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Transcriptomic analysis of COVID?19 lungs and bronchoalveolar lavage fluid samples reveals predominant B cell activation responses to infection.

ABSTRACT: The outbreak of the 2019 coronavirus disease (named, COVID?19), caused by the novel SARS?CoV?2 virus, represents a worldwide severe threat to public health. It is of the utmost importance to characterize the immune responses against the SARS?CoV?2 and the mechanisms of hyperinflammation, in order to design better therapeutic strategies for COVID?19. In the present study, a transcriptomic analysis was performed to profile the immune signatures in lung and the bronchoalveolar lavage fluid samples from COVID?19 patients and controls. Our data concordantly revealed increased humoral responses to infection. The elucidation of the host responses to SARS?CoV?2 infection may further improve our understanding of COVID?19 pathogenesis and suggest better therapeutic strategies.

SUBMITTER: Cavalli E

PROVIDER: S-EPMC7447313 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Transcriptomic analysis of COVID‑19 lungs and bronchoalveolar lavage fluid samples reveals predominant B cell activation responses to infection.

Cavalli Eugenio E Petralia Maria Cristina MC Basile Maria Sofia MS Bramanti Alessia A Bramanti Placido P Nicoletti Ferdinando F Spandidos Demetrios A DA Shoenfeld Yehuda Y Fagone Paolo P

International journal of molecular medicine 20200812 4

The outbreak of the 2019 coronavirus disease (named, COVID‑19), caused by the novel SARS‑CoV‑2 virus, represents a worldwide severe threat to public health. It is of the utmost importance to characterize the immune responses against the SARS‑CoV‑2 and the mechanisms of hyperinflammation, in order to design better therapeutic strategies for COVID‑19. In the present study, a transcriptomic analysis was performed to profile the immune signatures in lung and the bronchoalveolar lavage fluid samples ...[more]

PMID: 32945352

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Project description:BackgroundIt is now possible to comprehensively characterize the microbiota of the lungs using culture-independent, sequencing-based assays. Several sample types have been used to investigate the lung microbiota, each presenting specific challenges for preparation and analysis of microbial communities. Bronchoalveolar lavage fluid (BALF) enables the identification of microbiota specific to the lower lung but commonly has low bacterial density, increasing the risk of false-positive signal from contaminating DNA. The objectives of this study were to investigate the extent of contamination across a range of sample densities representative of BALF and identify features of contaminants that facilitate their removal from sequence data and aid in the interpretation of BALF sample 16S sequencing data.ResultsUsing three mock communities across a range of densities ranging from 8E+?02 to 8E+?09 16S copies/ml, we assessed taxonomic accuracy and precision by 16S rRNA gene sequencing and the proportion of reads arising from contaminants. Sequencing accuracy, precision, and the relative abundance of mock community members decreased with sample input density, with a significant drop-off below 8E+?05 16S copies/ml. Contaminant OTUs were commonly inversely correlated with sample input density or not reproduced between technical replicates. Removal of taxa with these features or physical concentration of samples prior to sequencing improved both sequencing accuracy and precision for samples between 8E+?04 and 8E+?06 16S copies/ml. For the lowest densities, below 8E+?03 16S copies/ml BALF, accuracy and precision could not be significantly improved using these approaches. Using clinical BALF samples across a large density range, we observed that OTUs with features of contaminants identified in mock communities were also evident in low-density BALF samples.ConclusionRelative abundance data and community composition generated by 16S sequencing of BALF samples across the range of density commonly observed in this sample type should be interpreted in the context of input sample density and may be improved by simple pre- and post-sequencing steps for densities above 8E+?04 16S copies/ml.

Dataset Information

Transcriptomic analysis of COVID?19 lungs and bronchoalveolar lavage fluid samples reveals predominant B cell activation responses to infection.

Publications

Transcriptomic analysis of COVID‑19 lungs and bronchoalveolar lavage fluid samples reveals predominant B cell activation responses to infection.

Similar Datasets

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