| Abstract [eng] |
2015 marks the advent of high-throughput single cell RNA sequencing (scRNAseq) technologies, which enabled measuring gene expression levels in thousands of cells in a single experiment. One of the methods, inDrops, elegantly harnessed the throughput of droplet microfluidics. However, the complexity of inDrops called for a detailed public protocol before it could be widely adopted. This thesis describes efforts to improve the accessibility of inDrops, as well as its application in two projects, where scRNAseq was used for unbiased cataloguing of cell types. In the first project we sought to better understand the composition of the airway epithelium and its dynamics during recovery. Apart from identifying known cell populations, scRNAseq revealed a novel rare cell type, which we called pulmonary ionocytes. We further characterized ionocytes by gaining insight into their specification and establishing their relevance to cystic fibrosis. In the second project, we sought to estimate the conservation of tumor-infiltrating myeloid cells between human and mouse. Our analysis revealed a one-to-one human-mouse match in dendritic cell and monocyte subsets, partial conservation of neutrophil states, and species differences in macrophages. Neutrophil diversity was largely novel, and a subset of neutrophils was established to have tumor-promoting functions. We hope our study will help focusing efforts in drug and disease mechanism research to human-relevant aspects of mouse biology. |
