Biology subjects

Short, K. R.

Publications and source records attributed to Short, K. R..

12 recordsLinked to original sources

bioRxiv2026

IL-1β and TNF drive endothelial dysfunction and coagulopathy in acute COVID-19.

Vascular dysfunction and coagulopathy are hallmarks of severe COVID-19. How SARS-CoV-2 infection drives endothelial dysfunction, despite the virus not infecting or replicating in endothelial cells, remains controversial. Here, we used an in vitro co-culture model of the human pulmonary epithelial-endothelial cell barrier to investigate which inflammatory mediators drive endothelial dysfunction during SARS-CoV-2 infection. SARS-CoV-2 infection of primary human bronchial epithelial cells increased adjacent endothelial cell expression of the leukocyte adhesion marker ICAM-1, disrupted endothelial VE-cadherin junctions, promoted endothelial cell death, and promoted platelet adherence to gaps in the endothelial monolayers. Dexamethasone treatment rescued these dysregulated endothelial phenotypes in infected co-cultures, confirming that inflammatory signalling was the primary driver of SARS-CoV-2-induced endothelial dysfunction. Specifically, epithelial-derived TNF and IL-1{beta} promoted endothelial dysfunction, as inhibition of TNF or IL-1R signalling blocked SARS-CoV-2-induced endothelial dysfunction in co-cultures. SARS-CoV-2-infected wild-type mice, but not TNF, IL-1{beta}, or TNF/IL-1{beta}- deficient mice, displayed increased endothelial ICAM-1 expression, while an anti-IL-1{beta} monoclonal antibody prevented SARS-CoV-2-induced ICAM-1 expression and fibrin deposition in aged K18-ACE2 mice. Our data indicate that TNF and IL-1{beta} are the specific cytokines that drive multiple aspects of endothelial dysfunction during acute SARS-CoV-2 infection, and that inhibiting their signalling pathways may provide therapeutic benefit in preventing vascular complications of COVID-19.

cell biology↗

bioRxiv2026

AVE0991, a Mas receptor agonist, increases influenza and COVID-19 severity in vivo.

Dysregulation of the renin-angiotensin system (RAS) contributes to severe influenza and COVID-19, potentially via impaired ACE2/Ang-(1-7)/Mas receptor (MasR) signalling. AVE0991, an orally bioavailable MasR agonist, protects against non-infectious lung inflammation, but its effects in viral respiratory disease are unknown. We evaluated AVE0991 in human lung epithelial cells and murine models of influenza A virus (IAV) and SARS-CoV-2 infection. In vitro, AVE0991 suppressed cytokines IL-6 and TNF- to both IAV and SARS-CoV-2 and reduced IAV titres. Unexpectedly, in vivo treatment worsened disease. These findings highlight discordant in vitro and in vivo effects and underscore the need for careful evaluation of RAS-targeted therapies in acute viral infection.

microbiology↗

bioRxiv2026

Influenza A virus infection perturbs host cell glycosylation

Glycosylation is critical for viral-host cell interactions in influenza A virus (IAV) infection, but we lack a comprehensive understanding of how IAV infection shapes the host glycoproteome and the implications of these changes. Here, we used a liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to perform proteomic, glycomic, and glycoproteomic characterisation of the dynamic subcellular responses to an in vitro time course infection of human A549 cells with two IAV strains (A/X-31, H3N2; and A/Puerto Rico/8/1934, H1N1). IAV infection resulted in only modest changes to the subcellular proteome, but robust and significant changes to the host secreted and organelle glycome and glycoproteome. Infection with either virus resulted in a widespread reduction in sialic acid across the N- and O-glyco(proteo)me; increased abundance of oligomannose, paucimannose, and phosphorylated glycans; and shorter hybrid/complex glycans. Reduced sialylation was consistent with desialylation of glycans by viral neuraminidase (NA), but with specific features of the glycan and protein controlling the extent of desialylation. Desialylation was greater when glycans were fucosylated; when the sialic acid was attached via an 2,3 linkage or positioned on the 3 arm; on larger, more complex glycans; and when present on proteins that are more accessible to IAV NA. Subtle but prolonged activation of the unfolded protein response in infection led to a doubling of oligomannose N-glycosylation. Glycans were shorter in infection, implicating IAV-induced disruption of Golgi glycoprotein flux as a mechanism that reduces host glycoprotein sialylation and promotes virion release, independent of NA activity. Our data provide important insights into the host glycoproteome during influenza virus infection, furthering our understanding of how influenza NA acts upon host glycans, and how cell stresses in infection perturb key mediators of protein stability and function, cell signalling and immunity.

biochemistry↗

bioRxiv2025

Omicron evolution drives increased ciliated cell tropism and dysfunction in nasal epithelia.

SARS-CoV-2 Omicron variants demonstrate greater replication efficiency in the upper respiratory tract than both ancestral virus and Delta variant, potentially due to stronger interactions with motile cilia in human nasal epithelial cells. Despite the emergence of numerous Omicron variants, there has been no comprehensive investigation comparing their interactions with ciliated cells. Here, we use differentiated primary human nasal epithelial cell (NEC) cultures to compare an ancestral isolate (QLD02) to Omicron variants BA.1, BA.5 and XBB. Transcriptomic analysis revealed that BA.5 and XBB infection, unlike BA.1 and QLD02, drives a distinct host response, defined by the profound downregulation of genes essential for cilium assembly and function at 48 hours post-infection. The BA.5/XBB signature was also characterized by the strong upregulation of pro-apoptotic and inflammatory pathways. Immunofluorescence of nucleocapsid-positive cells in NECs showed a significant 13-fold increase for BA.5 relative to QLD02. Additionally, BA.1 and BA.5 exhibited greater tropism for ciliated cells (7.6-fold for BA.1, 9-fold for BA.5) than QLD02. BA.5 and BA.1 infection were associated with elevated apoptosis in both infected and bystander cells, however, the total number of ciliated cells remained unchanged. Consistent with this, BA.5 infection significantly reduced DNAH5 outer dynein arm protein in the cilia, indicating dysfunction of cilia motility rather than overt cilia loss. Overall, we demonstrate a stepwise evolution at the nasal barrier: while enhanced ciliated cell tropism and elevated apoptosis are conserved features of Omicron infection, ciliary dysfunction, evident at both the transcriptional and protein level, is a more pronounced phenotype emerging with BA.5 and preserved in the XBB variant. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/689397v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@11b1b60org.highwire.dtl.DTLVardef@a25e0borg.highwire.dtl.DTLVardef@1cc3904org.highwire.dtl.DTLVardef@b35447_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Maternal exercise during lactation reprograms obesity-related changes in mammary metabolism to optimize milk fatty acids and offspring energy expenditure

Maternal obesity alters breast milk composition in ways that may predispose infants to excess adiposity. While maternal exercise during lactation has been associated with favorable shifts in milk metabolites in humans, the mechanisms by which exercise remodels the mammary gland and milk lipid profile to influence offspring metabolism remain unclear. We developed a mouse model incorporating daily moderate treadmill exercise during lactation, indirect calorimetry, stable isotope tracer respirometry, and mammary epithelial cell (MEC) proteomics in lean (LN) and diet-induced obese (OB) dams. Maternal obesity broadly remodeled the MEC proteome, reducing enzymes of de novo fatty acid synthesis and altering lipid transport and oxidative pathways. These molecular adaptations corresponded to higher milk triglyceride content and shifts in fatty acid composition, including an elevated omega-6 to omega-3 fatty acid ratio. The exercise (EX) intervention during lactation reset MEC protein networks, enhancing translational and vesicle transport pathways while reducing fatty acid desaturation, relative to the sedentary (SED) group. In OB dams, exercise increased milk medium-chain fatty acid (MCFA) levels and partially corrected the n6/n3 FA ratio. Offspring nursed by OB-EX dams exhibited higher whole-body energy expenditure, increased fatty acid oxidation, and improved metabolic flexibility compared to litters consuming OB-SED milk. Together, maternal exercise during lactation remodels mammary metabolism and milk fatty acid composition in obese dams, enhancing neonatal lipid oxidation and energy expenditure. These findings highlight lactation as a modifiable window, wherein maternal activity influences milk composition and infant metabolic health. New and noteworthyMaternal obesity alters milk fatty acid composition, with consequences for infant metabolism. Exercise during lactation in obese dams remodeled the mammary epithelial cell proteome, increasing medium-chain fatty acids in milk and enhancing lipid oxidation and energy expenditure in offspring.

physiology↗

bioRxiv2023

Evidence for vagal sensory neural involvement in influenza pathogenesis and disease

Influenza A virus (IAV) is a common respiratory pathogen and a global cause of significant and often severe morbidity. Although inflammatory immune responses to IAV infections are well described, little is known about how neuroimmune processes contribute to IAV pathogenesis. In the present study, we employed surgical, genetic, and pharmacological approaches to manipulate pulmonary vagal sensory neuron innervation and activity in the lungs to explore potential crosstalk between pulmonary sensory neurons and immune processes. Intranasal inoculation of mice with H1N1 strains of IAV resulted in stereotypical antiviral lung inflammation and tissue pathology, changes in breathing, loss of body weight and other clinical signs of severe IAV disease. Unilateral cervical vagotomy and genetic ablation of pulmonary vagal sensory neurons had a moderate effect on the pulmonary inflammation induced by IAV infection, but significantly worsened clinical disease presentation. Inhibition of pulmonary vagal sensory neuron activity via inhalation of the charged sodium channel blocker, QX-314, resulted in a moderate decrease in lung pathology, but again this was accompanied by a paradoxical worsening of clinical signs. Notably, vagal sensory ganglia neuroinflammation was induced by IAV infection and this was significantly potentiated by QX-314 administration. This vagal ganglia hyperinflammation was characterized by alterations in IAV-induced host defense gene expression, increased neuropeptide gene and protein expression, and an increase in the number of inflammatory cells present within the ganglia. These data suggest that pulmonary vagal sensory neurons play a role in the regulation of the inflammatory process during IAV infection and suggest that vagal neuroinflammation may be an important contributor to IAV pathogenesis and clinical presentation. Targeting these pathways could offer therapeutic opportunities to treat IAV-induced morbidity and mortality. Author summaryInfluenza viruses are a common respiratory pathogen that represent a constant and pervasive threat to human health. Although the inflammatory and immune responses to influenza viral infections are well described, little is known about the role the nervous system plays in the formation and progression of disease. The lungs receive a rich supply of sensory nerve fibers from the vagus nerve. These nerves are critical for protecting the lungs against harmful stimuli and play an important defence role against pathogens, including viruses. Here we use several complex animal models to demonstrate the impact lung sensory neurons have on influenza viral infection and disease outcome. We demonstrate that ablation of lung sensory neurons and inhibition of their neural activity significantly worsens the clinical outcome in mice infected with influenza virus, however with only a moderate impact on lung pathology. Interestingly, when the activity of these neurons is inhibited during influenza viral infection, this drives a hyper neuroinflammatory response within the vagal sensory ganglia, where their cell bodies are located. Our work provides new insights into how these lung sensory neurons are involved in influenza viral infections and may offer therapeutic opportunities to treat influenza-induced morbidity and mortality.

neuroscience↗

bioRxiv2023

Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature

ObjectivesSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a "preeclampsia-like syndrome". However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection. MethodsWe utilized whole-transcriptome, digital spatial profiling, to examine gene expression patterns in placental tissues from participants who contracted SARS-CoV-2 in the third trimester of their pregnancy (n=7) and those collected prior to the start of the coronavirus disease 2019 (COVID-19) pandemic (n=9). ResultsThrough comprehensive spatial transcriptomic analyses of the trophoblast and villous core stromal cell subpopulations in the placenta, we identified signatures associated with hypoxia and placental dysfunction during SARS-CoV-2 infection in pregnancy. Notably, genes associated with vasodilation (NOS3), oxidative stress (GDF15, CRH), and preeclampsia (FLT1, EGFR, KISS1, PAPPA2), were enriched with SARS-CoV-2. Pathways related to increased nutrient uptake, vascular tension, hypertension, and inflammation, were also enriched in SARS-CoV-2 samples compared to uninfected controls. ConclusionsOur findings demonstrate the utility of spatially resolved transcriptomic analysis in defining the underlying pathogenic mechanisms of SARS-CoV-2 in pregnancy, particularly its role in placental dysfunction. Furthermore, this study highlights the significance of digital spatial profiling in mapping the intricate crosstalk between trophoblasts and villous core stromal cells, thus shedding light on pathways associated with placental dysfunction in pregnancies with SARS-CoV-2 infection. Graphical abstractIn this study, using spatial digital profiling transcriptomic approaches, we demonstrate that SARS-CoV-2 infection in pregnancy disrupts optimal placental function by altering the genomic architecture of trophoblasts and villous core stromal cells.

developmental biology↗

bioRxiv2022

Oxysterols drive inflammation via GPR183 during influenza virus and SARS-CoV-2 infection

RationaleSevere viral respiratory infections are often characterized by extensive myeloid cell infiltration and activation and persistent lung tissue injury. However, the immunological mechanisms driving excessive inflammation in the lung remain elusive. ObjectivesTo identify the mechanisms that drive immune cell recruitment in the lung during viral respiratory infections and identify novel drug targets to reduce inflammation and disease severity. MethodsPreclinical murine models of influenza virus and SARS-CoV-2 infection. ResultsOxidized cholesterols and the oxysterol-sensing receptor GPR183 were identified as drivers of monocyte-macrophage infiltration to the lung during influenza virus (IAV) and SARS-CoV-2 infections. Both IAV and SARS-CoV-2 infections upregulated the enzymes cholesterol 25-hydroxylase (CH25H) and cytochrome P450 family 7 subfamily member B1 (CYP7B1) in the lung, resulting in local production of the oxidized cholesterols 25-hydroxycholesterol and 7,25-dihydroxycholesterol (7,25-OHC). Loss-of-function mutation of GPR183, or treatment with a GPR183 antagonist, reduced macrophage infiltration and inflammatory cytokine production in the lungs of IAV- or SARS-CoV-2-infected mice. The GPR183 antagonist also significantly attenuated the severity of SARS-CoV-2 infection by reducing weight loss and viral loads. ConclusionThis study demonstrates that oxysterols drive inflammation in the lung and provides the first preclinical evidence for therapeutic benefit of targeting GPR183 during severe viral respiratory infections. Author SummaryViral infections trigger oxysterol production in the lung, attracting macrophages via GPR183. Blocking GPR183 reduced inflammation and disease severity in SARS-CoV-2 infection, making GPR183 a putative target for therapeutic intervention.

immunology↗

bioRxiv2022

ACE2 is necessary for SARS-CoV-2 infection and sensing by macrophages but not sufficient for productive viral replication

Macrophages are key cellular contributors to COVID-19 pathogenesis. Whether SARS-CoV-2 can enter macrophages, replicate and release new viral progeny remains controversial. Similarly, whether macrophages need to sense replicating virus to drive cytokine release is also unclear. Macrophages are heterogeneous cells poised to respond to their local microenvironment, and accordingly, the SARS-CoV-2 entry receptor ACE2 is only present on a subset of macrophages at sites of human infection. Here, we use in vitro approaches to investigate how SARS-CoV-2 interacts with ACE2-negative and ACE2-positive human macrophages and determine how these macrophage populations sense and respond to SARS-CoV-2. We show that SARS-CoV-2 does not replicate within ACE2-negative human macrophages and does not induce pro-inflammatory cytokine expression. By contrast, ACE2 expression in human macrophages permits SARS-CoV-2 entry, replication, and virion release. ACE2-expressing macrophages sense replicating virus to trigger pro-inflammatory and anti-viral programs that limit virus release. These combined findings resolve several controversies regarding macrophage-SARS-CoV-2 interactions and identify a signaling circuit by which macrophages sense SARS-CoV-2 cell entry and respond by restricting viral replication. One sentence summaryLack of macrophage ACE2 expression precludes SARS-CoV-2 entry and sensing, while ACE2-expressing macrophages sense intramacrophage SARS-CoV-2 replication to induce rapid anti-viral responses that limit new virion release.

immunology↗

bioRxiv2022

COVID-19 vaccine booster induces a strong CD8+ T cell response against Omicron variant epitopes in HLA-A*02:01+ individuals

The >30 mutated residues in the Omicron spike protein have led to its rapid classification as a new SARS-CoV-2 variant of concern. As a result, Omicron may escape from the immune system, decreasing the protection provided by COVID-19 vaccines. Preliminary data shows a weaker neutralizing antibody response to Omicron compared to the ancestral SARS-CoV-2 virus, which can be increased after a booster vaccine. Here, we report that CD8+ T cells can recognize Omicron variant epitopes presented by HLA-A*02:01 in both COVID-19 recovered and vaccinated individuals, even 6 months after infection or vaccination. Additionally, the T cell response was stronger for Omicron variant epitopes after the vaccine booster. Altogether, T cells can recognize Omicron variants, especially in vaccinated individuals after the vaccine booster. One-Sentence SummaryCD8+ T cells response against Omicron variant epitopes is stronger after the vaccine booster.

immunology↗

bioRxiv2021

Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells

Children typically experience more mild symptoms of COVID-19 when compared to adults. There is a strong body of evidence that children are also less susceptible to SARS-CoV-2 infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remains to be determined. Here, we use primary nasal epithelial cells from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the nasal epithelial cells of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the nasal epithelial cells of children. Importantly, the Delta variant also replicated to significantly lower titres in the nasal epithelial cells of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.

microbiology↗

bioRxiv2021

Endothelial cells elicit a pro-inflammatory response to SARS-COV-2 without productive viral infection

ObjectivesThrombotic and microvascular complications are frequently seen in deceased COVID-19 patients. However, whether this is caused by direct viral infection of the endothelium or inflammation-induced endothelial activation remains highly contentious. MethodsHere, we use patient autopsy samples, primary human endothelial cells and an in vitro model of the pulmonary epithelial-endothelial cell barrier to show that primary human endothelial cells express very low levels the SARS-CoV-2 receptor ACE2 and the protease TMPRSS2. ResultsAccordingly, endothelial cells can only be infected when SARS-CoV-2 is present at very high concentrations. However, this is not a productive infection (i.e. no infectious virus is produced) and viral entry induces an inflammatory response. We also show that SARS-CoV-2 does not infect endothelial cells in 3D vessels under flow conditions. We further demonstrate that in a co-culture model endothelial cells are not infected with SARS-CoV-2. They do however sense and respond to infection in the adjacent epithelial cells, increasing ICAM-1 expression and releasing pro-inflammatory cytokines. ConclusionsTaken together, these data suggest that in vivo, endothelial cells are unlikely to be infected with SARS-CoV-2 and that infection is only likely to occur if the adjacent pulmonary epithelium is denuded (basolateral infection) or a high viral load is present in the blood (apical infection). In such a scenario, whilst SARS-CoV-2 infection of the endothelium can occur, it does not contribute to viral amplification. However, endothelial cells are still likely to play a key role in SARS-CoV-2 pathogenesis by sensing adjacent infection and mounting a pro-inflammatory response to SARS-CoV-2.

cell biology↗