Next Generation Sequencing of SARS-CoV-2 infected lung epithelial cells derived from iPSC

We present evidence on how a lung epithelial cell culture system based on human induced pluripotent stem cells (hiPSC) could emerge as a relevant and sensitive platform for modelling SARS-CoV-2 infection. In order to develop a human model system, we differentiated hiPSC into lung epithelial lineage (airway and alveolar cells) through a three-step protocol. De novo generated cells were authenticated by spatiotemporal expression of stage specific markers including SOX2, FOXJ1 and CC10 in proximal cells and SOX9, FOXP2, SFTPC, MUC5AC, and CC10 in distal cells. Further we showed upregulation of ACE2 and TMPRSS2, the two proteins responsible for SARS-CoV-2 binding and invasion into the host lung in our iPSC-derived proximal and distal lung epithelial cells. In order to find out whether our in-house created lung cell culture system was permissive to SARS-CoV-2 infection, two viral doses representing two multiplicities of infections (MOIs) was tested. Plaque assay, RT-PCR, and ICC results demonstrated that the virus was able to enter and replicate inside these cells in a reproducible manner. Further, transcriptomics (RNA seq) data uncovered a robust epithelial cell-specific response to virus infection including perturbation of metabolic processes, disruption in alveolar and airway maturation program, in addition to the well-known upregulation of antiviral defense and immune responses. Overall design: We generated lung epithelial cells from induced pluripotent stem cells and infected them with SARS-CoV-2 virus at different MOI and different time points. RNA was isolated and sequenced from the control uninfected and SARS-CoV-2 infected cells. We tried to understand the CoVID-19 disease pathology, inflammatory profile, lung structural and functional patterns post infection.