Supplementary MaterialsSupplementary figures 41467_2019_11632_MOESM1_ESM

Supplementary MaterialsSupplementary figures 41467_2019_11632_MOESM1_ESM. Source Data file. Abstract Human lung tissue-resident NK cells (trNK cells) are likely to play an important role in host responses towards viral infections, inflammatory conditions and cancer. However, detailed insights into these cells are still largely lacking. Here we show, using RNA sequencing and flow cytometry-based FGF9 analyses, that subsets of human lung CD69+CD16? NK cells display hallmarks of tissue-residency, including high expression of CD49a, CD103, and (CD49a), (Hobit), (CD62L), transcripts compared to the CD69?subset (Fig.?2k). All of these genes have previously been described as hallmarks of CD8+ TRM cells and have been shown to be involved in tissue-retention23. Furthermore, the CD69+CD49a+CD103+ NK cell subset expressed significantly higher levels of (CD103), (CD29), and compared to the CD69? subset (Fig.?2k and Supplementary Fig.?3b). Notably, the CD69+CD49a+CD103+ subset only differed from the CD69+CD49a+CD103? subset with lower expression of a handful of genes, including and (Supplementary Fig.?3b). Taken together, the gene expression signatures of CD69+CD49a+CD103? and CD69+CD49a+CD103+ NK cells strongly indicate that they represent trNK cells. Since CD69 is commonly considered a hallmark marker of tissue-resident lymphocytes, we additionally analyzed whether the CD69sp subset in the lung also expressed genes associated with tissue-residency despite the lack of CD49a and CD103. Relatively few differentially expressed genes were, however, detected when comparing the CD69sp and CD69?subsets with each other (Fig.?2j, k and Supplementary Fig.?3b), although several of them have been associated with tissue-residency, such as in the former subset (Fig.?2j, k and Supplementary Fig.?3b). This indicates that CD69spCD16?NK cells in the human lung have a GSK5182 less distinct tissue-resident phenotype. In addition to the identification of genes directly involved in tissue-retention, a number of genes involved in regulating NK cell function were also differentially expressed in the CD69+CD49a+CD103? and CD69+CD49a+CD103+ NK cell subsets compared to the CD69?subset, including higher expression of (NKp65)and lower expression of (NKp80), (CD127) in the former subsets (Fig.?2k, Supplementary Fig.?3b, and Supplementary data?1). Of note, the CD69sp subset differed from the CD69?, CD69+CD49a+CD103?, and CD69+CD49a+CD103+ subsets GSK5182 with lower expression of (Granulysin) and (Granzyme B) (Fig.?2k, Supplementary Fig.?3b), indicating that CD69spCD16?NK cells have reduced cytotoxic capacity. Transcription factors control the expression of a large number of genes, and therefore differences GSK5182 in expression of transcription factors are likely to reflect important differences in the biology of NK cells. The CD69+CD49a+CD103? and CD69+CD49a+CD103+ subsets indeed differed in their expression profile of a number of transcription factors compared to the CD69?subset (Fig.?2k and Supplementary Fig.?3b), further strengthening the notion that these cells constitute a distinct population of cells. For example, the CD69+CD49a+CD103?and CD69+CD49a+CD103+ subsets had increased expression of compared to the CD69? NK cell subset (Fig.?2k and GSK5182 Supplementary Fig.?3b). Moreover, the CD69+CD49a+CD103+ subset expressed higher levels of the transcription factors compared to the CD69?subset (Fig.?2k, Supplementary Fig.?3b, and GSK5182 supplementary data?1). Taken together, the combined gene and protein expression analyses showed that CD69+CD49a+CD103?CD16? and CD69+CD49a+CD103+CD16? NK cells were distinct from both CD69spCD16? and CD69?CD16? NK cells, and had a transcriptional signature indicative of tissue-residency in human lung. In contrast, CD69spCD16? NK cells in human lung were overall more similar to CD69?CD16? NK cells and, to a lesser extent, expressed genes associated with tissue-residency. TrNK cells differ between tissues and from CD8+ TRM cells Recently, the transcriptome of trNK cells in human bone marrow was published20 and was found to share a transcriptional signature with human spleen CD8+ TRM cells1. It however remains unknown whether trNK cells are unique for their respective tissue environment, and to what extent they share a common transcriptional signature. We therefore next compared the profile of differentially expressed genes in lung trNK cells (CD69+CD49a+CD103+CD16? trNK cells versus CD69?CD16? NK cells), with available published data on bone marrow trNK cells (CXCR6+CD69+CD54+ trNK cells versus CXCR6?CD56bright NK cells)20, as well as with CD8+ TRM cells in human lung and spleen (CD69+CD45RA?CCR7? TRM cells versus CD69?CD45RA?CCR7?CD8+ TEM cells)1. Out of the differentially expressed genes detected in trNK cells in lung (padj? ?0.05), a substantial number were also differentially expressed in trNK cells in bone marrow (Fig.?3a), as well as in CD8+ TRM cells in lung (Fig.?3b). In contrast, substantially fewer genes were commonly differentially expressed (i.e., co-regulated) in trNK.