Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium

Satria P. Sajuthi; Peter DeFord; Nathan D. Jackson; Michael T. Montgomery; Jamie L. Everman; Cydney L. Rios; Elmar Pruesse; James D. Nolin; Elizabeth G. Plender; Michael E. Wechsler; Angel CY Mak; Celeste Eng; Sandra Salazar; Vivian Medina; Eric M. Wohlford; Scott Huntsman; Deborah A. Nickerson; Soren Germer; Michael C. Zody; Gonçalo Abecasis; Hyun Min Kang; Kenneth M. Rice; Rajesh Kumar; Sam Oh; Jose Rodriguez-Santana; Esteban G. Burchard; Max A. Seibold

infections, but also provide evidence that this subfamily of viruses drives an enhanced 408 cytotoxic immune response. Our work provides a set of biomarkers that can be easily 409 examined in COVID-19 patients, through analysis of nasal swabs, to determine the 410 relative importance of these mechanisms and genes in governing susceptibility to 411 infection, severe illness and death. cells. However, we caution that a cell may not need to be TMPRSS2 + to be susceptible 420 to infection, since it has been demonstrated the TMPRSS2 protein is secreted from 421 nasal airway epithelial cells 26 . We also caution that scRNA-seq data are known to 422 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.034454 doi: bioRxiv preprint exhibit biases in gene detection, and thus the level and frequency of ACE2 expression 423 across cells may be much higher than we observe here. In line with this possibility we 424 observe more moderate levels of ACE2 expression in our bulk RNA-seq data on nasal 425 brushings. 426 427 Airway inflammation caused by type 2 cytokine production from infiltrating immune cells 428 plays a prominent role in the control of cellular composition, expression, and thus 429 biology of the airway epithelium 11, 13, 23, 27 . Moreover, while T2 airway inflammation is an 430 important driver of T2-high asthma and COPD disease endotypes, it is also associated 431 with atopy in the absence of lung disease, a very common phenotype in both children 432 and adults. In fact, among the children in this study, we find that 43% of non-asthmatics 433 were scored as T2-high based on expression profile, further substantiating the high 434 prevalence of T2 airway inflammation outside of those with lung disease. Our data 435 suggest that airway epithelial TMPRSS2 expression is highly upregulated by T2 436 inflammation, and specifically by IL-13. Both our network and single cell data show that 437 TMPRSS2 is most prominent in less developed "early secretory" cells as well as in more 438 mature mucus secretory cells. Based on our in vitro data, IL-13 upregulates TMPRSS2 439 across nearly all types of epithelial cells, but the core of this effect appears to be in the 440 induced metaplasia. In contrast to enhanced levels of TMPRSS2, T2 inflammation, 446 whether observed in vivo or induced with IL-13 stimulation, precipitated a dramatic 447 reduction in levels of epithelial ACE2, thus complicating expectations for how T2 448 inflammation might affect overall risk for a poor COVID-19 outcome. Germane to this 449 question, a recent study of 85 fatal COVID-19 subjects found that 81.2% of them 450 exhibited very low levels of blood eosinophil levels 4 . Blood eosinophil levels are a 451 strong, well-known predictor of airway T2 inflammation and were strongly correlated 452 with T2 status in our study as well 11, 23 . Together, these studies provisionally suggest 453 that T2 inflammation may predispose individuals to experience better COVID-19 454 outcomes through a decrease in airway levels of ACE2 that override any countervailing 455 effect from increased expression of TMPRSS2. However, both in vitro experiments 456 examining IL-13 effects on SARS-CoV-2 infection and empirical data on COVID-19 457 outcomes among T2-high and T2-low patients will certainly be needed to determine 458 whether this common airway inflam