Project description:Analysis of breast cancer survivors' gut microbiota after lifestyle intervention, during the COVID-19 lockdown, by 16S sequencing of fecal samples.
Project description:COVID-19 induces profound B-cell dysregulation, notably a marked expansion of plasmablasts (PB), whose functional role remains unclear. This study aimed to characterize PB dynamics and functions in COVID-19 and their association with disease severity. We performed longitudinal immune profiling in a prospective cohort of 50 patients with COVID-19 (cohort 1), including flow cytometry-based B-cell immunophenotyping and multiplex cytokine analysis at days 1, 7, 14, and 30. A second retrospective cohort of 282 corticosteroid-naïve patients (cohort 2) was used to validate PB dynamics, model PB trajectories, and perform transcriptomic profiling of sorted PB. PB expansion occurred early in COVID-19 and was positively correlated with maximal disease severity (r=0.53, p<0.0001). Two distinct PB expansion trajectories were identified: one rapidly resolving, and one persistent and amplified, the latter being associated with higher severity scores and 30-day mortality (31% vs. 5%, p<0.001). In cohort 1, BAFF levels at day 7 correlated positively with both PB proportion (r=0.59, p=0.002) and maximal disease severity (r=0.74, p<0.001). Transcriptomic profiling of PB in cohort 2 revealed severity-specific signatures: in severe cases, early PB upregulated genes related to purine metabolism and CD39 expression, suggesting a pro-inflammatory role. In non-severe cases, PB expressed interferon-related and CIITA-mediated MHC-II programs, indicative of antiviral function. PB display dual functional profiles in COVID-19, acting either as regulators of antiviral immunity or as amplifiers of inflammation in severe disease. These findings support exploring therapeutic strategies targeting the BAFF-PB axis in severe COVID-19.
Project description:The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Here we define multiple pathways by which the gut microbiome protects mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). SCFAs reduced viral burdens in the airways and intestines by downregulating the SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2), and enhancing adaptive immunity in male animals. In order to identify other mechanisms by which SCFAs influence the outcome of SARS-CoV-2 infection, we performed RNA-seq on lungs from male GF mice given control or SCFA water for two weeks. We identified a novel role for the gut microbiome in regulating systemic coagulation response by limiting megakaryocyte proliferation and platelet turnover via the Sh2b3-Mpl axis. Taken together, our findings have unraveled novel functions of SCFAs and fiber-fermenting gut bacteria that might be leveraged as pan-coronavirus therapeutics to dampen viral entry and hypercoagulation and promote adaptive anti-viral immunity.
Project description:Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA-Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups.
Project description:To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. To further exploring the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases.
Project description:We used total RNA of nasopharyngeal swabs from COVID-19 patients to identify their gene expression profile. Multiple biological process were significantly enriched in either asymptomatic or mildly symptomatic patients. These significantly expressed genes were suggested to contribute to the severity of the disease. We also performed metagenomics analysis to identify differences in the microbiome profile of the two groups of patients.
Project description:The 3p21.31 locus, which locus contains a chemokine receptor (CKR) cluster, is the most robust genomic region associated with COVID-19 severity. We tested expression quantitative trait loci (eQTL) targeting the 3p21.31 CKR cluster linked to COVID-19 hospitalization in Europeans from the COVID-19 HGI meta-analysis. Among these, CCRL2, a key regulator of neutrophil trafficking, was targeted by neutrophil-restricted eQTLs. We confirmed these eQTLs in an Italian COVID-19 cohort. Haplotype analysis revealed a link between an increased CCRL2 expression and COVID-19 severity and hospitalization. By the exposure of neutrophils to a TLR8 ligand, reflecting a viral infection, we revealed specific chromatin domains within the 3p21.31 locus exclusive to neutrophils. In addition, the identified variants mapped within these regions altered the binding motif of neutrophils expressed transcription factors. These results support that CCRL2 eQTL variants contribute to the risk of severe COVID-19 by selectively affecting neutrophil’s function
Project description:We investigated the association between endogenous vitamin D and the severity of COVID-19 as well as the mechanisms of action of vitamin D supplementation. Vitamin D deficiency and insufficiency were associated with increased severity and unfavourable outcome after 28 days. Vitamin D levels were negatively associated with biomarkers of COVID-19 severity. Vitamin D supplementation after challenge of mice with COVID-19 plasma led to reduced levels of TNFα, IL-6, IFNγ and MPO in the lung, as well as down-regulation of pro-inflammatory pathways as derived from RNA-seq experiments. Thus, vitamin D demonstrates a protective effect against severity and unfavorable outcome in COVID-19, possibly through attenuation of tissue-specific hyperinflammation.