PBECs from asthma patients display a shift in cell-type composition and a reduced inflammatory response to RSV infection

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Respiratory syncytial virus (RSV) during infancy is associated with subsequent childhood asthma symptoms. In addition, RSV infections can cause asthma exacerbations by infecting the epithelial layer of the airways, which induces an innate and adaptive immune response. The type-I interferon antiviral response by the epithelial cells induced by RSV infection has been shown to be reduced in asthma in most - but not all - studies. However, the molecular mechanisms that cause this difference between the healthy and asthmatic bronchial epithelium in response to viral infection are not completely understood. In this study, we investigated the transcriptional response of primary bronchial epithelial cells (PBECs) from asthma patients and healthy donors to RSV infection. The PBECs obtained from bronchial brushes were cultured at air-liquid interface conditions for 3 weeks followed by infection with RSV, UV-inactivated RSV or control suspension. Three days after infection, cells were processed for bulk or single-cell RNA sequencing. Transepithelial electrical resistance measurements showed that the barrier function of PBECs from healthy donors is superior to that of PBECs from asthma patients. In the bulk transcriptomic data, a pro-inflammatory response to RSV was observed in both conditions, but was stronger for the healthy PBECs. Cell type deconvolution on the bulk RNA-sequencing data revealed an increase in proportion of ciliated cells (p=0,023) and a decrease in basal cells (p=0,047) after RSV infection in asthma, but not in healthy PBECs. To further analyze the response to RSV infection in a cell-type specific fashion, we performed single-cell RNA sequencing, which revealed the presence of a strong NF-kB response from the basal and secretory cells, which was reduced in PBECs from asthma patients. Our results highlight that the response to RSV infection is altered in the bronchial epithelial cells in asthma, with a reduced inflammatory response and a shift in cell-type composition after viral infection.