SINGLE-CELL TRANSCRIPTOMICS IDENTIFIES THE IMPAIRED ANTIFIBROTIC FUNCTION OF PULMONARY NK CELLS IN SEVERE COVID-19 PATIENTS

Abstract

Intro: Pulmonary fibrosis has been reported as a common complication of severe COVID-19, especially in patients who have undergone ARDS or mechanical ventilation treatment. As innate lymphocytes, NK cells play important roles in antiviral immunity and inhibit the progression of organ fibrosis.The exploration of key NK populations will clarify their role in the progression of COVID-19 and provide crucial cues for the treatment of post-COVID pulmonary fibrosis. Methods: Single-cell transcriptome data from bronchoalveolar lavage fluid (BALF) of COVID-19 patients and healthy donors were analyzed on normalized expression matrices of all cells screened. After annotation according to the marker genes, NK cells were extracted for further clustering and subsequent analyses of gene expression profiling, gene set enrichment, and molecular interaction. Findings: Reduced-dimensional clustering showed that NK cells in BALF were divided into 10 subpopulations. Compared with healthy persons, NK cells in the lungs of COVID-19 patients showed higher activated features and up-regulation of IFN-related genes. However, the GZMs+PRF1+ subpopulation was only 30% of the total NK cells and highly expressed apoptotic genes of Bax and BCL2L11 in severe patients, which may lead to insufficiency and poor cytotoxicity. In severe patients, AREG+ subpopulation was enriched in the lungs and decreased the expression of TNFSF10, FasL, and CCR2, which indicated under-recruitment and impaired antifibrosis function. Conclusion: Our data showed that NK cells decreased in BALF of severe COVID-19 patients, especially the effector/cytotoxic NK subset very significantly decreased. The impaired activity of antifibrotic NK cells may be associated with collagen deposition and senescent cell accumulation in the lungs with severe SARS-COV-2 infection. Improving the antiviral function and antifibrosis ability may be valid measures to prevent severe COVID-19 and reduce fibrosis complications.