scPheno: A deep generative model to integrate scRNA-seq with disease phenotypes and its application on prediction of COVID-19 pneumonia and severe assessment

Cell-to-cell variability is orchestrated by transcriptional variations participating in different biological processes. However, the dissection of transcriptional variability in specific biological process at single-cell level remains unavailable. Here, we present a deep generative model scPheno to integrate scRNA-seq with disease phenotypes to unravel the invisible phenotype-related transcriptional variations. We applied scPheno on COVID-19 blood scRNA-seq to separate transcriptional variations in regulating COVID-19 host immunity and transcriptional variations in maintaining cell-type identity. In silico, we found CLU+IFI27+S100A9+ monocyte as the efficient cellular marker for the prediction of COVID-19 diagnosis. Inspiringly, using only 4 genes upregulated in CLU+IFI27+S100A9+ monocytes can predict the COVID-19 diagnosis of individuals from different country with an accuracy up to 81.3%. We also found C1+CD163+ monocyte and 8 C1+CD163+ monocyte-upregulated genes as the efficient biomarkers for the prediction of severity assessment. Overall, scPheno is an effective method in dissecting the transcriptional basis of phenotype variations at single-cell level.