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:Whole transcriptome analysis performed on lung samples from dead covid-19 patients and healthy non-covid-19 individuals of multiple age groups.
Project description:High throughput sequencing is performed on mRNA isolated from whole blood of adult Covid-19 patients, bacterial coinfection with Covid-19 and healthy controls in a South Indian cohort. Samples were collected from individuals at the time of hospitalization or visit to clinic. The Covid-19 samples are categorized by severeity.
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:MicroRNAs (miRNAs) have been shown to play important roles in the pathogenesis of viral infections, but little is known about the miRNA alternations associated with SARS-CoV-2 infection. Here, we performed high throughout sequencing to detect miRNAs in the plasma samples collected from 61 healthy controls, 16 asymptomatic individuals and 100 symptomatic COVID-19 patients. In total, we identified 2,336 known miRNAs and 361 novel miRNAs, including 75 differentially expressed miRNAs with p value<0.05 between various groups. We also found a number of miRNAs that were associated with various clinical presentations and viral persistence of COVID-19, such as hsa-miR-370-3p, hsa-miR-146a-3p, hsa-miR-885-5p, hsa-miR-214-3p and hsa-miR-10b-5p. Further analysis of the target genes, gene ontology and KEGG pathways revealed a panel of miRNAs that were linked to immune responses, viral infections, inflammation and apoptosis. Our findings may help understand the contribution of miRNAs to the pathogenesis of COVID-19 and identify potential biomarkers and molecular targets for the diagnosis and treatment of SARS-CoV-2 infection.
Project description:Characterization of the transcriptional signatures of 771 human genes and 19 coronavirus genes in skin samples collected from the borders of hospital-acquired sacral pressure injuries (HASPIs) that developed in individuals with and without COVID-19. Samples included pressure ulcers from individuals without COVID-19 (10), pressure ulcers from individuals with COVID-19 (5), as well as pressure ulcers with thrombotic vasculopathy histopathology from individuals with COVID-19 (8).
Project description:Purpose: Recent studies have focused their attention on conjunctivitis as one of the symptoms of coronavirus disease 2019 (COVID-19). Therefore, tear samples were taken from COVID-19 patients and the presence of SARS-CoV-2 was evidenced using Real Time reverse transcription polymerase chain reaction. Methods: The main aim of this study was to analyze mRNA expression in the tears of patients with COVID-19 viral infection compared with healthy subjects using Next Generation Sequencing (NGS). Results: The functional evaluation of the transcriptome highlighted 25 genes that differ statistically between healthy individuals and patients affected by COVID-19 disease. In particular, the NGS analysis identified the presence of several genes involved in B cell signaling and keratinization. In particular, the genes involved in B cell signaling were downregulated in the tears of COVID-19 patients, while those involved in keratinization were upregulated. Conclusions: The results indicated that COVID-19 may induce a process of ocular keratinization and a defective B cell response.
Project description:Although most SARS-CoV-2-infected individuals experience mild COVID-19, some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly upregulation of the TNF/IL-1beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1beta-driven inflammation, and this was not seen in patients with milder COVID-19 infection. Based on this, we propose that the type I IFN response exacerbates inflammation in patients with severe COVID-19 infection.
Project description:COVID-19 is characterized by systemic proinflammatory shifts with development of serious alterations in the functioning of the immune system. Investigations of the gene expression changes accompanying infection state provide insight towards understanding of the molecular and cellular processes depending on the sickness severity and virus variant. Severe Delta COVID-19 have been characterized by the appearance of the monocyte subset enriched for the proinflammatory gene expression signatures and shift of the ligand-receptor interactions. We profiled the chromatin accessibility landscape of 140,000 nuclei of the PBMC samples from healthy people or individuals with COVID-19. We investigated cis-regulatory elements and identified core transcription factors governing the gene expression state in immune cells during COVID-19. For the severe cases we discovered that regulome and chromatin co-accessibility modules significantly altered across many cell types. Moreover, cases with the Delta variant are accompanied by specific monocyte subtype discovered with the scATAC-seq data. From our analysis follows that immune cells of individuals with severe Delta COVID-19 undergo significant remodeling of the chromatin accessibility landscape and development of the proinflammatory expression pattern. With a gene regulatory network modeling approach we investigated core transcription factors governing cell state and identified the most pronounced chromatin changes in CD14+ monocytes from individuals with severe Delta COVID-19. Together, our results provide novel insight into the cis-regulatory module organization and their impact on gene activity in immune cells during SARS-CoV-2 infection.
Project description:COVID-19 exhibits extensive clinical heterogeneity ranging from asymptomatic infection to death. Unraveling the basis of immune response differences across individuals is critical for developing effective therapeutics and prophylactics. We longitudinally assessed 192 surface protein markers, the transcriptome, and T-cell receptor sequence profiles simultaneously in single peripheral immune cells from COVID-19 patients, and compared to age-matched healthy control samples.