standard of care guidelines for the management of CF CRS, but treatment of upper airway disease may ameliorate lower airway disease. We sought to inform future treatment guidelines by determining whether changes to sinus microbial community diversity and specific taxa known to cause CF lung disease are associated with increased respiratory disease and inflammation. MethodsWe performed 16S rRNA gene sequencing, supplemented with cytokine analyses, microscopy, and bacterial culturing, on samples from the sinuses of 27 adults with CF CRS at the University of Pittsburghs CF Sinus Clinic. At each study visit, participants underwent endoscopic paranasal sinus sampling and clinical evaluation. We identified key drivers of microbial community composition and evaluated relationships between diversity and taxa with disease outcomes and inflammation. FindingsSinus community diversity was low and the composition was unstable, with many participants exhibiting alternating dominance between Pseudomonas aeruginosa and Staphylococci over time. Despite a tendency for dominance by these two taxa, communities were highly individualized and shifted composition during exacerbation of sinus disease symptoms. Exacerbations were also associated with communities dominated by Staphylococcus spp. Reduced microbial community diversity was linked to worse sinus disease and the inflammatory status of the sinuses (including increased IL-1{beta}). Increased IL-1{beta} was also linked to worse sinus endoscopic appearance, and other cytokines were linked to microbial community dynamics. InterpretationTo our knowledge, this is the largest longitudinal study of microbial communities and cytokine secretion in CF CRS. Our work revealed previously unknown instability of sinus microbial communities and a link between inflammation, lack of microbial community diversity, and worse sinus disease. FundingCystic Fibrosis Foundation and US National Institutes of Health. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSA search of the PubMed database on October 11, 2021 with the terms [cystic fibrosis sinus microbiome] yielded 16 results, and we have identified seven primary research articles on the CF CRS microbiome (including re-analyses of existing datasets). Most are cross-sectional cohort analyses, along with one prior longitudinal study of four adults at the University of Auckland, New Zealand. Together, these prior studies reveal similarities between CF CRS and CF sputum microbiomes, including low community diversity associated with sinus disease, the presence of common CF-associated microbes in the sinuses, and prevalence of sinus communities dominated by P. aeruginosa or Staphylococcus aureus. High levels of IL-1{beta} are linked to the presence of nasal polyps in CF CRS, and polymorphisms in the IL-1 receptor antagonist gene are associated with risk of CRS outside of the context of CF. Two prior studies of this cohort have been performed by our laboratory. One describes clinical indicators of CF sinus disease and the other links sinus infection biogeography to P. aeruginosa evolutionary genomics. Added value of this studyOur study is the first to examine longitudinal relationships between the host immune response (through cytokine profiling) and microbiota dynamics in CF CRS, including linking elevated IL-1{beta} to worse sinus disease through reduced sinus microbial community diversity. The longitudinal nature of our study also allowed us to uncover striking temporal instability of microbial communities in approximately half of our cohorts sinus microbial communities over two years, including switching between communities dominated by P. aeruginosa and Staphylococcus spp. This instability could hinder attempts to link the relative abundance of taxa to clinical outcomes of interest in cross-sectional studies (e.g., markers of disease progression). We also identified patterns of synergy and antagonism between specific taxa, and impacts of the host immune response in the sinuses on community composition. Implications of all the available evidenceTogether with prior CF CRS microbiome studies, our study underscores similarities between sinus and lower respiratory tract microbial community structure in CF, and we show how community structure tracks with inflammation and several disease measures. This work strongly suggests that clinical management of CRS could be leveraged to improve overall respiratory health in CF. Our work implicates elevated IL-1{beta} in reduced microbiota diversity and worse sinus disease in CF CRS, suggesting applications for existing therapies targeting IL-1{beta}. Finally, the widespread use of highly effective CFTR modulator therapy has led to less frequent availability of spontaneous expectorated sputum for microbiological surveillance of lung infections. A better understanding of CF sinus microbiology could provide a much-needed alternative site for monitoring respiratory infection status by important CF pathogens.

microbiology↗

bioRxiv2018

A Dual Controllability Analysis of Influenza Virus-Host Protein-Protein Interaction Networks for Antiviral Drug Target Discovery

Host factors of influenza virus replication are often found in key topological positions within protein-protein interaction networks. This work explores how protein states can be manipulated through controllability analysis: the determination of the minimum manipulation needed to drive the cell system to any desired state. Here, we complete a two-part controllability analysis of two protein networks: a host network representing the healthy cell state and an influenza A virus-host network representing the infected cell state. This knowledge can be utilized to understand disease dynamics and isolate proteins for study as drug target candidates. Both topological and controllability analyses provide evidence of wide-reaching network effects stemming from the addition of viral-host protein interactions. Virus interacting and driver host proteins are significant both topologically and in controllability, therefore playing important roles in cell behavior during infection. 24 proteins are identified as holding regulatory roles specific to the infected cell by measures of topology, controllability, and functional role. These proteins are recommended for further study as potential antiviral drug targets.\n\nImportanceSeasonal outbreaks of influenza A virus are a major cause of illness and death around the world each year, with a constant threat of pandemic infection. Even so, the FDA has only approved four treatments, two of which are unsuited for at risk groups such as children and those with breathing complications. This research aims to increase the efficiency of antiviral drug target discovery using existing protein-protein interaction data and network analysis methods. Controllability analyses identify key regulating host factors of the infected cells progression, findings which are supported by biological context. These results are beneficial to future studies of influenza virus, both experimental and computational.

systems biology↗